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- PDB-7mmr: Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7mmr | ||||||
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Title | Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-NrdI complex from Aerococcus urinae in Oxidized Form with Cu(I) bound | ||||||
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![]() | OXIDOREDUCTASE/FMN Binding Protein / ribonucleotide reductase / beta subunit / RNR / R2 / class Ie / NrdI / FLAVOPROTEIN / OXIDOREDUCTASE-FMN Binding Protein complex | ||||||
Function / homology | ![]() ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein modification process / FMN binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Palowitch, G.M. / Boal, A.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Ribonucleotide Reductase 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 | ![]() | 377.6 KB | Display | ![]() |
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PDB format | ![]() | 306.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.6 MB | Display | ![]() |
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Full document | ![]() | 5.6 MB | Display | |
Data in XML | ![]() | 66.6 KB | Display | |
Data in CIF | ![]() | 90.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mmpC ![]() 7mmqC ![]() 7mmsC ![]() 7mmtC ![]() 7mmuC ![]() 7mmwC ![]() 6eboS 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 8 molecules ABCDEGFH
#1: Protein | Mass: 38764.375 Da / Num. of mol.: 4 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: Protein | Mass: 15929.860 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 556 molecules ![](data/chem/img/CU1.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CU1 / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-TRS / | #6: Chemical | ChemComp-CA / #7: Chemical | ChemComp-FMN / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.27 % / Mosaicity: 0.499 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 17% (w/v) PEG 3350, 0.1 M calcium chloride, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 146267 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.031 / Rrim(I) all: 0.084 / Χ2: 0.9 / Net I/σ(I): 9.3 / Num. measured all: 1050183 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2→34.32 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.382 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.16 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: 76.47 Å2 / Biso mean: 27.852 Å2 / Biso min: 10.44 Å2
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Refinement step | Cycle: final / Resolution: 2→34.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Rfactor Rfree error: 0
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