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Yorodumi- PDB-2x3l: Crystal Structure of the Orn_Lys_Arg decarboxylase family protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x3l | ||||||
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Title | Crystal Structure of the Orn_Lys_Arg decarboxylase family protein SAR0482 from Methicillin-resistant Staphylococcus aureus | ||||||
Components | ORN/LYS/ARG DECARBOXYLASE FAMILY PROTEIN | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information Aspartate Aminotransferase, domain 1 - #150 / Molybdopterin biosynthesis moea protein, domain 2 / Molybdopterin biosynthesis moea protein, domain 2 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H. | ||||||
Citation | Journal: J.Struct.Funct.Genomics / Year: 2010 Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs. Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x3l.cif.gz | 339.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x3l.ent.gz | 290.9 KB | Display | PDB format |
PDBx/mmJSON format | 2x3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x3l_validation.pdf.gz | 465.5 KB | Display | wwPDB validaton report |
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Full document | 2x3l_full_validation.pdf.gz | 474.7 KB | Display | |
Data in XML | 2x3l_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 2x3l_validation.cif.gz | 44.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/2x3l ftp://data.pdbj.org/pub/pdb/validation_reports/x3/2x3l | HTTPS FTP |
-Related structure data
Related structure data | 2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3fC 2x3gC 2x3mC 2x3nC 2x3oC 2x48C 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2x7iC 2xu2C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 51122.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: 252 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q6GJJ0, UniProt: A0A7U7ETV2*PLUS #2: Chemical | #3: Chemical | ChemComp-SM / #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | pH: 8 Details: 20% PEG4000, 0.1 M TRIS-CL, PH8.0, 0.32 M MGCL2, 0.8% ETHYLENE GLYCOL. THE CRYSTAL WAS SOAKED WITH 20 MM SAMARIUM ACETATE AND 5MM PLP. THE CRYSTALS WERE CRYOPROTECTED WITH 22% PEG4000, 0.1M ...Details: 20% PEG4000, 0.1 M TRIS-CL, PH8.0, 0.32 M MGCL2, 0.8% ETHYLENE GLYCOL. THE CRYSTAL WAS SOAKED WITH 20 MM SAMARIUM ACETATE AND 5MM PLP. THE CRYSTALS WERE CRYOPROTECTED WITH 22% PEG4000, 0.1M TRIS-CL, PH8.0, 0.3 M MGCL2, 2.0% ETHYLENE GLYCOL, 19% PEG400 DILUTED WITH A 50MM PLP SOLUTION 1:10 (FINAL CONCENTRATIONS ABOUT 17% PEG400 AND 5MM PLP) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 25, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.17 Å / Num. obs: 50798 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.7 / % possible all: 98.7 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2→29.17 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.868 / SU B: 14.06 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE IS ONLY ORDERED FROM RESIDUE 5 TO 443. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE IS ONLY ORDERED FROM RESIDUE 5 TO 443. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.754 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.17 Å
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Refine LS restraints |
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