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Yorodumi- PDB-4xbv: R2-like ligand-binding oxidase with anaerobically reconstituted d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xbv | ||||||
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Title | R2-like ligand-binding oxidase with anaerobically reconstituted diiron cofactor | ||||||
Components | Ribonuleotide reductase small subunit | ||||||
Keywords | OXIDOREDUCTASE / R2-like ligand-binding oxidase / diiron 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 / MOLECULAR REPLACEMENT / Resolution: 1.799 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 | 4xbv.cif.gz | 235.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xbv.ent.gz | 192.9 KB | Display | PDB format |
PDBx/mmJSON format | 4xbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/4xbv ftp://data.pdbj.org/pub/pdb/validation_reports/xb/4xbv | HTTPS FTP |
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-Related structure data
Related structure data | 4xb9C 4xbwC 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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Unit cell |
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-Components
#1: Protein | Mass: 36962.809 Da / Num. of mol.: 2 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 #2: Chemical | ChemComp-FE2 / #3: Chemical | #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: 2.39 Å3/Da / Density % sol: 48.49 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 27.5% (w/v) PEG 1500, 0.1 M HEPES-Na, pH7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2013 |
Radiation | Monochromator: Si(111) monochromator and Rh mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 1.799→50 Å / Num. obs: 66383 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 29.08 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.35 |
Reflection shell | Resolution: 1.799→1.91 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 1.75 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HR4 Resolution: 1.799→48.622 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.93 / 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: 40.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.799→48.622 Å
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Refine LS restraints |
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LS refinement shell |
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