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Yorodumi- PDB-2vba: beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound amino-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vba | ||||||
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Title | beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound amino- thiazole inhibitor | ||||||
Components | 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1 | ||||||
Keywords | TRANSFERASE / CYTOPLASM / ANTIBIOTIC / AMINO-THIAZOLE / 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: 1.36 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 | 2vba.cif.gz | 684.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vba.ent.gz | 573.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/2vba ftp://data.pdbj.org/pub/pdb/validation_reports/vb/2vba | HTTPS FTP |
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-Related structure data
Related structure data | 2vb7C 2vb8C 2vb9C 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-P4T / | #3: 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 0.01M LIGAND IN 30% PEG8000, 0.1M AMMONIUM SULPHATE, 0.1M TRIS PH7.5, 0.005M TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97881 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97881 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→20 Å / Num. obs: 685131 / % possible obs: 92.3 % / Observed criterion σ(I): 5 / Redundancy: 3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.35→1.45 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6.2 / % possible all: 72.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EK4 Resolution: 1.36→19.87 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.18 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.044 / 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: 17.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.36→19.87 Å
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Refine LS restraints |
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