[English] 日本語

- PDB-8rtp: Bilirubin oxidase from Myrothecium verrucaria in complex with NAD+ -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8rtp | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Bilirubin oxidase from Myrothecium verrucaria in complex with NAD+ | ||||||||||||
![]() | Bilirubin oxidase | ||||||||||||
![]() | OXIDOREDUCTASE / Trp-His cross link / complex / NAD+ | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Svecova, L. / Koval, T. / Kolenko, P. / Ostergaard, L.H. / Dohnalek, J. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Bilirubin oxidase - answers to questions on ligand binding and Trp-His covalent link formation Authors: Svecova, L. / Koval, T. / Kolenko, P. / Ostergaard, L.H. / Dohnalek, J. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 268.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 4.8 MB | Display | |
Data in XML | ![]() | 60.3 KB | Display | |
Data in CIF | ![]() | 85.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rtoC ![]() 8rtqC ![]() 8rtrC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
2 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 60009.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Covalent link between side chains of Trp396 and His398. Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Sugars , 2 types, 4 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#3: Polysaccharide | Source method: isolated from a genetically manipulated source |
-Non-polymers , 8 types, 1032 molecules 














#4: Chemical | ChemComp-CU / #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-PGR / | #9: Chemical | #10: Chemical | ChemComp-GOL / | #11: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|---|
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.6 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 3.1 Details: 14% (w/v) PEG 3350, 0.1 M succinic acid, pH 3.1, protein concentration 25 mg/ml. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.992 Å / Num. obs: 87859 / % possible obs: 98.9 % / Observed criterion σ(I): -3.7 / Redundancy: 5.4 % / Biso Wilson estimate: 26.5 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.055 / Rrim(I) all: 0.128 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2 / Num. unique obs: 4073 / CC1/2: 0.723 / Rpim(I) all: 0.354 / Rrim(I) all: 0.782 / % possible all: 90.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions. The last refinement cycle was performed against all measured reflections.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.582 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.992 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|