[English] 日本語
![](img/lk-miru.gif)
- PDB-8awp: Crystal structure of a manganese-containing cupin (tm1459) from T... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8awp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant 208 (V19I/R23H/M38I/I60F/C106Q) | ||||||
![]() | Cupin_2 domain-containing protein | ||||||
![]() | METAL BINDING PROTEIN / cupin / alkene cleavage / amino acid oxidation | ||||||
Function / homology | Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / Cupin type-2 domain-containing protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grininger, C. / Steiner, K. / Gruber, K. / Pavkov-Keller, T. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Engineering TM1459 for Stabilisation against Inactivation by Amino Acid Oxidation Authors: Grill, B. / Pavkov-Keller, T. / Grininger, C. / Darnhofer, B. / Gruber, K. / Hall, M. / Schwab, H. / Steiner, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 66.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 43.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 430.4 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8awnC ![]() 8awoC ![]() 1vj2S 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: 13165.018 Da / Num. of mol.: 2 / Mutation: V19I, R23H, M38I, I60F, C106Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8 Gene: TM_1459 Production host: ![]() ![]() References: UniProt: Q9X1H0 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.83 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 14.2 mg/ml protein concentration 1.6M Sodium citrate tribasic dihydrate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.595→45.77 Å / Num. obs: 27169 / % possible obs: 99.41 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.26 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06499 / Rpim(I) all: 0.02775 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.595→1.652 Å / Rmerge(I) obs: 0.7128 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 2590 / CC1/2: 0.837 / CC star: 0.955 / Rpim(I) all: 0.2985 / % possible all: 96.23 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1vj2 Resolution: 1.595→45.77 Å / SU ML: 0.1448 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8737 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: 26.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.595→45.77 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|