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Yorodumi- PDB-2yvw: Crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yvw | ||||||
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Title | Crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Aquifex aeolicus VF5 | ||||||
Components | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||
Keywords | TRANSFERASE / PEPTIDOGLYCAN / UDP-N-ACETYLGLUCOSAMINE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / cytoplasm Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Kitamuta, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Aquifex aeolicus VF5 Authors: Kitamura, Y. / Yokoyama, S. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yvw.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yvw.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/2yvw ftp://data.pdbj.org/pub/pdb/validation_reports/yv/2yvw | HTTPS FTP |
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-Related structure data
Related structure data | 1uaeS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47322.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) References: UniProt: O67315, UDP-N-acetylglucosamine 1-carboxyvinyltransferase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-EPU / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.2 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 7.4 Details: 40% (v/v) PEG 400, 0.1M Imidazole, pH 7.4, MICRO BATCH, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 21, 2007 |
Radiation | Monochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→50 Å / Num. obs: 52283 / % possible obs: 98.7 % / Redundancy: 10.4 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 33.47 |
Reflection shell | Resolution: 1.81→1.87 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 6.24 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UAE Resolution: 1.81→43.64 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 91872.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.8358 Å2 / ksol: 0.366653 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.81→43.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.92 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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