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Yorodumi- PDB-2vb8: beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound inhibi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vb8 | ||||||
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Title | beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound inhibitor thiolactomycin | ||||||
Components | 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1 | ||||||
Keywords | TRANSFERASE / CYTOPLASM / ANTIBIOTIC / THIOLACTOMYCIN / ACYLTRANSFERASE / LIPID SYNTHESIS / FATTY ACID SYNTHESIS / FATTY ACID BIOSYNTHESIS | ||||||
Function / homology | Function and homology information monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Pappenberger, G. / Schulz-Gasch, T. / Bailly, J. / Hennig, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Structure-Assisted Discovery of an Aminothiazole Derivative as a Lead Molecule for Inhibition of Bacterial Fatty-Acid Synthesis. Authors: Pappenberger, G. / Schulz-Gasch, T. / Kusznir, E. / Mueller, F. / Hennig, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vb8.cif.gz | 362.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vb8.ent.gz | 296.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vb8_validation.pdf.gz | 336 KB | Display | wwPDB validaton report |
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Full document | 2vb8_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 2vb8_validation.xml.gz | 71.1 KB | Display | |
Data in CIF | 2vb8_validation.cif.gz | 122 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/2vb8 ftp://data.pdbj.org/pub/pdb/validation_reports/vb/2vb8 | HTTPS FTP |
-Related structure data
Related structure data | 2vb7C 2vb9C 2vbaC 1ek4S 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42656.203 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PQE80 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 References: UniProt: P0A953, beta-ketoacyl-[acyl-carrier-protein] synthase I #2: Chemical | ChemComp-TLM / #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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: CRYSTALLIZATION CONDITIONS: HANGING DROP AGAINST 3% PEG 400, 1.9 M AMMONIUM SULPHATE, 0.1 M TRIS PH 7.5; SOAK WITH 0.3MM LIGAND IN 2.3M AMMONIUM SULPHATE, 0.1M TRIS PH7.5, 3% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9511 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 8, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9511 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 515847 / % possible obs: 95.8 % / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 2.68 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.51 / % possible all: 78 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EK4 Resolution: 1.52→119.52 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.222 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.069 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.85 Å2
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Refinement step | Cycle: LAST / Resolution: 1.52→119.52 Å
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Refine LS restraints |
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