[English] 日本語
![](img/lk-miru.gif)
- PDB-4wwb: High-resolution structure of the Ni-bound form of the Y135F mutan... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4wwb | ||||||
---|---|---|---|---|---|---|---|
Title | High-resolution structure of the Ni-bound form of the Y135F mutant of C. metallidurans CnrXs | ||||||
![]() | Nickel and cobalt resistance protein CnrR | ||||||
![]() | METAL BINDING PROTEIN / Nickel sensor | ||||||
Function / homology | Heavy-metal resistance protein / Heavy-metal resistance / periplasmic space / CARBON DIOXIDE / FORMIC ACID / : / NICKEL (II) ION / Nickel and cobalt resistance protein CnrR![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Volbeda, A. / Coves, J. / Maillard, A.P. / Kuennemann, S. / Grosse, C. / Schleuder, G. / Petit-Haertlein, I. / de Rosny, E. / Nies, D.H. | ||||||
![]() | ![]() Title: Response of CnrX from Cupriavidus metallidurans CH34 to nickel binding. Authors: Maillard, A.P. / Kunnemann, S. / Groe, C. / Volbeda, A. / Schleuder, G. / Petit-Hartlein, I. / de Rosny, E. / Nies, D.H. / Coves, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 121.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 94.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 429.5 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wwdC ![]() 4wwfC ![]() 2y39S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | biological unit is the same as asym. |
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 13295.874 Da / Num. of mol.: 1 / Fragment: Metal-sensor domain of CnrX / Mutation: Y135F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 6 types, 240 molecules ![](data/chem/img/NI.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/K.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/K.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NI / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-CO2 / | #5: Chemical | ChemComp-K / | #6: Chemical | ChemComp-FMT / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.2 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, HEPES, sodium/potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979725 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.107→39.066 Å / Num. all: 42671 / Num. obs: 42671 / % possible obs: 98.9 % / Redundancy: 8.4 % / Rpim(I) all: 0.036 / Rrim(I) all: 0.103 / Rsym value: 0.089 / Net I/av σ(I): 5.069 / Net I/σ(I): 16.6 / Num. measured all: 358094 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2Y39 Resolution: 1.11→30 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.98 / WRfactor Rfree: 0.1244 / WRfactor Rwork: 0.1087 / FOM work R set: 0.9483 / SU B: 0.595 / SU ML: 0.014 / SU R Cruickshank DPI: 0.0257 / SU Rfree: 0.0248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.99 Å2 / Biso mean: 8.822 Å2 / Biso min: 2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.11→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.11→1.139 Å / Total num. of bins used: 20
|