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Yorodumi- PDB-6g58: Structure of the alanine racemase from Staphylococcus aureus in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g58 | |||||||||
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Title | Structure of the alanine racemase from Staphylococcus aureus in complex with a pyridoxal 5' phosphate-derivative | |||||||||
Components | Alanine racemase 1 | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / pyridoxal 5 phosphate dependent / D-alanine biosynthesis | |||||||||
Function / homology | Function and homology information alanine racemase / D-alanine biosynthetic process / alanine racemase activity / pyridoxal phosphate binding Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Hoegl, A. / Sieber, S.A. / Schneider, S. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Nat Chem / Year: 2018 Title: Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics. Authors: Hoegl, A. / Nodwell, M.B. / Kirsch, V.C. / Bach, N.C. / Pfanzelt, M. / Stahl, M. / Schneider, S. / Sieber, S.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g58.cif.gz | 335 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g58.ent.gz | 270.8 KB | Display | PDB format |
PDBx/mmJSON format | 6g58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g58_validation.pdf.gz | 953.9 KB | Display | wwPDB validaton report |
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Full document | 6g58_full_validation.pdf.gz | 936.6 KB | Display | |
Data in XML | 6g58_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 6g58_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/6g58 ftp://data.pdbj.org/pub/pdb/validation_reports/g5/6g58 | HTTPS FTP |
-Related structure data
Related structure data | 6g56C 6g59C 4a3qS S: Starting model for refinement 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: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1 - 382 / Label seq-ID: 23 - 404
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45285.801 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal strep-tag / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: alr1, alr, SAV2070 / Production host: Escherichia coli (E. coli) / References: UniProt: P63479, alanine racemase |
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-Non-polymers , 8 types, 507 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-MPD / ( #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-MRD / ( | #8: Chemical | ChemComp-GOL / | #9: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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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: 3.3 Å3/Da / Density % sol: 62.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 0.1 M Sodium acetate pH 4, 10 %(v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.4 Å / Num. obs: 95389 / % possible obs: 99 % / Redundancy: 6.7 % / Biso Wilson estimate: 28.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8791 / CC1/2: 0.45 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4A3Q Resolution: 1.9→49.4 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 5.279 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.089 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.78 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→49.4 Å
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Refine LS restraints |
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