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Yorodumi- PDB-6qk2: R2-like ligand-binding oxidase Y715F mutant with anaerobically re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qk2 | ||||||
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Title | R2-like ligand-binding oxidase Y715F mutant with anaerobically reconstituted Mn/Fe cofactor | ||||||
Components | Ribonucleotide reductase small subunit | ||||||
Keywords | OXIDOREDUCTASE / R2-LIKE LIGAND-BINDING OXIDASE / MN/FE COFACTOR / RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT FOLD / METALLOPROTEIN OXIDOREDUCTASE | ||||||
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: 1.596 Å | ||||||
Authors | Griese, J.J. / Hogbom, M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: Key Structural Motifs Balance Metal Binding and Oxidative Reactivity in a Heterobimetallic Mn/Fe Protein. Authors: Kisgeropoulos, E.C. / Griese, J.J. / Smith, Z.R. / Branca, R.M.M. / Schneider, C.R. / Hogbom, M. / Shafaat, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qk2.cif.gz | 238.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qk2.ent.gz | 193.9 KB | Display | PDB format |
PDBx/mmJSON format | 6qk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/6qk2 ftp://data.pdbj.org/pub/pdb/validation_reports/qk/6qk2 | HTTPS FTP |
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-Related structure data
Related structure data | 6qjvC 6qk0C 6qk1C 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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-Components
#1: Protein | Mass: 36946.809 Da / Num. of mol.: 2 / Mutation: Y175F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria) Strain: HTA426 / 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: 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: 2.39 Å3/Da / Density % sol: 48.58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 30% (W/V) PEG 1500, 0.1 M HEPES-NA PH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.596→50 Å / Num. obs: 94346 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 23.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.07 / Net I/σ(I): 15.29 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 14804 / CC1/2: 0.735 / Rrim(I) all: 0.878 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4hr4 Resolution: 1.596→48.592 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.596→48.592 Å
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Refine LS restraints |
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LS refinement shell |
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