RCSB PDB - 193L: THE 1.33 A STRUCTURE OF TETRAGONAL HEN EGG WHITE LYSOZYME St...
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`Macromolecular Structures
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`Biological Assembly 1 
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`193L
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`Macromolecule Content
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`• Unique protein chains: 1
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`THE 1.33 A STRUCTURE OF TETRAGONAL HEN EGG WHITE LYSOZYME
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`DOI: 10.2210/pdb193l/pdb
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`Classification: HYDROLASE (O-GLYCOSYL)
`Deposited: 1995-09-01 Released: 1995-12-07
`Deposition author(s): Vaney, M.C., Maignan, S., Ries-Kautt, M., Ducruix, A.
`Organism: Gallus gallus
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`Structural Biology Knowledgebase: 193L (1 model >23 annotations)
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`Experimental Data Snapshot
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`wwPDB Validation
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`Full Report
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`Method: X-RAY DIFFRACTION
`Resolution: 1.33 Å
`R-Value Free: 0.226
`R-Value Work: 0.184
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`Literature
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`High-resolution structure (1.33 A) of a HEW lysozyme tetragonal crystal grown in the APCF
`apparatus. Data and structural comparison with a crystal grown under microgravity from
`SpaceHab-01 mission.
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`Vaney, M.C., Maignan, S., Ries-Kautt, M., Ducriux, A.
`
`(1996) Acta Crystallogr.,Sect.D 52: 505-517
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`PubMed: 15299672
`DOI: 10.1107/S090744499501674X
`Primary Citation of Related Structures: 193L 194L
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`Also Cited By: 1HF4
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`PubMed Abstract:
`Crystals of tetragonal hen egg-white lysozyme were grown using Advanced Protein Crystallization Facility (APCF)
`apparatus under a microgravity environment (SpaceHab-01 mission) and ground control conditions. Crystals were
`grown from NaCl as a crystallizing agent at pH 4.3. The X-ray diffraction patterns of the best diffracting ground- and
`space-grown crystals were recorded using synchrotron radiation and an image plate on the W32 beamline at LURE.
`Both ground- and space-grown crystals showed nearly equivalent maximum resolution of 1.3-1.4 A. Refinements
`were carried out with the program X-PLOR with final R values of 18.45 and 18.27% for structures from ground- and
`space- grown crystals, respectively. The two structures are nearly identical with the root-mean-square difference on
`all protein atoms being 0.13 A. Some residues of the two refined structures show multiple alternative conformations.
`Two ions were localized into the electron-density maps of the two structures: one chloride ion at the interface
`between two symmetry-related molecules and one sodium ion stabilizing the loop Ser60-Leu75. The sodium ion is
`surrounded by six ligands which form a bipyramid around it at distances of 2.2-2.6 A.
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`Keywords:
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`Organizational Affiliation:
`Laboratoire de Biologie Structurale, Bâtimet 34, UMR 9920, CNRS, Université Paris-Sud, Gif sur Yvette, France.
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`Macromolecules
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`Classification: HYDROLASE (O-GLYCOSYL)
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`
`Total Structure Weight: 14389.68
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`Macromolecule Entities
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`Molecule
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`LYSOZYME
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`Chains
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`A
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`Length
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`129
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`Organism
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`Gallus gallus
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`Details
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`EC#: 3.2.1.17 IUBMB
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`LYZ Gene View
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`
`http://www.rcsb.org/pdb/explore/explore.do?structureId=193L
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`APOTEX EX1045
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`RCSB PDB - 193L: THE 1.33 A STRUCTURE OF TETRAGONAL HEN EGG WHITE LYSOZYME St...
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`Small Molecules
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`Ligands
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`2 Unique
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`ID
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`CL
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`NA
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`
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`Chains
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`Name / Formula / InChI Key
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`2D Diagram
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`& Interactions
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`3D Interactions
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`A
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`A
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`CHLORIDE ION
`Cl
`VEXZGXHMUGYJMC-UHFFFAOYSA-M
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`SODIUM ION
`Na
`FKNQFGJONOIPTF-UHFFFAOYSA-N
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`Ligand Explorer
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`Binding Pocket (JSmol)
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`Ligand Explorer
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`Binding Pocket (JSmol)
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`Experimental Data & Validation
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`Experimental Data
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`Method: X-RAY DIFFRACTION
`Resolution: 1.33 Å
`R-Value Free: 0.226
`R-Value Work: 0.184
`Space Group: P 4 2 2
`3
`1
`Electron Density Server: EDS
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`
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`Entry History
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`Deposition Data
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`Unit Cell:
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`View Full Validation Report or Ramachandran Plots
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`Structure Validation
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`Length (Å)
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`Angle (°)
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`a = 78.54
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`b = 78.54
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`c = 37.77
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`α = 90.00
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`β = 90.00
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`γ = 90.00
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`Revision History
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`
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`
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`
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`Deposited Date: 1995-09-01
`Released Date: 1995-12-07
`Deposition author(s): Vaney, M.C., Maignan, S., Ries-Kautt, M., Ducruix, A.
