[English] 日本語
![](img/lk-miru.gif)
- PDB-5exe: Crystal structure of oxalate oxidoreductase from Moorella thermoa... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5exe | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with carboxy-TPP adduct | ||||||
![]() | (Oxalate oxidoreductase subunit ...) x 3 | ||||||
![]() | OXIDOREDUCTASE / oxalate / OFOR / thiamine | ||||||
Function / homology | ![]() oxalate oxidoreductase / oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / oxalate catabolic process / thiamine pyrophosphate binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gibson, M.I. / Chen, P.Y.-T. / Drennan, C.L. | ||||||
![]() | ![]() Title: One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography. Authors: Gibson, M.I. / Chen, P.Y. / Johnson, A.C. / Pierce, E. / Can, M. / Ragsdale, S.W. / Drennan, C.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 468.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 371 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 98.5 KB | Display | |
Data in CIF | ![]() | 150.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5exdC ![]() 5c4iS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Oxalate oxidoreductase subunit ... , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 43737.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 39073 / References: UniProt: Q2RI41, oxalate oxidoreductase #2: Protein | Mass: 33960.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 39073 / References: UniProt: Q2RI40, oxalate oxidoreductase #3: Protein | Mass: 34277.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 39073 / References: UniProt: Q2RI42, oxalate oxidoreductase |
---|
-Non-polymers , 5 types, 2444 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/5SR.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/5SR.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SF4 / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.41 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Crystals were grown in a Coy anaerobic chamber under an Ar/H2 gas mixture. OOR was mixed with the well solution containing PEG 3000 and Tacsimate (pH 7.0), in drops composed of 1 uL well ...Details: Crystals were grown in a Coy anaerobic chamber under an Ar/H2 gas mixture. OOR was mixed with the well solution containing PEG 3000 and Tacsimate (pH 7.0), in drops composed of 1 uL well solution and 1 uL OOR (30 mg/ml) with the addition of 0.2 uL of 100 mM oxalic acid (pH 8.0) to the crystallization drop |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→50 Å / Num. obs: 200377 / % possible obs: 94.4 % / Redundancy: 5.9 % / Rsym value: 0.129 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 1.9 / % possible all: 75 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5C4I Resolution: 1.88→48.704 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.64 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→48.704 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|