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Yorodumi- PDB-3vx3: Crystal structure of [NiFe] hydrogenase maturation protein HypB f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vx3 | ||||||
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Title | Crystal structure of [NiFe] hydrogenase maturation protein HypB from Thermococcus kodakarensis KOD1 | ||||||
Components | ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog | ||||||
Keywords | ADP BINDING PROTEIN / Mrp/MinD family ATPase / [NiFe] hydrogenase maturation | ||||||
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 kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Sasaki, D. / Watanabe, S. / Miki, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Identification and Structure of a Novel Archaeal HypB for [NiFe] Hydrogenase Maturation Authors: Sasaki, D. / Watanabe, S. / Matsumi, R. / Shoji, T. / Yasukochi, A. / Tagashira, K. / Fukuda, W. / Kanai, T. / Atomi, H. / Imanaka, T. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vx3.cif.gz | 198.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vx3.ent.gz | 160.9 KB | Display | PDB format |
PDBx/mmJSON format | 3vx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vx3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3vx3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3vx3_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 3vx3_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/3vx3 ftp://data.pdbj.org/pub/pdb/validation_reports/vx/3vx3 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27622.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK2007 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: Q5JIH4 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.0M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 3, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 40492 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rsym value: 0.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.529 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→40.22 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.403 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.133 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→40.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.156 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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