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Yorodumi- PDB-5dd8: The Crystal structure of HucR mutant (HucR-E48Q) from Deinococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dd8 | ||||||
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Title | The Crystal structure of HucR mutant (HucR-E48Q) from Deinococcus radiodurans | ||||||
Components | Transcriptional regulator, MarR familyTranscriptional regulation | ||||||
Keywords | Transcription regulator / HucR / Transcription factor / MarR | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Deochand, D.K. / Perera, I.C. / Crochet, R.B. / Gilbert, N.C. / Newcomer, M.E. / Grove, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol Biosyst / Year: 2016 Title: Histidine switch controlling pH-dependent protein folding and DNA binding in a transcription factor at the core of synthetic network devices. Authors: Deochand, D.K. / Perera, I.C. / Crochet, R.B. / Gilbert, N.C. / Newcomer, M.E. / Grove, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dd8.cif.gz | 137.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dd8.ent.gz | 107.6 KB | Display | PDB format |
PDBx/mmJSON format | 5dd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/5dd8 ftp://data.pdbj.org/pub/pdb/validation_reports/dd/5dd8 | HTTPS FTP |
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-Related structure data
Related structure data | 2fbkS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 8 - 179 / Label seq-ID: 8 - 179
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-Components
#1: Protein | Mass: 19736.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Gene: DR_1159 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RV71 #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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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: 2.1 Å3/Da / Density % sol: 41.5 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 22% (w/v) PEG 3350, 500 mM MgCl2, 100 mM Bis-Tris (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 23, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→38.91 Å / Num. obs: 19997 / % possible obs: 99 % / Redundancy: 10.7 % / Rsym value: 0.106 / Net I/σ(I): 2.1 |
Reflection shell | Resolution: 2.05→2.12 Å / Rsym value: 0.689 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FBK Resolution: 2.05→38.91 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 13.911 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.194 / 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: 62.797 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→38.91 Å
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Refine LS restraints |
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