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- PDB-1kgn: R2F from Corynebacterium Ammoniagenes in its oxidised, Fe contain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kgn | ||||||
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Title | R2F from Corynebacterium Ammoniagenes in its oxidised, Fe containing, form | ||||||
![]() | Ribonucleotide reductase protein R2F | ||||||
![]() | METAL BINDING PROTEIN / helix bundle / arm exchange / radical protein | ||||||
Function / homology | ![]() ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hogbom, M. / Huque, Y. / Sjoberg, B.M. / Nordlund, P. | ||||||
![]() | ![]() Title: Crystal structure of the di-iron/radical protein of ribonucleotide reductase from Corynebacterium ammoniagenes. Authors: Hogbom, M. / Huque, Y. / Sjoberg, B.M. / 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 | ![]() | 285.2 KB | Display | ![]() |
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PDB format | ![]() | 227.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456 KB | Display | ![]() |
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Full document | ![]() | 472.2 KB | Display | |
Data in XML | ![]() | 59.3 KB | Display | |
Data in CIF | ![]() | 90.9 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is one dimer. The asymmetric unit contains two of these dimers |
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Components
#1: Protein | Mass: 37959.023 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pIG056 / Production host: ![]() ![]() #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.73 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG4000, sodium citrate, ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||
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: Sep 30, 2000 |
Radiation | Monochromator: asymmetrically cut Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. all: 101333 / Num. obs: 101333 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.048 |
Reflection shell | Resolution: 1.85→1.88 Å / Rmerge(I) obs: 0.26 / % possible all: 94.7 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 193418 |
Reflection shell | *PLUS % possible obs: 94.7 % / Rmerge(I) obs: 0.26 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.85→30 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.158 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |