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Open data
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Basic information
Entry | Database: PDB / ID: 5auo | ||||||
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Title | Crystal structure of the HypAB-Ni complex (AMPPCP) | ||||||
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![]() | 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.7 KB | Display | ![]() |
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PDB format | ![]() | 69.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 758.3 KB | Display | ![]() |
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Full document | ![]() | 760.2 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5aunC ![]() 5aupC ![]() 5auqC ![]() 3a43S ![]() 3vx3S 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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1 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 15711.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: hypA, TK2008 / Production host: ![]() ![]() |
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#2: Protein | Mass: 27622.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK2007 / Production host: ![]() ![]() |
-Non-polymers , 7 types, 185 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | ChemComp-NI / | ||||
#5: Chemical | ChemComp-CL / | ||||
#6: Chemical | ChemComp-ACP / | ||||
#7: Chemical | #8: Chemical | ChemComp-GOL / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.2 / Details: magnesium chloride, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: 1.8→50 Å / Num. obs: 72200 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 1.2 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3A43, 3VX3 Resolution: 1.8→40.949 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 24.54 / Stereochemistry target values: ML Details: THE STRUCTURAL FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→40.949 Å
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Refine LS restraints |
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LS refinement shell |
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