[English] 日本語
Yorodumi- PDB-2vr1: Crystal structure of Biotin carboxylase from E. coli in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vr1 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Biotin carboxylase from E. coli in complex with ATP analog, ADPCF2P. | ||||||
Components | BIOTIN CARBOXYLASE | ||||||
Keywords | LIGASE / NUCLEOTIDE-BINDING / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / BIOTIN CARBOXYLASE / FAS / BIOTIN / BACTERIAL / ATP-BINDING | ||||||
Function / homology | Function and homology information biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / negative regulation of fatty acid biosynthetic process / fatty acid biosynthetic process / protein homodimerization activity / ATP binding / metal ion binding ...biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / negative regulation of fatty acid biosynthetic process / fatty acid biosynthetic process / protein homodimerization activity / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Mochalkin, I. / Waldrop, G.L. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Structural Evidence for Substrate-Induced Synergism and Half-Sites Reactivity in Biotin Carboxylase. Authors: Mochalkin, I. / Miller, J.R. / Evdokimov, A. / Lightle, S. / Yan, C. / Stover, C.K. / Waldrop, G.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vr1.cif.gz | 181.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vr1.ent.gz | 143.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/2vr1 ftp://data.pdbj.org/pub/pdb/validation_reports/vr/2vr1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2c00C 2j9gC 2vpqC 2vqdC 1dv2S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 49386.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24182, biotin carboxylase #2: Chemical | #3: Chemical | ChemComp-ATF / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.46 % / Description: NONE |
---|---|
Crystal grow | Details: 0.1M KCL, 3-8% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Date: May 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 32843 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.83 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.3 / % possible all: 96.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DV2 Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 20.689 / SU ML: 0.222 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.773 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.83 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|