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Yorodumi- PDB-2hf8: Crystal structure of HypB from Methanocaldococcus jannaschii in t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hf8 | ||||||
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Title | Crystal structure of HypB from Methanocaldococcus jannaschii in the triphosphate form, in complex with zinc | ||||||
Components | Probable hydrogenase nickel incorporation protein hypB | ||||||
Keywords | HYDROLASE / METAL BINDING PROTEIN / alpha and beta protein / P-loop containing nucleoside triphosphate hydrolase | ||||||
Function / homology | Function and homology information nickel cation binding / protein maturation / GTPase activity / GTP binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Gasper, R. / Scrima, A. / Wittinghofer, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural insights into HypB, a GTP-binding protein that regulates metal binding. Authors: Gasper, R. / Scrima, A. / Wittinghofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hf8.cif.gz | 96.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hf8.ent.gz | 76.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hf8_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2hf8_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2hf8_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 2hf8_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/2hf8 ftp://data.pdbj.org/pub/pdb/validation_reports/hf/2hf8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological unit is composed of chain A and B |
-Components
#1: Protein | Mass: 24988.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: hypB / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q57884 #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | #5: 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: 2.29 Å3/Da / Density % sol: 46.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 175 mM maleic acid disodium salt, 52.5 mM HCl, 14% PEG3350, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9785 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2005 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Av σ(I) over netI: 20.54 / Number: 194237 / Rmerge(I) obs: 0.048 / D res high: 2.1 Å / Num. obs: 51141 / % possible obs: 98.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.1→20 Å / Num. all: 51141 / Num. obs: 51141 / % possible obs: 98.6 % / Observed criterion σ(F): 3 / Redundancy: 3.76 % / Biso Wilson estimate: 24.484 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.54 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 1.94 % / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 9.3 / Num. measured obs: 13086 / Num. unique all: 6342 / % possible all: 93.1 |
-Phasing
Phasing | Method: SAD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD | D res high: 2.1 Å / D res low: 20 Å / FOM : 0.39 / Reflection: 27579 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MAD set site |
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Phasing MAD shell |
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Phasing dm | FOM : 0.72 / FOM acentric: 0.74 / FOM centric: 0.62 / Reflection: 27579 / Reflection acentric: 24064 / Reflection centric: 3515 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→19.92 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.579 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.188 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.353 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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