+Open data
-Basic information
Entry | Database: PDB / ID: 1amk | ||||||
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Title | LEISHMANIA MEXICANA TRIOSE PHOSPHATE ISOMERASE | ||||||
Components | TRIOSE PHOSPHATE ISOMERASETriosephosphate isomerase | ||||||
Keywords | GLUCONEOGENESIS / TIM / 2-PG / PGA / FATTY ACID BIOSYNTHESIS | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Williams, J.C. / Wierenga, R. | ||||||
Citation | 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. / Lambeir, A.M. / Wierenga, R.K. #1: Journal: Eur.J.Biochem. / Year: 1994 Title: Triose-Phosphate Isomerase of Leishmania Mexicana Mexicana. Cloning and Characterization of the Gene, Overexpression in Escherichia Coli and Analysis of the Protein Authors: Kohl, L. / Callens, M. / Wierenga, R.K. / Opperdoes, F.R. / Michels, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1amk.cif.gz | 63 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1amk.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 1amk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/1amk ftp://data.pdbj.org/pub/pdb/validation_reports/am/1amk | HTTPS FTP |
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-Related structure data
Related structure data | 5timS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27209.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania mexicana (eukaryote) / 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: 51 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.85 Details: 100 MM ACETIC ACID/NAOH 4.5 20% PEG 6000 1 MM DTT, EDTA, 1 MM AZIDE, 5% ETHYLENE GLYCOL, 10 MM 2-PHOSPHOGLYCOLIC ACID. CRYSTAL WAS MOVED INTO 100 MM CITRATE PH 5.85 20 % PEG 6000, 1 MM DTT, ...Details: 100 MM ACETIC ACID/NAOH 4.5 20% PEG 6000 1 MM DTT, EDTA, 1 MM AZIDE, 5% ETHYLENE GLYCOL, 10 MM 2-PHOSPHOGLYCOLIC ACID. CRYSTAL WAS MOVED INTO 100 MM CITRATE PH 5.85 20 % PEG 6000, 1 MM DTT, 1 MM EDTA, 1 MM AZIDE BEFORE DATA COLLECTION. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Feb 22, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→22 Å / Num. obs: 22669 / % possible obs: 89.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 6 / % possible all: 84.3 |
Reflection | *PLUS Lowest resolution: 22 Å / Num. measured all: 123706 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 84.3 % / Rmerge(I) obs: 0.116 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5TIM Resolution: 1.83→22 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET / Bsol: 262.9 Å2 / ksol: 0.802 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→22 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor all: 0.107 / Rfactor Rwork: 0.107 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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