[English] 日本語
![](img/lk-miru.gif)
- PDB-3pin: Crystal structure of Mxr1 from Saccharomyces cerevisiae in comple... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3pin | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mxr1 from Saccharomyces cerevisiae in complex with Trx2 | ||||||
![]() |
| ||||||
![]() | ELECTRON TRANSPORT/Oxidoreductase / methionine-S-sulfoxide reductase / thioredoxin / ELECTRON TRANSPORT-Oxidoreductase complex | ||||||
Function / homology | ![]() membrane fusion priming complex / protein deglutathionylation / L-methionine-(S)-S-oxide reductase activity / TP53 Regulates Metabolic Genes / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / Interconversion of nucleotide di- and triphosphates / vacuole inheritance / The NLRP3 inflammasome / vacuole fusion, non-autophagic ...membrane fusion priming complex / protein deglutathionylation / L-methionine-(S)-S-oxide reductase activity / TP53 Regulates Metabolic Genes / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / Interconversion of nucleotide di- and triphosphates / vacuole inheritance / The NLRP3 inflammasome / vacuole fusion, non-autophagic / sulfate assimilation / disulfide oxidoreductase activity / Detoxification of Reactive Oxygen Species / fungal-type vacuole / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / deoxyribonucleotide biosynthetic process / Oxidative Stress Induced Senescence / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / glutathione metabolic process / cell redox homeostasis / protein transport / cellular response to oxidative stress / Golgi membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ma, X.X. / Guo, P.C. / Shi, W.W. / Luo, M. / Tan, X.F. / Chen, Y. / Zhou, C.Z. | ||||||
![]() | ![]() Title: Structural plasticity of the thioredoxin recognition site of yeast methionine S-sulfoxide reductase Mxr1 Authors: Ma, X.X. / Guo, P.C. / Shi, W.W. / Luo, M. / Tan, X.F. / Chen, Y. / Zhou, C.Z. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 111.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 86.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 435.2 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pilSC ![]() 3pimC ![]() 2fa4S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 11197.771 Da / Num. of mol.: 1 / Mutation: C34S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: TRX2 / Plasmid: pET28b / Production host: ![]() ![]() |
---|---|
#2: Protein | Mass: 20975.432 Da / Num. of mol.: 1 / Mutation: C23S, C25S, C44S, C68S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MXR1 / Plasmid: pET29b / Production host: ![]() ![]() References: UniProt: P40029, peptide-methionine (S)-S-oxide reductase |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.01 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 8.5 Details: 0.2M trimethylamine N-oxide, 0.1M Tris, 20% polyethylene glycol 2000 monomethyl ether, pH 8.5, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 8320 / % possible obs: 98 % |
Reflection shell | Resolution: 2.7→2.8 Å / % possible all: 98.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3PIL, 2FA4 Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.902 / SU B: 39.132 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.271 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.703→2.773 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|