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- PDB-2wvc: Structural and mechanistic insights into Helicobacter pylori NikR... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wvc | ||||||
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Title | Structural and mechanistic insights into Helicobacter pylori NikR function | ||||||
![]() | PUTATIVE NICKEL-RESPONSIVE REGULATOR | ||||||
![]() | TRANSCRIPTION / TRANSCRIPTION FACTOR / TRANSCRIPTION REGULATION / RHH / DNA-BINDING / METAL-BINDING / METALLOREGULATOR | ||||||
Function / homology | ![]() response to nickel cation / DNA-binding transcription repressor activity / nickel cation binding / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dian, C. / Bahlawane, C. / Muller, C. / Round, A. / Delay, C. / Fauquant, C. / Schauer, K. / de Reuse, H. / Michaud-Soret, I. / Terradot, L. | ||||||
![]() | ![]() Title: Structural and Mechanistic Insights Into Helicobacter Pylori Nikr Activation. Authors: Bahlawane, C. / Dian, C. / Muller, C. / Round, A. / Fauquant, C. / Schauer, K. / De Reuse, H. / Terradot, L. / Michaud-Soret, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.4 KB | Display | ![]() |
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PDB format | ![]() | 96.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.5 KB | Display | ![]() |
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Full document | ![]() | 473.2 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wvbC ![]() 2wvdC ![]() 2wveC ![]() 2wvfC ![]() 2ca9S 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 on special symmetry positions |
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Components
#1: Protein | Mass: 17008.080 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, HIS 74 TO GLY ENGINEERED RESIDUE IN CHAIN A, HIS 75 TO GLY ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.52 % / Description: NONE |
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Crystal grow | Details: 0.4-0.7 M AMMONIUM SULFATE, 100 MM CITRATE PH 5-5.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 2, 2009 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.78 Å / Num. obs: 20773 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 8.9 % / Biso Wilson estimate: 29.56 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.5 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CA9 Resolution: 2.1→35.006 Å / SU ML: 0.24 / σ(F): 1.15 / Phase error: 18.88 / Stereochemistry target values: ML Details: REFINED USING FOBS+ AND FOBS-, NOT FOBS TO VERIFY THE PRESENCE OF METAL IONS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.741 Å2 / ksol: 0.361 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→35.006 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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