[English] 日本語
![](img/lk-miru.gif)
- PDB-5g2z: Crystallographic structure of mutant W31A of thioredoxin from Lit... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5g2z | ||||||
---|---|---|---|---|---|---|---|
Title | Crystallographic structure of mutant W31A of thioredoxin from Litopenaeus vannamei | ||||||
![]() | THIOREDOXIN | ||||||
![]() | OXIDOREDUCTASE / THIOREDOXIN / SHRIMP / LITOPENAEUS VANNAMEI / MUTANT / DISULFIDE BOND | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Campos-Acevedo, A.A. / Rudino-Pinera, E. | ||||||
![]() | ![]() Title: Is dimerization a common feature in thioredoxins? The case of thioredoxin from Litopenaeus vannamei. Authors: Campos-Acevedo, A.A. / Sotelo-Mundo, R.R. / Perez, J. / Rudino-Pinera, E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 55.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 40.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 426.9 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g30C ![]() 5g31C ![]() 3zzxS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 11843.578 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: RESIDUE 11 IS A SER IN THE UNIPROT DEPOSIT B1PWB9, IN THIS STRUCTURE A PHE IS CLEARLY VISIBLE ON POSITION 11. Source: (gene. exp.) ![]() Plasmid: PET22B / Production host: ![]() ![]() References: UniProt: B1PWB9, thioredoxin-disulfide reductase #2: Water | ChemComp-HOH / | Sequence details | A SERINE IS PRESENT IN RESIDUE 11 FROM UNIPROT DEPOSIT B1PWB9, IN OUR STRUCTURE RESIDUE 11 IS A PHENILALAN | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.78 % / Description: NONE |
---|---|
Crystal grow | pH: 7 Details: 30% (W/V) POLYETHYLENE GLYCOL 3, 000. 100 MM TRIS BASE/HYDROCHLORIC ACID PH 7.0. 200 MM NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU-MSC R-AXIS IV / Detector: IMAGE PLATE / Date: Nov 18, 2014 / Details: VARIMAX-HR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→23.43 Å / Num. obs: 17415 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 23.21 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.88→1.92 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZZX Resolution: 1.88→23.429 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 22.19 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→23.429 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|