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- PDB-2vqd: Crystal Structure of Biotin Carboxylase from Pseudomonas aerugino... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vqd | ||||||
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Title | Crystal Structure of Biotin Carboxylase from Pseudomonas aeruginosa complexed with AMPCP | ||||||
![]() | BIOTIN CARBOXYLASE | ||||||
![]() | LIGASE / NUCLEOTIDE-BINDING / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / ATP-GRASP DOMAIN / BIOTIN CARBOXYLASE / BIOTIN / BACTERIA / ATP-BINDING | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mochalkin, I. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.4 KB | Display | ![]() |
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PDB format | ![]() | 78.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 763.8 KB | Display | ![]() |
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Full document | ![]() | 764.9 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2c00C ![]() 2j9gC ![]() 2vpqC ![]() 2vr1C ![]() 1dv2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() | ||
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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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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