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Yorodumi- PDB-4hr0: R2-like ligand-binding oxidase with aerobically reconstituted met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hr0 | ||||||
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Title | R2-like ligand-binding oxidase with aerobically reconstituted metal cofactor | ||||||
Components | Ribonuleotide reductase small subunit | ||||||
Keywords | OXIDOREDUCTASE / R2-like ligand-binding oxidase / heterodinuclear Mn/Fe cofactor / ribonucleotide reductase R2 subunit fold / metalloprotein / manganese / iron / fatty acid/long-chain hydrocarbon ligand | ||||||
Function / homology | Function and homology information deoxyribonucleotide biosynthetic process / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Geobacillus kaustophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.896 Å | ||||||
Authors | Griese, J.J. / Hogbom, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Direct observation of structurally encoded metal discrimination and ether bond formation in a heterodinuclear metalloprotein Authors: Griese, J.J. / Roos, K. / Cox, N. / Shafaat, H.S. / Branca, R.M.M. / Lehtio, J. / Graslund, A. / Lubitz, W. / Siegbahn, P.E.M. / Hogbom, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hr0.cif.gz | 117.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hr0.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 4hr0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hr0_validation.pdf.gz | 588.7 KB | Display | wwPDB validaton report |
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Full document | 4hr0_full_validation.pdf.gz | 589.6 KB | Display | |
Data in XML | 4hr0_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 4hr0_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/4hr0 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/4hr0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36962.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA246 / Gene: GK2771 / Plasmid: pET-46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5KW80, ribonucleoside-diphosphate reductase |
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-Non-polymers , 6 types, 103 molecules
#2: Chemical | ChemComp-MN3 / |
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#3: Chemical | ChemComp-FE / |
#4: Chemical | ChemComp-MN / |
#5: Chemical | ChemComp-NA / |
#6: Chemical | ChemComp-PLM / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.35 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12.5%(w/v) PEG 1500, 0.1M HEPES-Na, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 27, 2011 |
Radiation | Monochromator: Si (111) monochromator and Pt mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.896→50 Å / Num. all: 28825 / Num. obs: 28825 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 39.794 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.73 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2 / Num. unique all: 4531 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.896→39.153 Å / SU ML: 0.18 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 18.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.896→39.153 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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