[English] 日本語
Yorodumi- PDB-4jeq: Different Contribution of Conserved Amino Acids to the Global Pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jeq | ||||||
---|---|---|---|---|---|---|---|
Title | Different Contribution of Conserved Amino Acids to the Global Properties of Homologous Enzymes | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL | ||||||
Keywords | ISOMERASE / TIM BARREL / DISEASE MUTATION / PENTOSE SHUNT / GLUCONEOGENESIS / GLYCOLYSIS | ||||||
Function / homology | Function and homology information glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | TRYPANOSOMA CRUZI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å | ||||||
Authors | Hernandez-Santoyo, A. / Aguirre-Fuentes, Y. / Torres-Larios, A. / Gomez-Puyou, A. / De Gomez-Puyou, M.T. | ||||||
Citation | Journal: Proteins / Year: 2014 Title: Different contribution of conserved amino acids to the global properties of triosephosphate isomerases. Authors: Aguirre, Y. / Cabrera, N. / Aguirre, B. / Perez-Montfort, R. / Hernandez-Santoyo, A. / Reyes-Vivas, H. / Enriquez-Flores, S. / de Gomez-Puyou, M.T. / Gomez-Puyou, A. / Sanchez-Ruiz, J.M. / Costas, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4jeq.cif.gz | 555.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4jeq.ent.gz | 462.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jeq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/4jeq ftp://data.pdbj.org/pub/pdb/validation_reports/je/4jeq | HTTPS FTP |
---|
-Related structure data
Related structure data | 4hhpC 2j27S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26851.807 Da / Num. of mol.: 12 / Mutation: E104D Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Strain: MEXICAN NINOA / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04789, triose-phosphate isomerase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PEG / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.69 % |
---|---|
Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 8.6 Details: 25% w/v PEG monomethyl ether 2000, 0.1 M Tris, 0.01 M Nickel (II) chloride hexahydrate, 5% w/v n-dodecyl-N,N-dimethylamin-N-oxide , pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 281.15K |
-Data collection
Diffraction | Mean temperature: 113 K | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Type: OTHER / Wavelength: 0.9791 Å | ||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 28, 2010 Details: HIGH-RESOLUTION DOUBLE- CRYSTAL SI(220) SAGITTAL FOCUSING, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR | ||||||||||||||||||
Radiation | Monochromator: ROSENBAUM-ROCK MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.3→89.78 Å / Num. all: 122434 / Num. obs: 122434 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 36.51 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.086 / Net I/σ(I): 8.1 | ||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J27 Resolution: 2.303→61.577 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 28.35 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.303→61.577 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|