[English] 日本語
Yorodumi- PDB-5auq: Crystal structure of ATPase-type HypB in the nucleotide free state -
+Open data
-Basic information
Entry | Database: PDB / ID: 5auq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ATPase-type HypB in the nucleotide free state | ||||||
Components | ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog | ||||||
Keywords | HYDROLASE / ATPase | ||||||
Function / homology | Function and homology information ATP-dependent FeS chaperone activity / iron-sulfur cluster assembly / mitochondrial respiratory chain complex I assembly / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermococcus kodakaraensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.525 Å | ||||||
Authors | Watanabe, S. / Kawashima, T. / Nishitani, Y. / Miki, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5auq.cif.gz | 349.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5auq.ent.gz | 284.5 KB | Display | PDB format |
PDBx/mmJSON format | 5auq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5auq_validation.pdf.gz | 499 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5auq_full_validation.pdf.gz | 509.3 KB | Display | |
Data in XML | 5auq_validation.xml.gz | 60.4 KB | Display | |
Data in CIF | 5auq_validation.cif.gz | 82.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/5auq ftp://data.pdbj.org/pub/pdb/validation_reports/au/5auq | HTTPS FTP |
-Related structure data
Related structure data | 5aunC 5auoC 5aupC 3vx3S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27622.047 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK2007 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JIH4 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.16 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: Magnesium chloride, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→50 Å / Num. obs: 73757 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.51→2.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2 / % possible all: 99.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VX3 Resolution: 2.525→40.601 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.66 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.525→40.601 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|