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Yorodumi- PDB-4r1r: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH SUBSTRATE, GDP AND EFFEC... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 4r1r | ||||||
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| Title | RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH SUBSTRATE, GDP AND EFFECTOR DTTP FROM ESCHERICHIA COLI | ||||||
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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 informationribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / iron ion binding / ATP binding ...ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / iron ion binding / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / RIGID BODY / Resolution: 3.2 Å | ||||||
Authors | Eriksson, M. / Eklund, H. | ||||||
Citation | Journal: Structure / Year: 1997Title: 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. #1: Journal: Nature / Year: 1994Title: Structure of Ribonucleotide Reductase Protein R1 Authors: Uhlin, U. / Eklund, H. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4r1r.cif.gz | 443.2 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb4r1r.ent.gz | 363.6 KB | Display | PDB format |
| PDBx/mmJSON format | 4r1r.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4r1r_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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| Full document | 4r1r_full_validation.pdf.gz | 2.1 MB | Display | |
| Data in XML | 4r1r_validation.xml.gz | 79.7 KB | Display | |
| Data in CIF | 4r1r_validation.cif.gz | 104.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/4r1r ftp://data.pdbj.org/pub/pdb/validation_reports/r1/4r1r | HTTPS FTP |
-Related structure data
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Links
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Assembly
| Deposited unit | ![]()
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| 5 | x 6![]()
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| 10 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS oper:
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Components
| #1: Protein | Mass: 85845.023 Da / Num. of mol.: 3 / Mutation: C292A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() 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.) ![]() #3: Chemical | #4: Chemical | |
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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: 3.04 Å3/Da / Density % sol: 56.5 % | ||||||||||||||||||||||||||||||||||||
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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 FO 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 FO A 20-RESIDUE PEPTIDE CORRESPONDING TO THE C-TERMINUS OF THE R2 SUBUNIT AND IS ESSENTIAL FOR CRYSTALLIZATION. 10 MM DTTP AND 10 MM GDP WAS ADDED TO THE PROTEIN SOLUTION 48 H BEFORE FREEZING THE PROTEIN CRYSTALS | ||||||||||||||||||||||||||||||||||||
| Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
| Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Uhlin, U., (1993) FEBS Lett., 336, 148. | ||||||||||||||||||||||||||||||||||||
| Components of the solutions | *PLUS
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-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
| Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: MIRRORS |
| Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
| Reflection | Resolution: 3.2→45 Å / Num. obs: 53514 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 11.2 |
| Reflection shell | Resolution: 3.2→3.4 Å / Redundancy: 2 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.308 / % possible all: 93.6 |
| Reflection | *PLUS Rmerge(I) obs: 0.096 |
| Reflection shell | *PLUS % possible obs: 52.2 % |
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Processing
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| Refinement | Method to determine structure: RIGID BODY / Resolution: 3.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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| Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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| Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||
| Refine LS restraints | *PLUS
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