[English] 日本語
Yorodumi- PDB-1pvv: Refined Structure of Pyrococcus furiosus Ornithine Carbamoyltrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pvv | ||||||
---|---|---|---|---|---|---|---|
Title | Refined Structure of Pyrococcus furiosus Ornithine Carbamoyltransferase at 1.87 A | ||||||
Components | Ornithine carbamoyltransferaseOrnithine transcarbamylase | ||||||
Keywords | TRANSFERASE / dodecamer | ||||||
Function / homology | Function and homology information ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / arginine biosynthetic process / amino acid binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.87 Å | ||||||
Authors | Massant, J. / Wouters, J. / Glansdorff, N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Refined structure of Pyrococcus furiosus ornithine carbamoyltransferase at 1.87 A. Authors: Massant, J. / Wouters, J. / Glansdorff, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pvv.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pvv.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 1pvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/1pvv ftp://data.pdbj.org/pub/pdb/validation_reports/pv/1pvv | HTTPS FTP |
---|
-Related structure data
Related structure data | 1a1sS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 12|||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Components on special symmetry positions |
| |||||||||||||||||||||||||||
Details | The biological assembly is a dodecamer generated from the monomer in the asymmetric unit |
-Components
#1: Protein | Mass: 35229.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: ARGF OR PF0594 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q51742, ornithine carbamoyltransferase | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 67.02 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: sodium acetate, ammonium sulfate, glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.989 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.989 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→99 Å / Num. all: 42928 / Num. obs: 42928 / % possible obs: 98.5 % / Rmerge(I) obs: 0.033 |
Reflection shell | Resolution: 1.87→1.91 Å / Rmerge(I) obs: 0.187 / % possible all: 86.5 |
Reflection | *PLUS Num. measured all: 304009 |
Reflection shell | *PLUS % possible obs: 86.5 % |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: AB INITIO Starting model: PDB ENTRY 1A1S Resolution: 1.87→99 Å / Num. parameters: 10575 / Num. restraintsaints: 10110 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2648.48 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→99 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
LS refinement shell |
|