`
`• 2011-07-13
`Type: Version format compliance | Details: compliance with PDB Exchange Dictionary
`V4
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`
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`
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`The RCSB PDB is funded by a grant (DBI-1338415) from the National Science Foundation, the National Institutes of Health, and the US Department of Energy.
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`http://www.rcsb.org/pdb/explore/explore.do?structureId=193L
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`Remediated Sequence - 193L: THE 1.33 A STRUCTURE OF TETRAGONAL HEN EGG WHITE LYS...
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`An Information Portal to
`121414 Biological
`Macromolecular Structures
`
`193L
`THE 1.33 A STRUCTURE OF TETRAGONAL HEN EGG WHITE LYSOZYME
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`
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` Display Files
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`Sequence Display for the Entities in PDB 193L
`
`The graphical representation below shows this entry's sequences as reported in UniProtKB, in the sample (SEQRES), or as
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`observed in the experiment (ATOM). Different 3rd party annotations can be graphically mapped on the sequence and
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`displayed in the Jmol viewer. Read more about the sequence display on our help pages.
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`The structure 193L has in total 1 chains.
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`Redundancy Reduction and Sequence Clustering. View
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`the clustering results for 193L.
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`Chain A: LYSOZYME
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`Chain Downloadable Files
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`Download FASTA File
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`View Sequence & DSSP Image
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`Download Sequence Chain Image
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`Chain Info
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`Polymer: 1
`
`Length: 129 residues
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`Chain Type: polypeptide(L)
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`Reference: UniProtKB (P00698)
`
`Up-to-date UniProt Ids are provided by the SIFTS project
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`SEQRES sequence.
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`Details
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`Domain
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` d193la_ Lysozyme: 129
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`Assignment:SCOP
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`residues
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`[hide] [reference]
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`Secondary
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`40% helical (7 helices; 52
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`Structure:DSSP
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`residues)
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`[hide] [reference]
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`10% beta sheet (9 strands; 14
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`residues)
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`Structural Feature:Site
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` 193L_A_AC1_2 BINDING SITE
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`Record
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`FOR RESIDUE CL A 130
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`[hide] [reference]
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`(SOFTWARE)
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` 193L_A_AC2_6 BINDING SITE
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`FOR RESIDUE NA A 131
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`(SOFTWARE)
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`Structural
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` 0018 L-cystine RESID AA0025
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`Feature:Protein
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`PSI-MOD MOD:00034
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`Modification
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`[hide] [reference]
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` 360 sodium ion PDB:NA
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`Remediated Sequence - 193L: THE 1.33 A STRUCTURE OF TETRAGONAL HEN EGG WHITE LYS...
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`Symbols used in Protein Modification track:
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`* A modified residue or standard residue with an attachment
`
`| A cross-link between two residues
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`Polygon A cross-link with three or more reisdues (n-sided polygon, n = number of coordinating residues)
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`References
`
`The PDB to UniProt mapping is based on the data provided by the EBI SIFTS project. See also Velankar et al., Nucleic Acids Research 33, D262-265 (2005).
`
`SCOP Domain Assignment
`
`DSSP Secondary Structure
`
`SCOP: a structural classification of proteins database for the investigation of sequences and structures.
`
`Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
`
`Murzin A.G., Brenner S.E., Hubbard T., Chothia C.
`
`J Mol Biol 1995 Apr; 247(4); 536-40.
`
`PMID: 7723011
`
`Kabsch W., Sander C.
`
`Biopolymers 1983 Dec; 22(12); 2577-637.
`
`PMID: 6667333
`
`Site Record Structural Feature
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`Protein Modification Structural Feature
`
`MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active
`
`The RESID Database of Protein Modifications as a resource and annotation tool.
`
`sites.
`
`Golovin A., Dimitropoulos D., Oldfield T., Rachedi A., Henrick K.
`
`Proteins 2005 Jan; 58(1); 190-9.
`
`PMID: 15468317
`
`Garavelli J.S.
`
`Proteomics 2004 Jun; 4(6); 1527-33.
`
`PMID: 15174122
`
`Protein Modification Structural Feature
`
`The RCSB PDB is funded by a grant (DBI-1338415) from the National Science Foundation, the National Institutes of Health, and the US Department of Energy.
`
`The PSI-MOD community standard for representation of protein modification data.
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`Montecchi-Palazzi L., Beavis R., Binz P.A., Chalkley R.J., Cottrell J., Creasy D., Shofstahl J., Seymour S.L.,
`
`Garavelli J.S.
`
`Nat Biotechnol 2008 Aug; 26(8); 864-6.
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`PMID: 18688235
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