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Yorodumi- PDB-5cw8: Crystal structure of Mycobacterium tuberculosis KstR in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cw8 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis KstR in complex with 3-oxo-4-cholesten-26-oyl-CoA | ||||||
Components | HTH-type transcriptional repressor KstR | ||||||
Keywords | Transcription regulator / Transcriptional repressor / TetR family Transcriptional repressor / cholesterol catabolism / CoA thioester ligand / Structural Genomics / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Ho, N.A.T. / Dawes, S. / Kendall, S. / Casabon, I. / Crowe, A.M. / Baker, E.N. / Eltis, L.D. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC) | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: The Structure of the Transcriptional Repressor KstR in Complex with CoA Thioester Cholesterol Metabolites Sheds Light on the Regulation of Cholesterol Catabolism in Mycobacterium tuberculosis. Authors: Ho, N.A. / Dawes, S.S. / Crowe, A.M. / Casabon, I. / Gao, C. / Kendall, S.L. / Baker, E.N. / Eltis, L.D. / Lott, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cw8.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cw8.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 5cw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cw8_validation.pdf.gz | 869.6 KB | Display | wwPDB validaton report |
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Full document | 5cw8_full_validation.pdf.gz | 873.7 KB | Display | |
Data in XML | 5cw8_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 5cw8_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/5cw8 ftp://data.pdbj.org/pub/pdb/validation_reports/cw/5cw8 | HTTPS FTP |
-Related structure data
Related structure data | 3mnlC 5cxgC 5cxiC 3bjbS 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: 22352.510 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: kstR, Rv3574 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P96856 #2: Chemical | #3: Chemical | ChemComp-PGE / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.01 M nickel (II) chloride hexahydrate, 0.1 M Tris pH 8.5, 1.0 M lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→47.8 Å / Num. obs: 12603 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.197 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BJB Resolution: 2.6→47.797 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.89 / 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: 2.6→47.797 Å
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Refine LS restraints |
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LS refinement shell |
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