[English] 日本語
Yorodumi- PDB-4bi7: CRYSTAL STRUCTURE OF A MUTANT (C202A) OF TRIOSEPHOSPHATE ISOMERAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bi7 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF A MUTANT (C202A) OF TRIOSEPHOSPHATE ISOMERASE FROM GIARDIA LAMBLIA COMPLEXED WITH 2-PHOSPHOGLYCOLIC ACID | |||||||||
Components | TRIOSEPHOSPHATE ISOMERASE | |||||||||
Keywords | ISOMERASE | |||||||||
Function / homology | Function and homology information methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm Similarity search - Function | |||||||||
Biological species | GIARDIA INTESTINALIS (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Torres-Larios, A. / Enriquez-Flores, S. / Reyes-Vivas, H. / Oria-Hernandez, J. / Hernandez-Alcantara, G. | |||||||||
Citation | Journal: Plos One / Year: 2013 Title: Structural and Functional Perturbation of Giardia Lamblia Triosephosphate Isomerase by Modification of a Non-Catalytic, Non-Conserved Region. Authors: Hernandez-Alcantara, G. / Torres-Larios, A. / Enriquez-Flores, S. / Garcia-Torres, I. / Castillo-Villanueva, A. / Mendez, S.T. / De La Mora-De La Mora, I. / Gomez-Manzo, S. / Torres-Arroyo, ...Authors: Hernandez-Alcantara, G. / Torres-Larios, A. / Enriquez-Flores, S. / Garcia-Torres, I. / Castillo-Villanueva, A. / Mendez, S.T. / De La Mora-De La Mora, I. / Gomez-Manzo, S. / Torres-Arroyo, A. / Lopez-Velazquez, G. / Reyes-Vivas, H. / Oria-Hernandez, J. | |||||||||
History |
| |||||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4bi7.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bi7.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 4bi7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/4bi7 ftp://data.pdbj.org/pub/pdb/validation_reports/bi/4bi7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4bi5C 4bi6C 2dp3S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 27908.123 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) GIARDIA INTESTINALIS (eukaryote) / Strain: WB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: P36186, triose-phosphate isomerase |
---|---|
#2: Chemical | ChemComp-PGA / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.53 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 Details: PROTEIN WAS CRYSTALLYZED FROM 0.1 M MES MONOHYDRATE PH 6.5, 12 % W/V POLYETHYLENE GLYCOL 20,000 |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 28, 2010 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→38.7 Å / Num. obs: 44874 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4 / % possible all: 99.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DP3 Resolution: 1.6→38.69 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 23.123 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→38.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|