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Yorodumi- PDB-2v5a: CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E.COLI IN COMPLEX WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v5a | ||||||
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Title | CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E.COLI IN COMPLEX WITH POTENT INHIBITOR 3 | ||||||
Components | BIOTIN CARBOXYLASE | ||||||
Keywords | LIGASE / FATTY ACID BIOSYNTHESIS / BIOTIN CARBOXYLASE / NUCLEOTIDE-BINDING / ATP-BINDING / ANTIBACTERIAL / LIPID SYNTHESIS / FAS / BIOTIN / BACTERIAL / INHIBITOR | ||||||
Function / homology | Function and homology information biotin carboxylase / biotin carboxylase activity / acetyl-CoA carboxylase complex / 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 / biotin carboxylase activity / acetyl-CoA carboxylase complex / 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: 2.31 Å | ||||||
Authors | Mochalkin, I. / Miller, J.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: A Class of Selective Antibacterials Derived from a Protein Kinase Inhibitor Pharmacophore. Authors: Miller, J.R. / Dunham, S. / Mochalkin, I. / Banotai, C. / Bowman, M. / Buist, S. / Dunkle, B. / Hanna, D. / Harwood, H.J. / Huband, M.D. / Karnovsky, A. / Kuhn, M. / Limberakis, C. / Liu, J. ...Authors: Miller, J.R. / Dunham, S. / Mochalkin, I. / Banotai, C. / Bowman, M. / Buist, S. / Dunkle, B. / Hanna, D. / Harwood, H.J. / Huband, M.D. / Karnovsky, A. / Kuhn, M. / Limberakis, C. / Liu, J.Y. / Mehrens, S. / Mueller, W.T. / Narasimhan, L. / Ogden, A. / Ohren, J. / Prasad, J.V. / Shelly, J.A. / Skerlos, L. / Sulavik, M. / Thomas, V.H. / Vanderroest, S. / Wang, L. / Wang, Z. / Whitton, A. / Zhu, T. / Stover, C.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v5a.cif.gz | 185.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v5a.ent.gz | 147.5 KB | Display | PDB format |
PDBx/mmJSON format | 2v5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/2v5a ftp://data.pdbj.org/pub/pdb/validation_reports/v5/2v5a | HTTPS FTP |
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-Related structure data
Related structure data | 2v58C 2v59C 1dv2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24182, biotin carboxylase #2: Chemical | ChemComp-LZL / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.06 % / Description: NONE |
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Crystal grow | Details: 0.1 M POTASSIUM CHLORIDE, 4% (W/V) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 |
Detector | Date: Oct 31, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→20 Å / Num. obs: 41691 / % possible obs: 85.3 % / Observed criterion σ(I): 0 / Redundancy: 3.21 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.99 |
Reflection shell | Resolution: 2.31→2.39 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.74 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DV2 Resolution: 2.31→80.32 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.905 / SU B: 12.208 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.251 / 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: 29.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→80.32 Å
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Refine LS restraints |
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