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Yorodumi- PDB-5omk: R2-like ligand-binding oxidase with aerobically reconstituted met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5omk | ||||||
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Title | R2-like ligand-binding oxidase with aerobically reconstituted metal cofactor before photoconversion | ||||||
Components | Ribonucleotide reductase small subunit | ||||||
Keywords | OXIDOREDUCTASE / R2-LIKE LIGAND-BINDING OXIDASE / DIIRON 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 / FOURIER SYNTHESIS / Resolution: 1.704 Å | ||||||
Authors | Griese, J.J. / Hogbom, M. | ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: Driving Protein Conformational Changes with Light: Photoinduced Structural Rearrangement in a Heterobimetallic Oxidase. Authors: Maugeri, P.T. / Griese, J.J. / Branca, R.M. / Miller, E.K. / Smith, Z.R. / Eirich, J. / 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 | 5omk.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5omk.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 5omk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/5omk ftp://data.pdbj.org/pub/pdb/validation_reports/om/5omk | HTTPS FTP |
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-Related structure data
Related structure data | 5omjC 4hr0S 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 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: 2.34 Å3/Da / Density % sol: 47.33 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 25% (w/v) PEG 1500, 0.1 M HEPES-Na pH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 38162 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 34.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.7→1.81 Å / Redundancy: 6.3 % / Rmerge(I) obs: 3.077 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 6063 / CC1/2: 0.121 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4HR0 Resolution: 1.704→48.312 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.704→48.312 Å
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Refine LS restraints |
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LS refinement shell |
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