[English] 日本語
![](img/lk-miru.gif)
- PDB-2wvd: Structural and mechanistic insights into Helicobacter pylori NikR... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2wvd | ||||||
---|---|---|---|---|---|---|---|
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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 225.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 182.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2wvbC ![]() 2wvcC ![]() 2wveC ![]() 2wvfC ![]() 2ca9S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17154.205 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 96 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 96 TO SER ...ENGINEERED | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.8 % / Description: NONE |
---|---|
Crystal grow | Details: 0.4-0.7 M AMMONIUM SULFATE, 100 MM CITRATE PH 5-5.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 28, 2009 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→46.32 Å / Num. obs: 21767 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 48.78 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.6 / % possible all: 99.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CA9 Resolution: 2.65→38.958 Å / SU ML: 0.84 / σ(F): 1.18 / Phase error: 21.87 / Stereochemistry target values: ML Details: THE STRUCTURE WAS REFINED USING FOBS+ AND FOBS- AND NOT FOBS TO VERIFY THE PRESENCE OF METAL IONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.295 Å2 / ksol: 0.337 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.49 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→38.958 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|