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Yorodumi- PDB-3tzk: Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tzk | ||||||
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Title | Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92A) from Vibrio cholerae | ||||||
Components | 3-oxoacyl-[acyl-carrier protein] reductase | ||||||
Keywords | OXIDOREDUCTASE / Vibrio cholerae / 3-ketoacyl-(acyl-carrier-protein) reductase / FabG / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : Function and homology information | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Hou, J. / Chruszcz, M. / Zheng, H. / Grabowski, M. / Domagalski, M. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: J.Bacteriol. / Year: 2015 Title: Dissecting the Structural Elements for the Activation of beta-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae. Authors: Hou, J. / Zheng, H. / Chruszcz, M. / Zimmerman, M.D. / Shumilin, I.A. / Osinski, T. / Demas, M. / Grimshaw, S. / Minor, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tzk.cif.gz | 197.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tzk.ent.gz | 157.7 KB | Display | PDB format |
PDBx/mmJSON format | 3tzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tzk_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 3tzk_full_validation.pdf.gz | 453.8 KB | Display | |
Data in XML | 3tzk_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 3tzk_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/3tzk ftp://data.pdbj.org/pub/pdb/validation_reports/tz/3tzk | HTTPS FTP |
-Related structure data
Related structure data | 3op4C 3rroC 3rshC 3tzcC 3u09C 4i08C 4wjzC 4wk6C 5endC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26372.139 Da / Num. of mol.: 2 / Mutation: G92A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: MJ-1236 / Gene: VC2021, VCD_002346 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL References: UniProt: C3NP04, 3-oxoacyl-[acyl-carrier-protein] reductase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-UNX / #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: 2.09 Å3/Da / Density % sol: 41.08 % |
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Crystal grow | Method: vapor diffusion / pH: 9 Details: 0.1M Tris, 2.4M Ammonium Sulfate, pH 9.0, vapor diffusion |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 6, 2010 / Details: MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 9.2 % / Av σ(I) over netI: 43.96 / Number: 366074 / Rmerge(I) obs: 0.051 / Χ2: 0.9 / D res high: 1.8 Å / D res low: 27 Å / Num. obs: 39838 / % possible obs: 99.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.8→50 Å / Num. obs: 39838 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.051 / Χ2: 0.896 / Net I/σ(I): 14 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.345 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES WITH TLS ADDED. 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 max: 72.15 Å2 / Biso mean: 30.8079 Å2 / Biso min: 16.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -18.39 Å / Origin y: 7.635 Å / Origin z: 0.046 Å
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Refinement TLS group |
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