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Yorodumi- PDB-2x2g: CRYSTALLOGRAPHIC BINDING STUDIES WITH AN ENGINEERED MONOMERIC VAR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x2g | |||||||||
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Title | CRYSTALLOGRAPHIC BINDING STUDIES WITH AN ENGINEERED MONOMERIC VARIANT OF TRIOSEPHOSPHATE ISOMERASE | |||||||||
Components | TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL | |||||||||
Keywords | ISOMERASE / FATTY ACID BIOSYNTHESIS / GLUCONEOGENESIS / GLYCOLYSIS / GLYCOSOME / LIPID SYNTHESIS | |||||||||
Function / homology | Function and homology information glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm Similarity search - Function | |||||||||
Biological species | TRYPANOSOMA BRUCEI BRUCEI (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Salin, M. / Kapetaniou, E.G. / Vaismaa, M. / Lajunen, M. / Casteleijn, M.G. / Neubauer, P. / Salmon, L. / Wierenga, R. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Crystallographic Binding Studies with an Engineered Monomeric Variant of Triosephosphate Isomerase Authors: Salin, M. / Kapetaniou, E.G. / Vaismaa, M. / Lajunen, M. / Casteleijn, M.G. / Neubauer, P. / Salmon, L. / Wierenga, R. | |||||||||
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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x2g.cif.gz | 114.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x2g.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 2x2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/2x2g ftp://data.pdbj.org/pub/pdb/validation_reports/x2/2x2g | HTTPS FTP |
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-Related structure data
Related structure data | 2x16C 2x1rC 2x1sC 2x1tC 2x1uC 2vekS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25659.289 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-13,15-72,80-234,238-250 / Mutation: YES Source method: isolated from a genetically manipulated source Details: A MONOMERIC MUTANT OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, WHICH HAS A BOUND 3PGA MOLECULE IN AN ACTIVE SITE Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P04789, triose-phosphate isomerase #2: Chemical | ChemComp-3PG / | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 15 TO SER ENGINEERED RESIDUE IN CHAIN A, GLN 18 TO PRO ...ENGINEERED | |
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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: 2.24 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 20% PEG6000, 0.1M CITRATE, PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 30, 2009 / Details: MONTEL MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. obs: 32859 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 20.22 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.9 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VEK Resolution: 1.9→14.073 Å / SU ML: 0.22 / σ(F): 2 / Phase error: 21.52 / Stereochemistry target values: ML / Details: RESIDUES 13-18 ARE DISORDERED, WERE NOT MODELED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.221 Å2 / ksol: 0.418 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→14.073 Å
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Refine LS restraints |
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LS refinement shell |
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