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Yorodumi- PDB-4uig: Structure of the copper sensitive operon repressor from Streptomy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uig | ||||||
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Title | Structure of the copper sensitive operon repressor from Streptomyces lividans at pH6 | ||||||
Components | COPPER SENSITIVE OPERON REPRESSOR | ||||||
Keywords | TRANSCRIPTION / BACTERIAL PROTEINS / REGULON / REPRESSOR PROTEINS / STRESS / ALLOSTERY | ||||||
Function / homology | Function and homology information negative regulation of DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | STREPTOMYCES LIVIDANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Porto, T. / Hough, M.A. / Worrall, J.A.R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structural Insights Into Conformational Switching in the Copper Metalloregulator Csor from Streptomyces Lividans Authors: Porto, T.V. / Hough, M.A. / Worrall, J.A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uig.cif.gz | 32.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uig.ent.gz | 21.5 KB | Display | PDB format |
PDBx/mmJSON format | 4uig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uig_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 4uig_full_validation.pdf.gz | 435.2 KB | Display | |
Data in XML | 4uig_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 4uig_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/4uig ftp://data.pdbj.org/pub/pdb/validation_reports/ui/4uig | HTTPS FTP |
-Related structure data
Related structure data | 4adzS S: Starting model for refinement |
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Similar 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: 14762.569 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES LIVIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D6EK73 | ||
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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 6 Details: 0.01 M MAGNESIUM SULFATE, 0.05 M SODIUM CACODYLATE PH 6.0, 1.8 M LITHIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9163 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9163 Å / Relative weight: 1 |
Reflection | Resolution: 2→40.2 Å / Num. obs: 14603 / % possible obs: 99.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ADZ Resolution: 2→67.9 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.279 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
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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: 39.342 Å2
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Refinement step | Cycle: LAST / Resolution: 2→67.9 Å
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Refine LS restraints |
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