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- PDB-7q39: Ribonucleotide Reductase R2_genomic protein from Aquifex aeolicus -
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Open data
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Basic information
Entry | Database: PDB / ID: 7q39 | |||||||||
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Title | Ribonucleotide Reductase R2_genomic protein from Aquifex aeolicus | |||||||||
![]() | Ribonucleoside-diphosphate reductase subunit beta | |||||||||
![]() | OXIDOREDUCTASE / ribonucletotide reductase / R2 subunit | |||||||||
Function / homology | : ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Scaletti, E. / Rehling, D. / Stenmark, P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and Biochemical Investigation of Class I Ribonucleotide Reductase from the Hyperthermophile Aquifex aeolicus. Authors: Rehling, D. / Scaletti, E.R. / Rozman Grinberg, I. / Lundin, D. / Sahlin, M. / Hofer, A. / Sjoberg, B.M. / Stenmark, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 19 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7agjC ![]() 7aikC ![]() 7ailSC ![]() 7q3cC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42113.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M citrate pH 4.0, 1.0 M lithium chloride, 20 % PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.247 Å / Num. obs: 26173 / % possible obs: 100 % / Redundancy: 25.7 % / CC1/2: 1 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.1→2.16 Å / Num. unique obs: 2084 / CC1/2: 0.673 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7AIL Resolution: 2.1→47.247 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.658 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / ESU R: 0.227 / ESU R Free: 0.212 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.164 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→47.247 Å
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Refine LS restraints |
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LS refinement shell |
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