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Yorodumi- PDB-1z05: Crystal structure of the ROK family transcriptional regulator, ho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z05 | ||||||
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Title | Crystal structure of the ROK family transcriptional regulator, homolog of E.coli MLC protein. | ||||||
Components | transcriptional regulator, ROK familyTranscriptional regulation | ||||||
Keywords | TRANSCRIPTION / ROK family / transcriptional regulator / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Vibrio cholerae O1 biovar eltor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Minasov, G. / Brunzelle, J.S. / Shuvalova, L. / Collart, F.R. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the ROK family transcriptional regulator, homolog of E.coli MLC protein. Authors: Minasov, G. / Brunzelle, J.S. / Shuvalova, L. / Collart, F.R. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z05.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z05.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 1z05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/1z05 ftp://data.pdbj.org/pub/pdb/validation_reports/z0/1z05 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Probably a dimer. The secon part could be generated by the two fold axis: -y,-x,-z+1/2 |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47084.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar eltor (bacteria) Species: Vibrio cholerae / Strain: N16961 / Gene: AAF95155 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9KQJ1 |
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-Non-polymers , 5 types, 405 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-BME / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl, 1.5M Ammonium SO4, 12% Glycerol, 5mM beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 9, 2005 / Details: Mirror |
Radiation | Monochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 33945 / Num. obs: 33945 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 16.5 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 52.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 7.9 / Num. unique all: 3580 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.11 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL Isotropic thermal model: Individual isotropic b-factor refinement Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.342 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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