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Open data
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Basic information
Entry | Database: PDB / ID: 1kgp | ||||||
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Title | R2F from Corynebacterium Ammoniagenes in its Mn substituted form | ||||||
![]() | Ribonucleotide reductase protein R2F![]() | ||||||
![]() | METAL BINDING PROTEIN / ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() 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 | ![]() | 269.5 KB | Display | ![]() |
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PDB format | ![]() | 216.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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-MN / #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.08 % | ||||||||||||||||||||||||||||||||||||
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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: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 29, 2000 |
Radiation | Monochromator: diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→25 Å / Num. all: 77244 / Num. obs: 77244 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.071 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.209 / % possible all: 85.4 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 149319 |
Reflection shell | *PLUS % possible obs: 85.4 % |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.177 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |