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Yorodumi- PDB-1mrr: SUBSTITUTION OF MANGANESE FOR IRON IN RIBONUCLEOTIDE REDUCTASE FR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mrr | ||||||
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Title | SUBSTITUTION OF MANGANESE FOR IRON IN RIBONUCLEOTIDE REDUCTASE FROM ESCHERICHIA COLI. SPECTROSCOPIC AND CRYSTALLOGRAPHIC CHARACTERIZATION | ||||||
Components | RIBONUCLEOTIDE REDUCTASE R1 PROTEIN | ||||||
Keywords | REDUCTASE(ACTING ON CH2) | ||||||
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 / Resolution: 2.5 Å | ||||||
Authors | Eklund, H. / Nordlund, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1992 Title: Substitution of manganese for iron in ribonucleotide reductase from Escherichia coli. Spectroscopic and crystallographic characterization. Authors: Atta, M. / Nordlund, P. / Aberg, A. / Eklund, H. / Fontecave, M. #1: Journal: Nature / Year: 1990 Title: Three-Dimensional Structure of the Free Radical Protein of Ribonucleotide Reductase Authors: Nordlund, P. / Sjuberg, B.-M. / Eklund, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mrr.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mrr.ent.gz | 126.7 KB | Display | PDB format |
PDBx/mmJSON format | 1mrr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mrr_validation.pdf.gz | 381.1 KB | Display | wwPDB validaton report |
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Full document | 1mrr_full_validation.pdf.gz | 403.9 KB | Display | |
Data in XML | 1mrr_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 1mrr_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/1mrr ftp://data.pdbj.org/pub/pdb/validation_reports/mr/1mrr | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: (-0.82, -0.552, -0.151), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. | |
-Components
#1: Protein | Mass: 43369.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) References: UniProt: P69924, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-HG / #4: Water | ChemComp-HOH / | Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.92 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 37 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Num. obs: 22517 / % possible obs: 86 % / Rmerge(I) obs: 0.076 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.18 / Rfactor obs: 0.18 / Highest resolution: 2.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 5 Å / Rfactor obs: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.9 |