+Open data
-Basic information
Entry | Database: PDB / ID: 7vdy | ||||||
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Title | Crystal structure of O-ureidoserine racemase | ||||||
Components | O-ureido-serine racemase | ||||||
Keywords | ISOMERASE / racemase | ||||||
Function / homology | O-ureido-serine racemase / diaminopimelate epimerase activity / Diaminopimelate epimerase, DapF / Diaminopimelate epimerase / racemase and epimerase activity, acting on amino acids and derivatives / lysine biosynthetic process via diaminopimelate / antibiotic biosynthetic process / cytoplasm / O-ureido-serine racemase Function and homology information | ||||||
Biological species | Streptomyces lavendulae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Oda, K. / Matoba, Y. | ||||||
Funding support | 1items
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Citation | Journal: Proteins / Year: 2022 Title: Crystal structure of O-ureidoserine racemase found in the d-cycloserine biosynthetic pathway. Authors: Oda, K. / Sakaguchi, T. / Matoba, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vdy.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vdy.ent.gz | 97.1 KB | Display | PDB format |
PDBx/mmJSON format | 7vdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vdy_validation.pdf.gz | 454.4 KB | Display | wwPDB validaton report |
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Full document | 7vdy_full_validation.pdf.gz | 458.5 KB | Display | |
Data in XML | 7vdy_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 7vdy_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/7vdy ftp://data.pdbj.org/pub/pdb/validation_reports/vd/7vdy | HTTPS FTP |
-Related structure data
Related structure data | 1gqzS S: Starting model for refinement |
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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: 31491.559 Da / Num. of mol.: 2 / Fragment: O-ureido-serine racemase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Gene: dcsC, dapF / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D2Z026, O-ureido-serine racemase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.32 Å3/Da / Density % sol: 46.96 % / Mosaicity: 0.46 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.45 M ammonium sulfate, 10%(v/v) dioxane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 24, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.12→49.17 Å / Num. obs: 32385 / % possible obs: 99.4 % / Redundancy: 7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.052 / Rrim(I) all: 0.139 / Net I/σ(I): 9.6 / Num. measured all: 225765 / Scaling rejects: 305 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GQZ Resolution: 2.12→39.67 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.91 Å2 / Biso mean: 29.2221 Å2 / Biso min: 10.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.12→39.67 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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