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- PDB-1jqc: Mn substituted Ribonucleotide reductase R2 from E. Coli oxidized ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jqc | ||||||
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Title | Mn substituted Ribonucleotide reductase R2 from E. Coli oxidized by hydrogen peroxide and hydroxylamine | ||||||
![]() | Protein R2 of ribonucleotide reductase | ||||||
![]() | OXIDOREDUCTASE / Ribonucleotide reductase R2 / Radical protein / Mn substituted / oxidized By H2O2/NH2OH | ||||||
Function / homology | ![]() ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / iron ion binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hogbom, M. / Andersson, M.E. / Nordlund, P. | ||||||
![]() | ![]() Title: Crystal structures of oxidized dinuclear manganese centres in Mn-substituted class I ribonucleotide reductase from Escherichia coli: carboxylate shifts with implications for O2 activation and radical generation. Authors: Hogbom, M. / Andersson, M.E. / Nordlund, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.7 KB | Display | ![]() |
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PDB format | ![]() | 133.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.2 KB | Display | ![]() |
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Full document | ![]() | 465.8 KB | Display | |
Data in XML | ![]() | 36.4 KB | Display | |
Data in CIF | ![]() | 54.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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: 43426.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P69924, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-HG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.1 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: peg 4000, MES, EMTS, sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Details: Nordlund, P., (1989) FEBS Lett., 258, 251. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 7, 1999 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→29 Å / Num. all: 91243 / Num. obs: 91243 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.065 |
Reflection shell | Resolution: 1.61→1.71 Å / % possible all: 95.3 |
Reflection | *PLUS Lowest resolution: 29 Å |
Reflection shell | *PLUS % possible obs: 99.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.286 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.61→29 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 29 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.176 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.8 |