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Yorodumi- PDB-1ag1: MONOHYDROGEN PHOSPHATE BINDING TO TRYPANOSOMAL TRIOSEPHOSPHATE IS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ag1 | ||||||
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Title | MONOHYDROGEN PHOSPHATE BINDING TO TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE | ||||||
Keywords | ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE) / ISOMERASE (INTRAMOLECULAR OXIDOREDUCTASE) | ||||||
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 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | ||||||
Authors | Verlinde, C.L.M.J. / Hol, W.G.J. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 1991 Title: Anion binding at the active site of trypanosomal triosephosphate isomerase. Monohydrogen phosphate does not mimic sulphate. Authors: Verlinde, C.L. / Noble, M.E. / Kalk, K.H. / Groendijk, H. / Wierenga, R.K. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ag1.cif.gz | 106.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ag1.ent.gz | 82.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ag1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ag1_validation.pdf.gz | 392.4 KB | Display | wwPDB validaton report |
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Full document | 1ag1_full_validation.pdf.gz | 412.1 KB | Display | |
Data in XML | 1ag1_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 1ag1_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/1ag1 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/1ag1 | HTTPS FTP |
-Related structure data
Related structure data | 6timS 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
#1: Protein | Mass: 26865.832 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Organelle: GLYCOSOME / References: UniProt: P04789, triose-phosphate isomerase #2: Chemical | ChemComp-PO4 / | #3: Water | ChemComp-HOH / | |
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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: 2.39 Å3/Da / Density % sol: 48.59 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 2.4 M AMMONIUM SULFATE IN 0.2 MOPS BUFFER, PH 7.0 FOLLOWED BY TRANSFER TO 44% PEG-6000 CONTAINING 15 MM PHOSPHATE | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop / Details: Wierenga, R.K., (1984) J. Mol. Biol., 178, 487. | |||||||||||||||||||||||||||||||||||||||||||||
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: ELLIOTT GX-21 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Mar 1, 1990 / Details: STANDARD |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.36 Å / Num. obs: 17592 / % possible obs: 87.5 % / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Rmerge(I) obs: 0.063 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 6TIM Resolution: 2.36→6 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: A POSTERIORI / σ(F): 3 / Stereochemistry target values: TNT PROTGEO /
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Refinement step | Cycle: LAST / Resolution: 2.36→6 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5C / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.15 / Rfactor Rwork: 0.15 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |