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Yorodumi- PDB-2dp3: Crystal structure of a double mutant (C202A/A198V) of Triosephosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dp3 | ||||||
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Title | Crystal structure of a double mutant (C202A/A198V) of Triosephosphate isomerase from giardia lamblia | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / TRIOSEPHOSPHATE ISOMERASE / GIARDIA / ENZYME / ALPHA/BETA BARREL | ||||||
Function / homology | Function and homology information methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | ||||||
Biological species | Giardia intestinalis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Diaz, A. / Reyes-Vivas, H. / Lopez-Velazquez, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Disulfide Bridges in the Mesophilic Triosephosphate Isomerase from Giardia lamblia Are Related to Oligomerization and Activity Authors: Reyes-Vivas, H. / Diaz, A. / Peon, J. / Mendoza-Hernandez, G. / Hernandez-Alcantara, G. / De la Mora-De la Mora, I. / Enriquez-Flores, S. / Dominguez-Ramirez, L. / Lopez-Velazquez, G. #1: Journal: Proteins / Year: 2004 Title: An unusual triosephosphate isomerase from the early divergent eukaryote Giardia lamblia Authors: Lopez-Velazquez, G. / Molina-Ortiz, D. / Cabrera, N. / Peon-Peralta, J. / Reyes-Vivas, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dp3.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dp3.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 2dp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dp3_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 2dp3_full_validation.pdf.gz | 443.3 KB | Display | |
Data in XML | 2dp3_validation.xml.gz | 15 KB | Display | |
Data in CIF | 2dp3_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/2dp3 ftp://data.pdbj.org/pub/pdb/validation_reports/dp/2dp3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis: |
-Components
#1: Protein | Mass: 27936.176 Da / Num. of mol.: 1 / Mutation: C202A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Giardia intestinalis (eukaryote) / Strain: WB STRAIN / Gene: gltim / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYS / References: UniProt: P36186, triose-phosphate isomerase | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 5microL of C202A (13mg/mL) dissolved in 100mM triethanolamine, 10mM EDTA, mixed with 5microL of 2M ammonium sulfate,5% isopropanol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 11, 2004 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→28.65 Å / Num. obs: 18609 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.071 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 8.1 / Num. unique all: 2875 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1tcd, 1lyx, 1m6j Resolution: 2.1→28.65 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati sigma a obs: 0.09 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→28.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009
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