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- PDB-3zzx: Crystallographic structure of thioredoxin from Litopenaeus vannamei -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zzx | ||||||
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Title | Crystallographic structure of thioredoxin from Litopenaeus vannamei | ||||||
![]() | THIOREDOXIN | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Campos-Acevedo, A.A. / Sotelo-Mundo, R.R. / Rudino-Pinera, E. | ||||||
![]() | ![]() Title: Expression, Purification, Crystallization and X-Ray Crystallographic Studies of Different Redox States of the Active Site of Thioredoxin 1 from the Whiteleg Shrimp Litopenaeus Vannamei Authors: Campos-Acevedo, A.A. / Garcia-Orozco, K.D. / Sotelo-Mundo, R.R. / Rudino-Pinera, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61 KB | Display | ![]() |
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PDB format | ![]() | 45.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 491.7 KB | Display | ![]() |
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Full document | ![]() | 495.4 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aj6C ![]() 4aj7C ![]() 4aj8C ![]() 1xwaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 11958.710 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: B1PWB9, thioredoxin-disulfide reductase |
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-Non-polymers , 5 types, 118 molecules ![](data/chem/img/DTU.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DTU / ( | ||||||
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#3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.6 % / Description: DATA WERE COLLECTED AT LANEM |
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Crystal grow | pH: 4.6 Details: 2.0 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU-MSC R-AXIS IV++ / Detector: IMAGE PLATE / Date: Aug 11, 2011 / 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→25 Å / Num. obs: 55281 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.14 % / Biso Wilson estimate: 23.81 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.88→1.99 Å / Redundancy: 3.16 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.14 / % possible all: 91.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1XWA Resolution: 1.88→23.29 Å / SU ML: 0.51 / σ(F): 1.36 / Phase error: 23.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.292 Å2 / ksol: 0.384 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→23.29 Å
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Refine LS restraints |
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LS refinement shell |
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