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- PDB-6qk1: R2-like ligand-binding oxidase Y175F mutant with aerobically reco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qk1 | ||||||
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Title | R2-like ligand-binding oxidase Y175F mutant with aerobically reconstituted Mn/Fe cofactor | ||||||
![]() | Ribonucleotide reductase small subunit | ||||||
![]() | OXIDOREDUCTASE / R2-LIKE LIGAND-BINDING OXIDASE / MN/FE COFACTOR / RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT FOLD / METALLOPROTEIN OXIDOREDUCTASE | ||||||
Function / homology | ![]() deoxyribonucleotide biosynthetic process / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Griese, J.J. / Hogbom, M. | ||||||
![]() | ![]() Title: Key Structural Motifs Balance Metal Binding and Oxidative Reactivity in a Heterobimetallic Mn/Fe Protein. Authors: Kisgeropoulos, E.C. / Griese, J.J. / Smith, Z.R. / Branca, R.M.M. / Schneider, C.R. / Hogbom, M. / Shafaat, H.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.6 KB | Display | ![]() |
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PDB format | ![]() | 99 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 582.9 KB | Display | ![]() |
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Full document | ![]() | 583.5 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qjvC ![]() 6qk0C ![]() 6qk2C ![]() 4hr0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36946.809 Da / Num. of mol.: 1 / Mutation: Y175F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: HTA426 / Gene: GK2771 / Plasmid: pET-46 Ek/LIC / Production host: ![]() ![]() References: UniProt: Q5KW80, ribonucleoside-diphosphate reductase |
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-Non-polymers , 5 types, 122 molecules ![](data/chem/img/PLM.gif)
![](data/chem/img/MN3.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN3.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PLM / |
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#3: Chemical | ChemComp-MN3 / |
#4: Chemical | ChemComp-MN / |
#5: Chemical | ChemComp-FE / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 27.5% (W/V) PEG 1500, 0.1 M HEPES-NA PH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 35227 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 31.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.04 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.75→1.86 Å / Redundancy: 4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 5598 / CC1/2: 0.684 / Rrim(I) all: 0.876 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4hr0 Resolution: 1.754→38.854 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 24.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.754→38.854 Å
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Refine LS restraints |
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LS refinement shell |
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