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- PDB-7mmv: Crystal Structure of the Class Ie Ribonucleotide Reductase Beta S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7mmv | ||||||
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Title | Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae with Cu(I) bound (Cu sulfate soak) | ||||||
![]() | Ribonucleoside-diphosphate reductase | ||||||
![]() | OXIDOREDUCTASE / ribonucleotide reductase / beta subunit / RNR / R2 / class Ie / metal-free / METAL BINDING PROTEIN | ||||||
Function / homology | ![]() ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Palowitch, G.M. / Boal, A.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Ribonucleotide Reductas Authors: Palowitch, G.M. / Boal, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.8 KB | Display | ![]() |
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PDB format | ![]() | 112.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6eboS S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 39320.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ACS-120-V-Col10a / Gene: HMPREF9243_0731 / Production host: ![]() ![]() References: UniProt: F2I8X9, ribonucleoside-diphosphate reductase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.49 % / Mosaicity: 0.152 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 18% (w/v) PEG 3350, 0.2 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 19, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.78→50 Å / Num. obs: 62957 / % possible obs: 98 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.058 / Rrim(I) all: 0.158 / Χ2: 0.929 / Net I/σ(I): 6.7 / Num. measured all: 462174 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6EBO Resolution: 1.78→38.36 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.479 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.115 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.57 Å2 / Biso mean: 19.261 Å2 / Biso min: 11.15 Å2
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Refinement step | Cycle: final / Resolution: 1.78→38.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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