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- PDB-4mv3: Crystal Structure of Biotin Carboxylase from Haemophilus influenz... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mv3 | ||||||
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Title | Crystal Structure of Biotin Carboxylase from Haemophilus influenzae in Complex with AMPPCP and Bicarbonate | ||||||
![]() | Biotin carboxylase | ||||||
![]() | LIGASE / ATP-grasp | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Broussard, T.C. / Pakhomova, S. / Neau, D.B. / Champion, T.S. / Bonnot, R.J. / Waldrop, G.L. | ||||||
![]() | ![]() Title: Structural Analysis of Substrate, Reaction Intermediate, and Product Binding in Haemophilus influenzae Biotin Carboxylase. Authors: Broussard, T.C. / Pakhomova, S. / Neau, D.B. / Bonnot, R. / 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 | ![]() | 267.1 KB | Display | ![]() |
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PDB format | ![]() | 219 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 810.2 KB | Display | ![]() |
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Full document | ![]() | 816.7 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 30.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mv1C ![]() 4mv4C ![]() 4mv6C ![]() 4mv7C ![]() 4mv8C ![]() 4mv9C ![]() 4rzqC ![]() 1dv1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 51346.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P43873, biotin carboxylase, acetyl-CoA carboxylase |
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#2: Chemical | ChemComp-ACP / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-BCT / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.3 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M NaCl, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2013 / Details: KB mirrors |
Radiation | Monochromator: Cryogenically cooled double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→42.72 Å / Num. all: 48032 / Num. obs: 48032 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 25.11 Å2 / Rsym value: 0.04 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.69→1.78 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 7000 / Rsym value: 0.6 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1DV1 Resolution: 1.69→42.72 Å / SU ML: 0.16 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.63 / Stereochemistry target values: ML / Details: Hydrogens have been added to the riding positions
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→42.72 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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