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Yorodumi- PDB-2y70: CRYSTALLOGRAPHIC STRUCTURE OF GM23, MUTANT G89D, AN EXAMPLE OF CA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y70 | ||||||
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Title | CRYSTALLOGRAPHIC STRUCTURE OF GM23, MUTANT G89D, AN EXAMPLE OF CATALYTIC MIGRATION FROM TIM TO THIAMIN PHOSPHATE SYNTHASE. | ||||||
Components | TRIOSE-PHOSPHATE ISOMERASE | ||||||
Keywords | ISOMERASE | ||||||
Function / homology | Function and homology information glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | TRYPANOSOMA BRUCEI BRUCEI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Saab-Rincon, G. / Olvera, L. / Olvera, M. / Rudino-Pinera, E. / Soberon, X. / Morett, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Evolutionary Walk between (Beta/Alpha)(8) Barrels: Catalytic Migration from Triosephosphate Isomerase to Thiamin Phosphate Synthase. Authors: Saab-Rincon, G. / Olvera, L. / Olvera, M. / Rudino-Pinera, E. / Benites, E. / Soberon, X. / Morett, E. | ||||||
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. THE SHEETS PRESENTED AS "BA" 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. THE SHEETS PRESENTED AS "CA" 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. THE SHEETS PRESENTED AS "DA" 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 | 2y70.cif.gz | 399.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y70.ent.gz | 329.6 KB | Display | PDB format |
PDBx/mmJSON format | 2y70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y70_validation.pdf.gz | 496.1 KB | Display | wwPDB validaton report |
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Full document | 2y70_full_validation.pdf.gz | 527.4 KB | Display | |
Data in XML | 2y70_validation.xml.gz | 46.7 KB | Display | |
Data in CIF | 2y70_validation.cif.gz | 64.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/2y70 ftp://data.pdbj.org/pub/pdb/validation_reports/y7/2y70 | HTTPS FTP |
-Related structure data
Related structure data | 2y6zSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 26376.072 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CM1061 THIE- / References: UniProt: P04789, triose-phosphate isomerase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, SER 43 TO PRO ENGINEERED RESIDUE IN CHAIN A, THR 44 TO SER ...ENGINEERED | Sequence details | THE SEQUENCE DEPOSITED IN THIS ENTRY IS 87.9 PER CENT IDENTICAL TO UNIPROT P04789 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.91 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM 2M LI2SO4, 100 MM MES, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 27, 2006 Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING. |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 55952 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 39.92 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y6Z Resolution: 2.3→47.448 Å / SU ML: 0.35 / σ(F): 1.97 / Phase error: 25.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.987 Å2 / ksol: 0.371 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→47.448 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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