+Open data
-Basic information
Entry | Database: PDB / ID: 6zjk | ||||||
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Title | Ribonucleotide reductase R2 subunit from Clostridium botulinum | ||||||
Components | Ribonucleoside-diphosphate reductase subunit betaRibonucleotide reductase | ||||||
Keywords | METAL BINDING PROTEIN / ribonucleotide / reductase / nucleotide / R2 | ||||||
Function / homology | Function and homology information ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridium botulinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Martinez-Carranza, M. / Stenmark, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site. Authors: Martinez-Carranza, M. / Jonna, V.R. / Lundin, D. / Sahlin, M. / Carlson, L.A. / Jemal, N. / Hogbom, M. / Sjoberg, B.M. / Stenmark, P. / Hofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zjk.cif.gz | 543.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zjk.ent.gz | 446.6 KB | Display | PDB format |
PDBx/mmJSON format | 6zjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/6zjk ftp://data.pdbj.org/pub/pdb/validation_reports/zj/6zjk | HTTPS FTP |
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-Related structure data
Related structure data | 2rccS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43246.566 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (strain Loch Maree / Type A3) (bacteria) Strain: Loch Maree / Type A3 / Gene: nrdB, CLK_2200 / Production host: Escherichia coli (E. coli) References: UniProt: B1KYY8, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-FE / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.46 Å3/Da / Density % sol: 49.9 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: sodium bromide, Bis Tris propane pH 6.5, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 115 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Limit h max: 99 / Limit h min: -103 / Limit k max: 19 / Limit k min: -20 / Limit l max: 75 / Limit l min: -74 / Number: 123556 / Theta max: 13.345875285 ° / Theta min: 0.544372704633 ° |
Reflection | Resolution: 2→83.68 Å / Num. obs: 106664 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 39.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.71 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 7815 / CC1/2: 0.664 |
Cell measurement | Reflection used: 123556 / Theta max: 13.345875285 ° / Theta min: 0.544372704633 ° |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RCC Resolution: 2→83.67 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.53 / 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 max: 114.08 Å2 / Biso mean: 54.6969 Å2 / Biso min: 31.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→83.67 Å
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Refinement TLS params. | Method: refined / Origin x: -7.0152 Å / Origin y: 15.2283 Å / Origin z: 32.2143 Å
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Refinement TLS group |
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