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- PDB-6g59: Structure of the alanine racemase from Staphylococcus aureus in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6g59 | |||||||||
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Title | Structure of the alanine racemase from Staphylococcus aureus in complex with an pyridoxal-6- phosphate derivative | |||||||||
![]() | Alanine racemase 1 | |||||||||
![]() | BIOSYNTHETIC PROTEIN / pyridoxal 5 phosphate dependent / D-alanine biosynthesis | |||||||||
Function / homology | ![]() alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hoegl, A. / Sieber, S.A. / Schneider, S. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 316.8 KB | Display | ![]() |
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PDB format | ![]() | 257 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 972.7 KB | Display | ![]() |
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Full document | ![]() | 957.3 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 41.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6g56C ![]() 6g58C ![]() 4a3qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: -1 - 381 / Label seq-ID: 21 - 403
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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.) ![]() Gene: alr1, alr, SAV2070 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 185 molecules ![](data/chem/img/EM2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.96 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 0.1M Hepes pH7, 2M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: 1 / Resolution: 2.45→49.5 Å
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Refine LS restraints |
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