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Yorodumi- PDB-2x5f: Crystal structure of the methicillin-resistant Staphylococcus aur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x5f | ||||||
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Title | Crystal structure of the methicillin-resistant Staphylococcus aureus Sar2028, an aspartate_tyrosine_phenylalanine pyridoxal-5'-phosphate dependent aminotransferase | ||||||
Components | ASPARTATE_TYROSINE_PHENYLALANINE PYRIDOXAL-5' PHOSPHATE-DEPENDENT AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information Aspartate Aminotransferase, domain 1 / 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 / MAD / Resolution: 1.8 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.Genom. / 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. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Expression, Purification, Crystallization, Data Collection and Preliminary Biochemical Characterization of Methicillin-Resistant Staphylococcus Aureus Sar2028, an ...Title: Expression, Purification, Crystallization, Data Collection and Preliminary Biochemical Characterization of Methicillin-Resistant Staphylococcus Aureus Sar2028, an Aspartate/Tyrosine/Phenylalanine Pyridoxal-5'-Phosphate-Dependent Aminotransferase. Authors: Seetharamappa, J. / Oke, M. / Liu, H. / Mcmahon, S.A. / Johnson, K.A. / Carter, L. / Dorward, M. / Zawadzki, M. / Overton, I.M. / Van Niekirk, C.A.J. / Graham, S. / Botting, C.H. / Taylor, G. ...Authors: Seetharamappa, J. / Oke, M. / Liu, H. / Mcmahon, S.A. / Johnson, K.A. / Carter, L. / Dorward, M. / Zawadzki, M. / Overton, I.M. / Van Niekirk, C.A.J. / Graham, S. / Botting, C.H. / Taylor, G.L. / White, M.F. / Barton, G.J. / Coote, P.J. / 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 | 2x5f.cif.gz | 346.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x5f.ent.gz | 286 KB | Display | PDB format |
PDBx/mmJSON format | 2x5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x5f_validation.pdf.gz | 473.7 KB | Display | wwPDB validaton report |
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Full document | 2x5f_full_validation.pdf.gz | 482.3 KB | Display | |
Data in XML | 2x5f_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 2x5f_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/2x5f ftp://data.pdbj.org/pub/pdb/validation_reports/x5/2x5f | HTTPS FTP |
-Related structure data
Related structure data | 2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3fC 2x3gC 2x3lC 2x3mC 2x3nC 2x3oC 2x48C 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 2 / Auth seq-ID: 4 - 33 / Label seq-ID: 6 - 35
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48346.332 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): BL21(DE3) / References: UniProt: Q6GFC0, UniProt: A0A7U7EVR5*PLUS |
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-Non-polymers , 5 types, 236 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | PYRIDOXAL-5'-PHOSPHATE (PLP): THERE IS AN OXYGEN ATOM MISSING FROM PLP |
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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: 2.02 Å3/Da / Density % sol: 39.18 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 28% PEG3350, 0.1M HEPES PH 7.5. THE CRYSTALS WERE CRYOPROTECTED WITH 16% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→27.24 Å / Num. obs: 69033 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.01 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.8→27.24 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.395 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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: 7.184 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→27.24 Å
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Refine LS restraints |
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