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- PDB-6i94: R2-like ligand-binding oxidase G68L mutant with non-activated Mn/... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i94 | ||||||
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Title | R2-like ligand-binding oxidase G68L mutant with non-activated Mn/Mn cofactor (after aerobic reconstitution with Mn and Fe) | ||||||
![]() | 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: Chemical flexibility of heterobimetallic Mn/Fe cofactors: R2lox and R2c proteins. Authors: Kutin, Y. / Kositzki, R. / Branca, R.M.M. / Srinivas, V. / Lundin, D. / Haumann, M. / Hogbom, M. / Cox, N. / Griese, J.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124 KB | Display | ![]() |
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PDB format | ![]() | 96.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.7 KB | Display | ![]() |
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Full document | ![]() | 441.8 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i90C ![]() 6i92C ![]() 6i93C ![]() 6i95C ![]() 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
#1: Protein | Mass: 37018.910 Da / Num. of mol.: 1 / Mutation: G68L 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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#2: Chemical | #3: Chemical | ChemComp-OCA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 27.5% (W/V) PEG 1500, 0.1 M HEPES-NA PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 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: 1.7→50 Å / Num. obs: 37827 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 28.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.04 / Net I/σ(I): 18.05 |
Reflection shell | Resolution: 1.7→1.81 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 5904 / CC1/2: 0.709 / Rrim(I) all: 0.684 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4HR0 Resolution: 1.703→38.792 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 19.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.703→38.792 Å
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Refine LS restraints |
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LS refinement shell |
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