+Open data
-Basic information
Entry | Database: PDB / ID: 1av8 | ||||||
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Title | RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT FROM E. COLI | ||||||
Components | RIBONUCLEOTIDE REDUCTASE R2 | ||||||
Keywords | OXIDOREDUCTASE / DNA REPLICATION | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Han, S. / Arvai, A. / Tainer, J.A. | ||||||
Citation | Journal: Biochemistry / Year: 1998 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: Journal: J.Mol.Biol. / Year: 1993 Title: Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2 Authors: Nordlund, P. / Eklund, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1av8.cif.gz | 149.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1av8.ent.gz | 119.6 KB | Display | PDB format |
PDBx/mmJSON format | 1av8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1av8_validation.pdf.gz | 384 KB | Display | wwPDB validaton report |
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Full document | 1av8_full_validation.pdf.gz | 393.9 KB | Display | |
Data in XML | 1av8_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 1av8_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/1av8 ftp://data.pdbj.org/pub/pdb/validation_reports/av/1av8 | HTTPS FTP |
-Related structure data
Related structure data | 2av8C 1ribS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: (-0.394139, 0.916991, 0.061508), Vector: |
-Components
#1: Protein | Mass: 39603.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P69924, ribonucleoside-diphosphate reductase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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 | *PLUS Density % sol: 65 % | ||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
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: 2.8→100 Å / Num. obs: 299329 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rsym value: 0.089 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.8→2.92 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 10 / Rsym value: 0.284 / % possible all: 91.6 |
Reflection | *PLUS Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS % possible obs: 92 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RIB Resolution: 2.8→7 Å / Cross valid method: THROUGHOUT / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.8→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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