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Yorodumi- PDB-3f6o: Crystal structure of ArsR family transcriptional regulator, RHA00566 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f6o | ||||||
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Title | Crystal structure of ArsR family transcriptional regulator, RHA00566 | ||||||
Components | Probable transcriptional regulator, ArsR family protein | ||||||
Keywords | transcription regulator / ArsR family / transcriptional regulator / RHA00566 / MCSG / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / DNA-binding / Transcription / Transcription regulation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodococcus sp. RHA1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Dong, A. / Xu, X. / Zheng, H. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of ArsR family transcriptional regulator, RHA00566 Authors: Dong, A. / Xu, X. / Zheng, H. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f6o.cif.gz | 53.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f6o.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 3f6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f6o_validation.pdf.gz | 427.7 KB | Display | wwPDB validaton report |
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Full document | 3f6o_full_validation.pdf.gz | 428.3 KB | Display | |
Data in XML | 3f6o_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 3f6o_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/3f6o ftp://data.pdbj.org/pub/pdb/validation_reports/f6/3f6o | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13476.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. RHA1 (bacteria) / Gene: RHA1_ro06925 / Plasmid: PET DERIVATIVE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)DERIVATIVE / References: UniProt: Q0S195 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE PROTEIN WAS CRYSTALLIZED BY IN SITU PTOTEOLYSIS METHOD, THE PROTEIN WAS ...AUTHORS STATE THAT THE PROTEIN WAS CRYSTALLIZ | |
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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: 2.14 Å3/Da / Density % sol: 42.52 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop Details: 0.1M Bis-tris pH5.5 0.2M MgCl2 25%PEG3350 , VAPOR DIFFUSION, SITTING DROP, temperature 297K PH range: pH5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9199 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9199 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. all: 18153 / Num. obs: 18153 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1726 / Rsym value: 0.428 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.475 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.158 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.591 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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