+Open data
-Basic information
Entry | Database: PDB / ID: 4hqm | ||||||
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Title | The crystal structure of QsrR-menadione complex | ||||||
Components | QsrR protein | ||||||
Keywords | TRANSCRIPTION regulator / menadione-modified protein / DNA | ||||||
Function / homology | Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / 2-methylnaphthalene-1,4-diol / : Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Ji, Q. / Zhang, L. / Jones, M.B. / Sun, F. / Deng, X. / Liang, H. / Brugarolas, P. / Gao, N. / Peterson, S.N. / Lan, L. ...Ji, Q. / Zhang, L. / Jones, M.B. / Sun, F. / Deng, X. / Liang, H. / Brugarolas, P. / Gao, N. / Peterson, S.N. / Lan, L. / Bae, T. / He, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR. Authors: Ji, Q. / Zhang, L. / Jones, M.B. / Sun, F. / Deng, X. / Liang, H. / Cho, H. / Brugarolas, P. / Gao, Y.N. / Peterson, S.N. / Lan, L. / Bae, T. / He, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hqm.cif.gz | 49.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hqm.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 4hqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/4hqm ftp://data.pdbj.org/pub/pdb/validation_reports/hq/4hqm | HTTPS FTP |
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-Related 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: 13071.968 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: I3FJN1 #2: Chemical | Sequence details | THE AUTHOR STATES THAT THE RESIDUES AT POSITIONS 30 AND 33 ARE CONSISTENT | |
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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: 2.63 Å3/Da / Density % sol: 53.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M NaCl, 0.1 M Tris.HCl, pH 8.5, 25% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→20 Å / Num. obs: 8886 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→19.405 Å / SU ML: 0.99 / σ(F): 1.34 / Phase error: 38.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.476 Å2 / ksol: 0.311 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.55→19.405 Å
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Refine LS restraints |
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LS refinement shell |
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