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- PDB-4xb9: R2-like ligand-binding oxidase with aerobically reconstituted dii... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xb9 | ||||||
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Title | R2-like ligand-binding oxidase with aerobically reconstituted diiron cofactor | ||||||
![]() | Ribonuleotide reductase small subunit | ||||||
![]() | OXIDOREDUCTASE / R2-like ligand-binding oxidase / diiron cofactor / ribonucleotide reductase R2 subunit fold / metalloprotein | ||||||
Function / homology | ![]() deoxyribonucleotide biosynthetic process / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Griese, J.J. / Hogbom, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/Iron Cofactor. Authors: Griese, J.J. / Kositzki, R. / Schrapers, P. / Branca, R.M. / Nordstrom, A. / Lehtio, J. / Haumann, M. / Hogbom, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126 KB | Display | ![]() |
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PDB format | ![]() | 98.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 605.2 KB | Display | ![]() |
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Full document | ![]() | 606 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xbvC ![]() 4xbwC ![]() 5dcoC ![]() 5dcrC ![]() 5dcsC ![]() 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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Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) | ||||||||||||
Components on special symmetry positions |
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Components
#1: Protein | Mass: 36962.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: GK2771 / Plasmid: pET-46 Ek/LIC / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-PLM / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.46 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% (w/v) PEG1500, 0.1 M HEPES-Na, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: May 3, 2012 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.798→50 Å / Num. obs: 33183 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 30.24 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 18.94 |
Reflection shell | Resolution: 1.798→1.91 Å / Redundancy: 4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.14 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4HR0 Resolution: 1.798→48.533 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.798→48.533 Å
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Refine LS restraints |
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LS refinement shell |
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