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Yorodumi- PDB-1vfs: Crystal structure of D-cycloserine-bound form of alanine racemase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vfs | ||||||
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Title | Crystal structure of D-cycloserine-bound form of alanine racemase from D-cycloserine-producing Streptomyces lavendulae | ||||||
Components | alanine racemase | ||||||
Keywords | ISOMERASE / TIM-barrel / Greek-key motief | ||||||
Function / homology | Function and homology information alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding / cytosol Similarity search - Function | ||||||
Biological species | Streptomyces lavendulae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Noda, M. / Matoba, Y. / Kumagai, T. / Sugiyama, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural evidence that alanine racemase from a D-cycloserine-producing microorganism exhibits resistance to its own product. Authors: Noda, M. / Matoba, Y. / Kumagai, T. / Sugiyama, M. #1: Journal: J.Biol.Chem. / Year: 2004 Title: Self-protection mechanism in D-cycloserine-producing streptomyces lavendulae: Gene cloning, characterization, and kinetics of its alanine racemase and D-alanyl-D-alanine ligase. which are ...Title: Self-protection mechanism in D-cycloserine-producing streptomyces lavendulae: Gene cloning, characterization, and kinetics of its alanine racemase and D-alanyl-D-alanine ligase. which are traget enyzmes of D-cycloserine Authors: Noda, M. / Kawahara, Y. / Ichikawa, A. / Matoba, Y. / Matsuo, H. / Lee, D.G. / Kumagai, T. / Sugiyama, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vfs.cif.gz | 158.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vfs.ent.gz | 122.3 KB | Display | PDB format |
PDBx/mmJSON format | 1vfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vfs_validation.pdf.gz | 516.1 KB | Display | wwPDB validaton report |
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Full document | 1vfs_full_validation.pdf.gz | 535.5 KB | Display | |
Data in XML | 1vfs_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 1vfs_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/1vfs ftp://data.pdbj.org/pub/pdb/validation_reports/vf/1vfs | HTTPS FTP |
-Related structure data
Related structure data | 1vfhSC 1vftC 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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-Components
#1: Protein | Mass: 41049.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Gene: alr / Plasmid: pET-alr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q65YW7, alanine racemase #2: Chemical | ChemComp-CL / | #3: Chemical | #4: 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: 2.38 Å3/Da / Density % sol: 48.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 6, 2003 / Details: mirrors |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. all: 60275 / Num. obs: 60275 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.128 / Rsym value: 0.109 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.2 / Num. unique all: 8688 / Rsym value: 0.454 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1VFH Resolution: 1.9→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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