+
Open data
-
Basic information
Entry | Database: PDB / ID: 5aup | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the HypAB complex | ||||||
![]() |
| ||||||
![]() | METAL BINDING PROTEIN/HYDROLASE / protein complex / metallochaperone / METAL BINDING PROTEIN-HYDROLASE complex | ||||||
Function / homology | ![]() ATP-dependent FeS chaperone activity / iron-sulfur cluster assembly / nickel cation binding / protein maturation / mitochondrial respiratory chain complex I assembly / protein modification process / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity / zinc ion binding / ATP binding ...ATP-dependent FeS chaperone activity / iron-sulfur cluster assembly / nickel cation binding / protein maturation / mitochondrial respiratory chain complex I assembly / protein modification process / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity / zinc ion binding / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Watanabe, S. / Kawashima, T. / Nishitani, Y. / Miki, K. | ||||||
![]() | ![]() Title: Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer Authors: Watanabe, S. / Kawashima, T. / Nishitani, Y. / Kanai, T. / Wada, T. / Inaba, K. / Atomi, H. / Imanaka, T. / Miki, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 159.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 122.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 973.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 979.1 KB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 36.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5aunC ![]() 5auoC ![]() 5auqC ![]() 3a43S ![]() 3vx3S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 2 types, 4 molecules AHBI
#1: Protein | Mass: 15711.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: hypA, TK2008 / Production host: ![]() ![]() #2: Protein | Mass: 27622.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK2007 / Production host: ![]() ![]() |
---|
-Non-polymers , 4 types, 13 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.79 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: magnesium chloride, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 31382 / % possible obs: 99.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 9 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.7 / % possible all: 99.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3A43 and 3VX3 Resolution: 3.102→46.537 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 25.96 / Stereochemistry target values: ML Details: THE STRUCTURAL FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.102→46.537 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|