[English] 日本語
Yorodumi- PDB-3jzi: Crystal structure of biotin carboxylase from E. Coli in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jzi | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of biotin carboxylase from E. Coli in complex with benzimidazole series | ||||||
Components | Biotin carboxylase | ||||||
Keywords | LIGASE / Biotin carboxylase / AccC / Acetyl coenzyme-A carboxylase / ACCase / ATP-binding / Biotin / Fatty acid biosynthesis / Lipid synthesis / Nucleotide-binding | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Cheng, C. / Shipps, G.W. / Yang, Z. / Sun, B. / Kawahata, N. / Soucy, K. / Soriano, A. / Orth, P. / Xiao, L. / Mann, P. / Black, T. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Discovery and optimization of antibacterial AccC inhibitors. Authors: Cheng, C.C. / Shipps, G.W. / Yang, Z. / Sun, B. / Kawahata, N. / Soucy, K.A. / Soriano, A. / Orth, P. / Xiao, L. / Mann, P. / Black, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3jzi.cif.gz | 192.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3jzi.ent.gz | 149.9 KB | Display | PDB format |
PDBx/mmJSON format | 3jzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jzi_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3jzi_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3jzi_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 3jzi_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/3jzi ftp://data.pdbj.org/pub/pdb/validation_reports/jz/3jzi | HTTPS FTP |
-Related structure data
Related structure data | 3jzfC 1bncS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 53507.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: accC, fabG, b3256, JW3224 / Production host: Escherichia coli (E. coli) References: UniProt: P24182, biotin carboxylase, acetyl-CoA carboxylase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.75 % Description: Use of the IMCA-CAT beamline 17-ID at the Advanced Photon Source was supported by the companies of the Industrial Macromolecular Crystallography Association through a contract with the ...Description: Use of the IMCA-CAT beamline 17-ID at the Advanced Photon Source was supported by the companies of the Industrial Macromolecular Crystallography Association through a contract with the Center for Advanced Radiation Sources at the University of Chicago. Use of the Advanced Photon Source was supported by the U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. W-31-109-Eng-38. |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Co-crystallization. 8-10% PEG6000, 100mM Tris-HCl., VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 47651 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 43.2 Å2 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 98.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BNC Resolution: 2.31→19.97 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.13 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→19.97 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.31→2.37 Å / Total num. of bins used: 20
|