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Yorodumi- PDB-1rib: STRUCTURE AND FUNCTION OF THE ESCHERICHIA COLI RIBONUCLEOTIDE RED... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rib | ||||||
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Title | STRUCTURE AND FUNCTION OF THE ESCHERICHIA COLI RIBONUCLEOTIDE REDUCTASE PROTEIN R2 | ||||||
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: 2.2 Å | ||||||
Authors | Eklund, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Structure and function of the Escherichia coli ribonucleotide reductase protein R2. Authors: Nordlund, P. / Eklund, H. #1: Journal: Proteins / Year: 1993 Title: Recognition of Errors in Three-Dimensional Structures of Proteins Authors: Sippl, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rib.cif.gz | 156.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rib.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 1rib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rib_validation.pdf.gz | 388.7 KB | Display | wwPDB validaton report |
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Full document | 1rib_full_validation.pdf.gz | 406.1 KB | Display | |
Data in XML | 1rib_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1rib_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/1rib ftp://data.pdbj.org/pub/pdb/validation_reports/ri/1rib | 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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Atom site foot note | 1: ASN B 131 - ASP B 132 OMEGA =149.75 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-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 | #3: 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: 20 ℃ / 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: 2.2 Å / Num. obs: 27364 / % possible obs: 74 % / Num. measured all: 90054 / Rmerge(I) obs: 0.059 |
-Processing
Software |
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Refinement | Resolution: 2.2→7 Å / Rfactor Rwork: 0.175 / Rfactor obs: 0.175 / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 7 Å / σ(F): 0 / Rfactor all: 0.175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.84 |