[English] 日本語
![](img/lk-miru.gif)
- PDB-1uzr: Crystal Structure of the Class Ib Ribonucleotide Reductase R2F-2 ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1uzr | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Class Ib Ribonucleotide Reductase R2F-2 subunit from Mycobacterium tuberculosis | ||||||
![]() | RIBONUCLEOTIDE REDUCTASE R2-2 SMALL SUBUNIT | ||||||
![]() | REDUCTASE / RIBONUCLEOTIDE REDUCTASE / TUBERCULOSIS / R2F-2 / RADICAL GENERATION / SMALL SUBUNIT | ||||||
Function / homology | ![]() ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Uppsten, M. / Davis, J. / Rubin, H. / Uhlin, U. | ||||||
![]() | ![]() Title: Crystal Structure of the Biologically Active Form of Class Ib Ribonucleotide Reductase Small Subunit from Mycobacterium Tuberculosis Authors: Uppsten, M. / Davis, J. / Rubin, H. / Uhlin, U. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 189.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 152.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 498.6 KB | Display | |
Data in XML | ![]() | 37.7 KB | Display | |
Data in CIF | ![]() | 52.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1r2fS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-
Components
#1: Protein | Mass: 33842.078 Da / Num. of mol.: 3 / Fragment: RADICAL GENERATING SUBUNIT, RESIDUES 1-296 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q50549, UniProt: P9WH71*PLUS, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-FE / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.3 % |
---|---|
Crystal grow | pH: 5.6 / Details: 0.6 M AMSO4, 100MM NACT PH 5.6, 50MM NA/K TARTRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 15, 2003 |
Radiation | Monochromator: CRYOGENICALLY COOLED HIGH RESOLUTION SI (311) AND LOWER RESOLUTION SI (111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 77125 / % possible obs: 99 % / Redundancy: 4.84 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.2→2.25 Å / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.7 / % possible all: 93.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1R2F Resolution: 2.2→111.8 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.876 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.39 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→111.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|