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Open data
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Basic information
Entry | Database: PDB / ID: 7xl9 | ||||||
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Title | The structure of HucR with urate | ||||||
![]() | Transcriptional regulator, MarR family | ||||||
![]() | TRANSCRIPTION / HucR / Repressor / Uric acid / Urate | ||||||
Function / homology | ![]() response to stress / DNA-binding transcription factor activity / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, S.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The structure of Deinococcus radiodurans transcriptional regulator HucR retold with the urate bound. Authors: Rho, S. / Jung, W. / Park, J.K. / Choi, M.H. / Kim, M. / Kim, J. / Byun, J. / Park, T. / Lee, B.I. / Wilkinson, S.P. / Park, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.8 KB | Display | ![]() |
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PDB format | ![]() | 63.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 648.6 KB | Display | ![]() |
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Full document | ![]() | 652.3 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fbkS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21908.865 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: DR_1159 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-URC / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Bis-Tris pH 7.0, 0.5 M MgCl2 and PEG 3350 20-30% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→28 Å / Num. obs: 5988 / % possible obs: 100 % / Redundancy: 35.4 % / Biso Wilson estimate: 65.8 Å2 / CC1/2: 1 / Rrim(I) all: 0.18 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.58→2.65 Å / Num. unique obs: 564 / CC1/2: 0.66 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FBK Resolution: 2.58→27.98 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.934 / SU B: 37.592 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R: 1.107 / ESU R Free: 0.378 / 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: 92.953 Å2
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Refinement step | Cycle: 1 / Resolution: 2.58→27.98 Å
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Refine LS restraints |
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