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Yorodumi- PDB-3bjn: Crystal structure of C-terminal domain of putative transcriptiona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bjn | ||||||
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Title | Crystal structure of C-terminal domain of putative transcriptional regulator from Vibrio cholerae, targeted domain 79-240 | ||||||
Components | Transcriptional regulator, putativeTranscriptional regulation | ||||||
Keywords | TRANSCRIPTION REGULATOR / putative transcriptional regulator IclR / Vibrio cholerae / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Vibrio cholerae O1 biovar eltor str. N16961 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Chang, C. / Volkart, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of C-terminal domain of putative transcriptional regulator from Vibrio cholerae. Authors: Chang, C. / Volkart, L. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bjn.cif.gz | 47.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bjn.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/3bjn ftp://data.pdbj.org/pub/pdb/validation_reports/bj/3bjn | 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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-Components
#1: Protein | Mass: 18507.223 Da / Num. of mol.: 1 / Fragment: C-terminal domain: Residues 79-240 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar eltor str. N16961 (bacteria) Species: Vibrio cholerae / Strain: El Tor Inaba N16961 / Serotype O1 / Gene: VC_A0029 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q9KND6 | ||
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#2: Chemical | #3: 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: 2.84 Å3/Da / Density % sol: 56.71 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Tris-HCl pH 8.5, 3.0 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2007 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 26687 / Num. obs: 26456 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 56.1 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.62 / Num. unique all: 2394 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→35.76 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.778 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.084 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.831 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→35.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 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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