[English] 日本語
![](img/lk-miru.gif)
- PDB-7r1r: RIBONUCLEOTIDE REDUCTASE E441Q MUTANT R1 PROTEIN FROM ESCHERICHIA COLI -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7r1r | ||||||
---|---|---|---|---|---|---|---|
Title | RIBONUCLEOTIDE REDUCTASE E441Q MUTANT R1 PROTEIN FROM ESCHERICHIA COLI | ||||||
![]() |
| ||||||
![]() | COMPLEX (OXIDOREDUCTASE/PEPTIDE) / RIBONUCLEOTIDE REDUCTASE / DEOXYRIBONUCLEOTIDE SYNTHESIS / RADICAL CHEMISTRY / ALLOSTERIC REGULATION / SPECIFICITY / COMPLEX (OXIDOREDUCTASE-PEPTIDE) / COMPLEX (OXIDOREDUCTASE-PEPTIDE) complex | ||||||
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 / protein folding chaperone / iron ion binding / ATP 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 / iron ion binding / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Eriksson, M. / Eklund, H. | ||||||
![]() | ![]() 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: ![]() 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: ![]() Title: Structure of Ribonucleotide Reductase Protein R1 Authors: Uhlin, U. / Eklund, H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 439.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 364.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5r1rSC ![]() 6r1rC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
3 | ![]()
| ||||||||||||
4 | ![]()
| x 6||||||||||||
5 | ![]()
| ||||||||||||
6 | ![]()
| ||||||||||||
7 | ![]()
| ||||||||||||
8 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-
Components
#1: Protein | Mass: 85876.102 Da / Num. of mol.: 3 / Mutation: E441Q 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: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 56 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() ![]() ![]() |
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: 53836 / % possible obs: 91.3 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 3.1→3.2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.36 / % possible all: 81.4 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: RIGID BODY Starting model: PDB ENTRY 5R1R Resolution: 3.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
| ||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 53836 / Rfactor Rwork: 0.2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|