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Yorodumi- PDB-2vqd: Crystal Structure of Biotin Carboxylase from Pseudomonas aerugino... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vqd | ||||||
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Title | Crystal Structure of Biotin Carboxylase from Pseudomonas aeruginosa complexed with AMPCP | ||||||
Components | BIOTIN CARBOXYLASE | ||||||
Keywords | LIGASE / NUCLEOTIDE-BINDING / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / ATP-GRASP DOMAIN / BIOTIN CARBOXYLASE / BIOTIN / BACTERIA / ATP-BINDING | ||||||
Function / homology | Function and homology information biotin carboxylase / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Mochalkin, I. | ||||||
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vqd.cif.gz | 105.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vqd.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 2vqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vqd_validation.pdf.gz | 763.8 KB | Display | wwPDB validaton report |
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Full document | 2vqd_full_validation.pdf.gz | 764.9 KB | Display | |
Data in XML | 2vqd_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 2vqd_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/2vqd ftp://data.pdbj.org/pub/pdb/validation_reports/vq/2vqd | HTTPS FTP |
-Related structure data
Related structure data | 2c00C 2j9gC 2vpqC 2vr1C 1dv2S C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 50779.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P37798, biotin carboxylase | ||
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#2: Chemical | ChemComp-AP2 / | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-SO4 / | ||
#5: Water | ChemComp-HOH / | ||
Nonpolymer details | PHOSPHOMETSequence details | C-TERMINAL HIS-TAG PRESENT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.02 % / Description: NONE |
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Crystal grow | Details: 0.1M HEPES (PH 7.0), 0.2M MGCL2, 15-20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 |
Detector | Date: May 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 15777 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.86 / % possible all: 83.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DV2 Resolution: 2.41→63.37 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.916 / SU B: 18.358 / SU ML: 0.229 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.859 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 33.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→63.37 Å
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Refine LS restraints |
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