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Yorodumi- PDB-3cjn: Crystal structure of transcriptional regulator, MarR family, from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cjn | ||||||
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Title | Crystal structure of transcriptional regulator, MarR family, from Silicibacter pomeroyi | ||||||
Components | Transcriptional regulator, MarR familyTranscriptional regulation | ||||||
Keywords | TRANSCRIPTION REGULATOR / Transcriptional regulator / MarR family / Silicibacter pomeroyi / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription regulation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Silicibacter pomeroyi DSS-3 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Chang, C. / Volkart, L. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of MarR family transcriptional regulator from Silicibacter pomeroyi. Authors: Chang, C. / Volkart, L. / Freeman, L. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cjn.cif.gz | 42.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cjn.ent.gz | 32.7 KB | Display | PDB format |
PDBx/mmJSON format | 3cjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/3cjn ftp://data.pdbj.org/pub/pdb/validation_reports/cj/3cjn | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18475.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Silicibacter pomeroyi DSS-3 (bacteria) / Species: Silicibacter pomeroyiRuegeria pomeroyi / Strain: DSS-3 / DSM 15171 / Gene: SPO1458 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q5LTF6 |
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#2: Chemical | ChemComp-PO4 / |
#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: 2.26 Å3/Da / Density % sol: 45.62 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 Succinic acid pH 7.0, 12 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2007 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 12944 / Num. obs: 12941 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 21 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 77.2 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 21.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 14.5 / Num. unique all: 1263 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→43.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.913 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.144 / 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: 32.927 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→43.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→1.997 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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