[English] 日本語
![](img/lk-miru.gif)
- PDB-3dmr: STRUCTURE OF DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS AT PH 7.0 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3dmr | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS AT PH 7.0 | ||||||
![]() | DMSO REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / DMSO / MOLYBDOPTERIN / PH 7 | ||||||
Function / homology | ![]() trimethylamine-N-oxide reductase activity / respiratory dimethylsulfoxide reductase / trimethylamine-N-oxide reductase / trimethylamine-N-oxide reductase (cytochrome c) activity / molybdenum ion binding / molybdopterin cofactor binding / anaerobic respiration / outer membrane-bounded periplasmic space / electron transfer activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mcalpine, A.S. / Bailey, S. | ||||||
![]() | Journal: J.Biol.Inorg.Chem. / Year: 1997 Title: Molybdenum Active Centre of Dmso Reductase from Rhodobacter Capsulatus: Crystal Structure of the Oxidised Enzyme at 1.82-A Resolution and the Dithionite-Reduced Enzyme at 2.8-A Resolution Authors: Mcalpine, A.S. / Mcewan, A.G. / Shaw, A. / Bailey, S. #1: ![]() Title: Preliminary Crystallographic Studies of Dimethylsulfoxide Reductase from Rhodobacter Capsulatus Authors: Bailey, S. / Mcalpine, A.S. / Duke, E.M.H. / Benson, N. / Mcewan, A.G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 177.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 135 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 89524.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-6MO / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 33.9 % Description: DIFFERENCE MAPS PICKED OUT CHANGES FROM OXIDIZED STRUCTURE | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7 Details: 0.1M CITRATE BUFFER, PH 4.8 - 5.2 20 - 3% PEG 4000 20% ETHANOL. CRYSTALS SOAKED IN 0.1M MES. PH 7.0 BEFORE DATA COLLECTION. CRYSTALS WERE SOAKED IN 0.1M MES BUFFER AT PH 7.0 FOR 10 MINUTES ...Details: 0.1M CITRATE BUFFER, PH 4.8 - 5.2 20 - 3% PEG 4000 20% ETHANOL. CRYSTALS SOAKED IN 0.1M MES. PH 7.0 BEFORE DATA COLLECTION. CRYSTALS WERE SOAKED IN 0.1M MES BUFFER AT PH 7.0 FOR 10 MINUTES BEFORE DATA COLLECTION. PH range: 4.8-5.2 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion / PH range low: 5.5 / PH range high: 4.7 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 21981 / % possible obs: 83.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.5→2.67 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3.2 / % possible all: 76.3 |
Reflection | *PLUS Num. measured all: 55133 / Rmerge(I) obs: 0.097 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: DIFFERENCE MAPS FROM OXIDISED STRUCTURE (BNL-5270) Resolution: 2.5→20 Å / Cross valid method: USE OF SINGLE FREE R SET / σ(F): 0
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
| ||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.181 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|