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Open data
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Basic information
Entry | Database: PDB / ID: 1pfr | ||||||
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Title | RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA CHAIN | ||||||
![]() | PROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE | ||||||
![]() | REDUCTASE / OXIDOREDUCTASE / DNA REPLICATION / IRON / ACTING ON RIBOSE 2'-OH | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Logan, D.T. / Su, X.D. / Aberg, A. / Regnstrom, K. / Hajdu, J. / Eklund, H. / Nordlund, P. | ||||||
![]() | ![]() Title: Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at a dinuclear iron site. Authors: Logan, D.T. / Su, X.D. / Aberg, A. / Regnstrom, K. / Hajdu, J. / Eklund, H. / Nordlund, P. #1: ![]() Title: Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2 Authors: Nordlund, P. / Eklund, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.4 KB | Display | ![]() |
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PDB format | ![]() | 122.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.8 KB | Display | ![]() |
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Full document | ![]() | 446.1 KB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 40.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xikC ![]() 1ribS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.824533, 0.547277, 0.14364), Vector: |
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Components
#1: Protein | Mass: 39587.883 Da / Num. of mol.: 2 / Mutation: S211A Source method: isolated from a genetically manipulated source Details: DIFERROUS FORM OF NON-HEME DINUCLEAR IRON SITE / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P69924, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-FE / #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: 2.1 Å3/Da / Density % sol: 34 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: HANGING DROP VAPOR DIFFUSION. CRYSTALLISED FROM 20% PEG 4000, 0.2M NACL, 0.1M MES PH 6.0, 1MM ETHYLMERCURY SALICYLATE., vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1992 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 95516 / % possible obs: 86 % / Observed criterion σ(I): 0 / Redundancy: 2.79 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 1.8 / % possible all: 34.1 |
Reflection | *PLUS Num. obs: 34220 / Num. measured all: 95516 |
Reflection shell | *PLUS % possible obs: 34.1 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: DIFERRIC FORM OF R2 PROTEIN, PDB ENTRY 1RIB Resolution: 2.2→15 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: THE STRUCTURE WAS REFINED FURTHER TO THAT DESCRIBED IN REFERENCE 1 USING TNT.
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 149.6 Å2 / ksol: 0.507 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.179 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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