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- PDB-1rnr: AUTOCATALYTIC GENERATION OF DOPA IN THE ENGINEERED PROTEIN R2 F20... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rnr | ||||||
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Title | AUTOCATALYTIC GENERATION OF DOPA IN THE ENGINEERED PROTEIN R2 F208Y FROM ESCHERICHIA COLI RIBONUCLEOTIDE REDUCTASE AND CRYSTAL STRUCTURE OF THE DOPA-208 PROTEIN | ||||||
![]() | RIBONUCLEOTIDE REDUCTASE R1 PROTEIN | ||||||
![]() | OXIDOREDUCTASE / REDUCTASE(ACTING ON CH2) | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Aberg, A. / Nordlund, P. | ||||||
![]() | ![]() Title: Autocatalytic generation of dopa in the engineered protein R2 F208Y from Escherichia coli ribonucleotide reductase and crystal structure of the dopa-208 protein. Authors: Aberg, A. / Ormo, M. / Nordlund, P. / Sjoberg, B.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150 KB | Display | ![]() |
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PDB format | ![]() | 124.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 384.6 KB | Display | ![]() |
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Full document | ![]() | 403.3 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43401.809 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P69924, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-HG / #4: Water | ChemComp-HOH / | Nonpolymer details | EACH CHAIN HAS A DINUCLEAR IRON SITE CONTAINING (2 FE+++). THE MERCURY ATOMS ARE FROM EMTS IN THE ...EACH CHAIN HAS A DINUCLEAR IRON SITE CONTAINING | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.58 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop / Details: Nordlund, P. (1989) FEBS Lett., 258, 251. | ||||||||||||||||||||||||||||||||||||
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: 60 Å / Num. obs: 24658 / % possible obs: 94.5 % / Num. measured all: 67726 / Rmerge(I) obs: 0.09 |
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Processing
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Refinement | Resolution: 2.5→10 Å / Rfactor Rwork: 0.186 / Rfactor obs: 0.186 Details: RESIDUES 341 - 375 OF BOTH CHAINS ARE NOT VISIBLE IN THE ELECTRON DENSITY MAPS AND THEREFORE WERE NOT REFINED. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Rfactor obs: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.8 |