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Yorodumi- PDB-2y61: Crystal structure of Leishmanial E65Q-TIM complexed with S-Glycid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y61 | |||||||||
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Title | Crystal structure of Leishmanial E65Q-TIM complexed with S-Glycidol phosphate | |||||||||
Components | TRIOSEPHOSPHATE ISOMERASE SYNONYM TRIOSE-PHOSPHATE ISOMERASE, TIM | |||||||||
Keywords | ISOMERASE / FATTY ACID BIOSYNTHESIS / TRANSITION STATE ANALOGUE / GLYCOLYSIS / PENTOSE SHUNT / GLUCONEOGENESIS / ENZYME-LIGAND COMPLEX | |||||||||
Function / homology | Function and homology information glycosome / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | |||||||||
Biological species | LEISHMANIA MEXICANA (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å | |||||||||
Authors | Venkatesan, R. / Alahuhta, M. / Pihko, P.M. / Wierenga, R.K. | |||||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: High resolution crystal structures of triosephosphate isomerase complexed with its suicide inhibitors: the conformational flexibility of the catalytic glutamate in its closed, liganded active site. Authors: Venkatesan, R. / Alahuhta, M. / Pihko, P.M. / Wierenga, R.K. | |||||||||
History |
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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 |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y61.cif.gz | 133.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y61.ent.gz | 102.3 KB | Display | PDB format |
PDBx/mmJSON format | 2y61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/2y61 ftp://data.pdbj.org/pub/pdb/validation_reports/y6/2y61 | HTTPS FTP |
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-Related structure data
Related structure data | 2y62C 2y63C 1n55S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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
#1: Protein | Mass: 27208.236 Da / Num. of mol.: 1 / Mutation: E65Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEISHMANIA MEXICANA (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: P48499, triose-phosphate isomerase | ||||||
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#2: Chemical | ChemComp-1GP / | ||||||
#3: Chemical | ChemComp-G3P / | ||||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Nonpolymer details | 1G3P, GOP: MICROHETEROGENEITY OBSERVED. S-GLYCIDOL PHOSPHATE BECAME GLYCEROL PHOSPHATE ESTER WITH ...1G3P, GOP: MICROHETER | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 0.48 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: 21% PEG6000, 0.1 M SODIUM ACETATE PH 4.5-5.5, 1MM DTT, 1MM EDTA, 1MM NAN3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.8997 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8997 Å / Relative weight: 1 |
Reflection | Resolution: 0.99→10 Å / Num. obs: 140160 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 0.99→1.02 Å / Redundancy: 4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.8 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N55 Resolution: 0.99→10 Å / Num. parameters: 22147 / Num. restraintsaints: 27895 / Cross valid method: FREE R-VALUE / σ(F): 0
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Refine analyze | Occupancy sum hydrogen: 1941.65 / Occupancy sum non hydrogen: 2322.88 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.99→10 Å
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Refine LS restraints |
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