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- PDB-2w6m: Crystal structure of Biotin carboxylase from E. coli in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2w6m | ||||||
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Title | Crystal structure of Biotin carboxylase from E. coli in complex with amino-oxazole fragment series | ||||||
![]() | BIOTIN CARBOXYLASE | ||||||
![]() | LIGASE / ATP-BINDING / FATTY ACID BIOSYNTHESIS / NUCLEOTIDE-BINDING / LIPID SYNTHESIS / ATP-GRASP DOMAIN / FRAGMENT SCREENING | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mochalkin, I. / Miller, J.R. | ||||||
![]() | ![]() Title: Discovery of Antibacterial Biotin Carboxylase Inhibitors by Virtual Screening and Fragment-Based Approaches. Authors: Mochalkin, I. / Miller, J.R. / Narasimhan, L.S. / Thanabal, V. / Erdman, P. / Cox, P. / Prasad, J.V. / Lightle, S. / Huband, M. / Stover, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197 KB | Display | ![]() |
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PDB format | ![]() | 156.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 40.1 KB | Display | |
Data in CIF | ![]() | 60.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2w6nC ![]() 2w6oC ![]() 2w6pC ![]() 2w6qC ![]() 2w6zC ![]() 2w70C ![]() 2w71C ![]() 2j9gS ![]() 2w7c 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
#1: Protein | Mass: 49386.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P24182, biotin carboxylase, acetyl-CoA carboxylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | (2-AMINO-OXAZOL-5-YL)-(3-BROMO-PHENYL)-METHANONE (OA1): INITIAL FRAGMENT SCREENING HIT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 50.89 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 74778 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.82 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.23 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.47 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2J9G Resolution: 2→80.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.831 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.14 / 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: 24.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2→80.06 Å
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Refine LS restraints |
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