[English] 日本語
![](img/lk-miru.gif)
- PDB-7qbk: Crystal structure of a second homolog of R2-like ligand-binding o... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7qbk | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a second homolog of R2-like ligand-binding oxidase in Sulfolobus acidocaldarius (SaR2loxII) | |||||||||||||||
![]() | R2-like ligand-binding oxidase (homolog II) from Sulfolobus acidocaldarius | |||||||||||||||
![]() | OXIDOREDUCTASE / R2LOX / R2-LIKE LIGAND-BINDING OXIDASE / MN/FE COFACTOR / RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT FOLD / METALLOPROTEIN / FERRITIN-LIKE SUPERFAMILY | |||||||||||||||
Function / homology | Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / deoxyribonucleotide biosynthetic process / Ribonucleotide reductase-like / Ferritin-like superfamily / oxidoreductase activity / : / MANGANESE (III) ION / Uncharacterized protein![]() | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Lebrette, H. / Diamanti, R. / Srinivas, V. / Hogbom, M. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: Comparative structural analysis provides new insights into the function of R2-like ligand-binding oxidase. Authors: Diamanti, R. / Srinivas, V. / Johansson, A.I. / Nordstrom, A. / Griese, J.J. / Lebrette, H. / Hogbom, M. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 87.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 52.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 436.2 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qbpC ![]() 4hr0S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37060.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Saci_1112 / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-MN3 / |
#3: Chemical | ChemComp-FE / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54.01 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 24% (w/v) polyethylene glycol 1500, 5% (v/v) formamide, 40 mM sodium propionate, 20 mM sodium cacodylate trihydrate, 40 mM bis-tris propane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→41.91 Å / Num. obs: 17196 / % possible obs: 91.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 41.35 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1587 / Rpim(I) all: 0.0948 / Rrim(I) all: 0.1858 / Net I/σ(I): 6.67 |
Reflection shell | Resolution: 2.26→2.341 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.442 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 1739 / CC1/2: 0.398 / CC star: 0.755 / Rpim(I) all: 0.8499 / Rrim(I) all: 1.683 / % possible all: 93.53 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4hr0 Resolution: 2.26→41.91 Å / SU ML: 0.3396 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.3506 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→41.91 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|