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Yorodumi- PDB-4xbw: R2-like ligand-binding oxidase with aerobically reconstituted dim... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xbw | |||||||||
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Title | R2-like ligand-binding oxidase with aerobically reconstituted dimanganese cofactor | |||||||||
Components | Ribonucleotide reductase small subunit | |||||||||
Keywords | OXIDOREDUCTASE / R2-like ligand-binding oxidase / dimanganese cofactor / ribonucleotide reductase R2 subunit fold / metalloprotein | |||||||||
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: 1.991 Å | |||||||||
Authors | Griese, J.J. / Hogbom, M. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/Iron Cofactor. Authors: Griese, J.J. / Kositzki, R. / Schrapers, P. / Branca, R.M. / Nordstrom, A. / Lehtio, J. / Haumann, 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 | 4xbw.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xbw.ent.gz | 94.5 KB | Display | PDB format |
PDBx/mmJSON format | 4xbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/4xbw ftp://data.pdbj.org/pub/pdb/validation_reports/xb/4xbw | HTTPS FTP |
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-Related structure data
Related structure data | 4xb9C 4xbvC 5dcoC 5dcrC 5dcsC 4hr4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) | |||||||||
Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36962.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria) Gene: GK2771 / Plasmid: pET-46 Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q5KW80, ribonucleoside-diphosphate reductase | ||||
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#2: Chemical | #3: Chemical | ChemComp-PLM / | #4: 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: 2.37 Å3/Da / Density % sol: 48.15 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 22.5 % (w/v) PEG1500, 0.1 M HEPES-Na, pH 7.0, 22.5 % (w/v) PEG1500, 0.1 M HEPES-Na, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: May 3, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 24406 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 38.12 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 21.93 |
Reflection shell | Resolution: 1.99→2.11 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 1.92 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4HR4 Resolution: 1.991→48.76 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.04 / 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: 55.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.991→48.76 Å
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Refine LS restraints |
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LS refinement shell |
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