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Open data
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Basic information
Entry | Database: PDB / ID: 2av8 | ||||||
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Title | Y122F MUTANT OF RIBONUCLEOTIDE REDUCTASE FROM ESCHERICHIA COLI | ||||||
![]() | RIBONUCLEOTIDE REDUCTASE R2 | ||||||
![]() | OXIDOREDUCTASE / DNA REPLICATION | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Han, S. / Arvai, A. / Tainer, J.A. | ||||||
![]() | ![]() Title: Characterization of Y122F R2 of Escherichia coli ribonucleotide reductase by time-resolved physical biochemical methods and X-ray crystallography. Authors: Tong, W. / Burdi, D. / Riggs-Gelasco, P. / Chen, S. / Edmondson, D. / Huynh, B.H. / Stubbe, J. / Han, S. / Arvai, A. / Tainer, J.A. #1: ![]() Title: Mechanism of Assembly of the Tyrosyl Radical-Dinuclear Iron Cluster Cofactor of Ribonucleotide Reductase Authors: Bollinger Junior, J.M. / Edmondson, D.E. / Huynh, B.H. / Filley, J. / Norton, J.R. / Stubbe, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152.1 KB | Display | ![]() |
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PDB format | ![]() | 120.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 388.1 KB | Display | ![]() |
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Full document | ![]() | 403.5 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1av8C ![]() 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: (0.999097, 0.037832, 0.019338), Vector: |
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Components
#1: Protein | Mass: 39587.883 Da / Num. of mol.: 2 / Mutation: Y122F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P69924, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-FE2 / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.6 Details: PROTEIN WAS CRYSTALLIZED FROM 80% SATURATED NACL, NEAR PHYSIOLOGICAL PH (PH 7.6) | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: IMAGE PLATE / Date: Aug 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→100 Å / Num. obs: 39923 / % possible obs: 95 % / Observed criterion σ(I): -3 / Rsym value: 0.058 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.46→2.55 Å / Redundancy: 2.55 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.302 / % possible all: 82.7 |
Reflection | *PLUS Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 83 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RIB Resolution: 2.46→7 Å / Cross valid method: THROUGHOUT / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.46→7 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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