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Yorodumi- PDB-5r1r: RIBONUCLEOTIDE REDUCTASE E441A MUTANT R1 PROTEIN FROM ESCHERICHIA COLI -
+Open data
-Basic information
Entry | Database: PDB / ID: 5r1r | ||||||
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Title | RIBONUCLEOTIDE REDUCTASE E441A MUTANT R1 PROTEIN FROM ESCHERICHIA COLI | ||||||
Components |
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Keywords | COMPLEX (OXIDOREDUCTASE/PEPTIDE) / RIBONUCLEOTIDE REDUCTASE / DEOXYRIBONUCLEOTIDE SYNTHESIS / RADICAL CHEMISTRY / ALLOSTERIC REGULATION / SPECIFICITY / COMPLEX (OXIDOREDUCTASE-PEPTIDE) / COMPLEX (OXIDOREDUCTASE-PEPTIDE) complex | ||||||
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 / protein folding chaperone / DNA replication / iron ion binding ...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 / protein folding chaperone / DNA replication / iron ion binding / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY / Resolution: 3.1 Å | ||||||
Authors | Eriksson, M. / Eklund, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1997 Title: A new mechanism-based radical intermediate in a mutant R1 protein affecting the catalytically essential Glu441 in Escherichia coli ribonucleotide reductase. Authors: Persson, A.L. / Eriksson, M. / Katterle, B. / Potsch, S. / Sahlin, M. / Sjoberg, B.M. #1: Journal: Structure / Year: 1997 Title: Binding of Allosteric Effectors to Ribonucleotide Reductase Protein R1: Reduction of Active-Site Cysteines Promotes Substrate Binding Authors: Eriksson, M. / Uhlin, U. / Ramaswamy, S. / Ekberg, M. / Regnstrom, K. / Sjoberg, B.M. / Eklund, H. #2: Journal: Nature / Year: 1994 Title: Structure of Ribonucleotide Reductase Protein R1 Authors: Uhlin, U. / Eklund, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5r1r.cif.gz | 437.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5r1r.ent.gz | 364.3 KB | Display | PDB format |
PDBx/mmJSON format | 5r1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5r1r_validation.pdf.gz | 411.9 KB | Display | wwPDB validaton report |
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Full document | 5r1r_full_validation.pdf.gz | 473 KB | Display | |
Data in XML | 5r1r_validation.xml.gz | 48.3 KB | Display | |
Data in CIF | 5r1r_validation.cif.gz | 72 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/5r1r ftp://data.pdbj.org/pub/pdb/validation_reports/r1/5r1r | HTTPS FTP |
-Related structure data
Related structure data | 6r1rC 7r1rC 1rlrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 85819.055 Da / Num. of mol.: 3 / Mutation: E441A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NRDA / Production host: Escherichia coli (E. coli) References: UniProt: P00452, ribonucleoside-diphosphate reductase #2: Protein/peptide | Mass: 2271.392 Da / Num. of mol.: 4 / Fragment: C-TERMINAL PORTION, 20 RESIDUES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P69924 #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: 3.02 Å3/Da / Density % sol: 56 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: PROTEIN WAS CRYSTALLIZED FROM 1.7 M LITHIUM SULFATE, AND 10 MM MAGNESIUM SULFATE IN 25 MM CITRATE BUFFER AT PH 6.0 THE PROTEIN SOLUTION CONTAINED 17 MG/ML R1 PROTEIN, 20 FOLD EXCESS OF A 20- ...Details: PROTEIN WAS CRYSTALLIZED FROM 1.7 M LITHIUM SULFATE, AND 10 MM MAGNESIUM SULFATE IN 25 MM CITRATE BUFFER AT PH 6.0 THE PROTEIN SOLUTION CONTAINED 17 MG/ML R1 PROTEIN, 20 FOLD EXCESS OF A 20-RESIDUE PEPTIDE CORRESPONDING TO THE C-TERMINUS OF THE R2 SUBUNIT AND IS ESSENTIAL FOR CRYSTALLIZATION | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Type: NSLS / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→40 Å / Num. obs: 53031 / % possible obs: 90.9 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 3.1→3.2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.29 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY Starting model: PDB ENTRY 1RLR Resolution: 3.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 52838 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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