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- PDB-6k2h: structural characterization of mutated NreA protein in nitrate bi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6k2h | ||||||
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Title | structural characterization of mutated NreA protein in nitrate binding site from staphylococcus aureus. | ||||||
![]() | NreA | ||||||
![]() | SIGNALING PROTEIN / Complex | ||||||
Function / homology | GAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / GAF domain-containing protein / GAF domain-containing protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sangare, L. / Chen, W. / Wang, C. / Chen, X. / Wu, M. / Zhang, X. / Zang, J. | ||||||
![]() | ![]() Title: Structural insights into the conformational change of Staphylococcus aureus NreA at C-terminus. Authors: Sangare, L. / Chen, W. / Wang, C. / Chen, X. / Wu, M. / Zhang, X. / Zang, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.5 KB | Display | ![]() |
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PDB format | ![]() | 28.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.5 KB | Display | ![]() |
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Full document | ![]() | 444.8 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6izjC ![]() 4pauS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17082.742 Da / Num. of mol.: 1 / Mutation: Y94A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: QU38_07700 / Production host: ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.66 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: HEPES, PEG monomethyl ether 10,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 12171 / % possible obs: 100 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.455 / Num. unique obs: 150995 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PAU Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.557 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.13 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.15 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→50 Å
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Refine LS restraints |
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