[English] 日本語
Yorodumi- PDB-6g59: Structure of the alanine racemase from Staphylococcus aureus in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g59 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the alanine racemase from Staphylococcus aureus in complex with an pyridoxal-6- 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 subsp. aureus Mu50 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | |||||||||
Authors | Hoegl, A. / Sieber, S.A. / Schneider, S. | |||||||||
Funding support | Germany, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6g59.cif.gz | 316.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6g59.ent.gz | 257 KB | Display | PDB format |
PDBx/mmJSON format | 6g59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/6g59 ftp://data.pdbj.org/pub/pdb/validation_reports/g5/6g59 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6g56C 6g58C 4a3qS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: -1 - 381 / Label seq-ID: 21 - 403
|
-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 subsp. aureus Mu50 (bacteria) Gene: alr1, alr, SAV2070 / Production host: Escherichia coli (E. coli) / References: UniProt: P63479, alanine racemase |
---|
-Non-polymers , 5 types, 185 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.96 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 0.1M Hepes pH7, 2M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→49.5 Å / Num. obs: 44955 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.2 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4399 / CC1/2: 0.5 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4A3Q Resolution: 2.45→49.5 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.93 / SU B: 15.869 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.206 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.447 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.45→49.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|