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Yorodumi- PDB-7ke2: Crystal structure of Staphylococcus aureus ketol-acid reductoisom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ke2 | ||||||
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Title | Crystal structure of Staphylococcus aureus ketol-acid reductoisomerase in complex with Mg2+ and NSC116565 | ||||||
Components | Ketol-acid reductoisomerase (NADP(+)) | ||||||
Keywords | ISOMERASE / Oxidoreductase / REDUCTOISOMERASE / INHIBITOR / METAL BINDING PROTEIN | ||||||
Function / homology | Function and homology information ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / isomerase activity / NADP binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Kurz, J.L. / Patel, K.P. / Guddat, L.W. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Chemistry / Year: 2021 Title: Discovery of a Pyrimidinedione Derivative with Potent Inhibitory Activity against Mycobacterium tuberculosis Ketol-Acid Reductoisomerase. Authors: Lin, X. / Kurz, J.L. / Patel, K.M. / Wun, S.J. / Hussein, W.M. / Lonhienne, T. / West, N.P. / McGeary, R.P. / Schenk, G. / Guddat, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ke2.cif.gz | 163.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ke2.ent.gz | 103.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ke2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/7ke2 ftp://data.pdbj.org/pub/pdb/validation_reports/ke/7ke2 | HTTPS FTP |
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-Related structure data
Related structure data | 7kh7C 5w3kS 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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Unit cell |
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-Components
#1: Protein | Mass: 37886.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ilvC, BMF23_13825, BO217_1422, ERS072840_02559 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: A0A145BYP4, ketol-acid reductoisomerase (NADP+) #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.37 Å3/Da / Density % sol: 48.02 % |
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Crystal grow | Temperature: 289.5 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 0.2 M sodium acetate pH 8.1, 32.5% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 12, 2020 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→43.18 Å / Num. obs: 22965 / % possible obs: 99.5 % / Redundancy: 6.58 % / Biso Wilson estimate: 48.62 Å2 / Rpim(I) all: 0.042 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.59→2.68 Å / Num. unique obs: 2131 / Rpim(I) all: 0.431 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5w3k Resolution: 2.59→43.18 Å / SU ML: 0.3858 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.5691 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→43.18 Å
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Refine LS restraints |
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LS refinement shell |
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