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Yorodumi- PDB-6c5n: Crystal structure of Staphylococcus aureus ketol-acid reductoisom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c5n | ||||||
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Title | Crystal structure of Staphylococcus aureus ketol-acid reductoisomerase with hydroxyoxamate inhibitor 1 | ||||||
Components | Ketol-acid reductoisomerase (NADP(+)) | ||||||
Keywords | OXIDOREDUCTASE / ketol-acid reductoisomerase / isomerase / inhibitor | ||||||
Function / homology | Function and homology information ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / amino acid biosynthetic process / NADP binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.673 Å | ||||||
Authors | Kandale, A. / Patel, K.M. / Zheng, S. / You, L. / Guddat, L.W. / Schenk, G. / Schembri, M.A. / McGeary, R.P. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: Design, synthesis, in vitro activity and crystallisation of novel N-isopropyl-N-hydroxyoxamate derivatives as ketol-acid reductosiomerase (KARI) inhibitor Authors: Kandale, A. / Patel, K.M. / Zheng, S. / You, L. / Guddat, L.W. / Schenk, G. / Schembri, M.A. / McGeary, R.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c5n.cif.gz | 168.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c5n.ent.gz | 129.5 KB | Display | PDB format |
PDBx/mmJSON format | 6c5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c5n_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6c5n_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6c5n_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 6c5n_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/6c5n ftp://data.pdbj.org/pub/pdb/validation_reports/c5/6c5n | HTTPS FTP |
-Related structure data
Related structure data | 5w3kS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37755.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / Gene: ilvC, SAB1941 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q2YUF3, ketol-acid reductoisomerase (NADP+) |
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-Non-polymers , 6 types, 847 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-IMD / | #7: 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: 2.31 Å3/Da / Density % sol: 46.78 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Imidazole pH8 17.5% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→46.63 Å / Num. obs: 79180 / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.67→1.7 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3915 / Rpim(I) all: 0.322 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W3K Resolution: 1.673→46.613 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 17.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.673→46.613 Å
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Refine LS restraints |
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LS refinement shell |
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