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Yorodumi- PDB-1qds: SUPERSTABLE E65Q MUTANT OF LEISHMANIA MEXICANA TRIOSEPHOSPHATE IS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qds | ||||||
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Title | SUPERSTABLE E65Q MUTANT OF LEISHMANIA MEXICANA TRIOSEPHOSPHATE ISOMERASE (TIM) | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE | ||||||
Keywords | ISOMERASE / TIM / LEISHMANIA / STABILITY / MUTAGENESIS / PKA | ||||||
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 / cytosol Similarity search - Function | ||||||
Biological species | Leishmania mexicana (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Lambeir, A.M. / Backmann, J. / Ruiz-Sanz, J. / Filimonov, V. / Nielsen, J.E. / Vriend, G. / Kursula, I. / Norledge, B.V. / Wierenga, R.K. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2000 Title: The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase. Authors: Lambeir, A.M. / Backmann, J. / Ruiz-Sanz, J. / Filimonov, V. / Nielsen, J.E. / Kursula, I. / Norledge, B.V. / Wierenga, R.K. #1: Journal: Protein Eng. / Year: 1999 Title: Structural and Mutagenesis Studies of Leishmania Triosephosphate Isomerase: a Point Mutation Can Convert a Mesophilic Enzyme into a Superstable Enzyme without Losing Catalytic Power Authors: Williams, J.C. / Zeelen, J.P. / Neubauer, G. / Vriend, G. / Backmann, J. / Michels, P.A.M. / Lambeir, A.-M. / Wierenga, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qds.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qds.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qds_validation.pdf.gz | 425.7 KB | Display | wwPDB validaton report |
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Full document | 1qds_full_validation.pdf.gz | 426.4 KB | Display | |
Data in XML | 1qds_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 1qds_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/1qds ftp://data.pdbj.org/pub/pdb/validation_reports/qd/1qds | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#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) / Plasmid: PET 3A / Production host: Escherichia coli (E. coli) / References: UniProt: P48499, triose-phosphate isomerase |
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#2: Chemical | ChemComp-PGA / |
#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: 2.5 Å3/Da / Density % sol: 50.8 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 16 % PEG 6000 10 MM PGA, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 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: Mar 22, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 17304 / Num. obs: 98464 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.169 / % possible all: 41.4 |
Reflection | *PLUS Num. obs: 17304 / Num. measured all: 98464 |
Reflection shell | *PLUS % possible obs: 41.4 % |
-Processing
Software |
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Refinement | Resolution: 2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: PROTEIN (CCP4)
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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