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Yorodumi- PDB-5i3h: Structure-Function Studies on Role of Hydrophobic Clamping of a B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i3h | ||||||
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Title | Structure-Function Studies on Role of Hydrophobic Clamping of a Basic Glutamate in Catalysis by Triosephosphate Isomerase | ||||||
Components | Triosephosphate isomerase, glycosomal | ||||||
Keywords | ISOMERASE / Triosephosphate Isomerase / Catalysis / Hydrophobic Clamping / PGA | ||||||
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 brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Drake, E.J. / Gulick, A.M. / Richard, J.P. / Zhai, X. / Kim, K. / Reinhardt, C.J. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Structure-Function Studies of Hydrophobic Residues That Clamp a Basic Glutamate Side Chain during Catalysis by Triosephosphate Isomerase. Authors: Richard, J.P. / Amyes, T.L. / Malabanan, M.M. / Zhai, X. / Kim, K.J. / Reinhardt, C.J. / Wierenga, R.K. / Drake, E.J. / Gulick, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i3h.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i3h.ent.gz | 87.1 KB | Display | PDB format |
PDBx/mmJSON format | 5i3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i3h_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 5i3h_full_validation.pdf.gz | 437.9 KB | Display | |
Data in XML | 5i3h_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 5i3h_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/5i3h ftp://data.pdbj.org/pub/pdb/validation_reports/i3/5i3h | HTTPS FTP |
-Related structure data
Related structure data | 5i3fC 5i3gC 5i3iC 5i3jC 5i3kC 3timS 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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Unit cell |
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-Components
#1: Protein | Mass: 26781.672 Da / Num. of mol.: 2 / Mutation: I172A, L232A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P04789, triose-phosphate isomerase #2: Chemical | #3: Chemical | ChemComp-PGA / | #4: 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: 2.31 Å3/Da / Density % sol: 46.7 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15-25% Peg 8000, 50-100 mM potassium acetate, 100 mM BTP pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 4, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→28.47 Å / Num. obs: 23315 / % possible obs: 98.38 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.25→2.299 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TIM Resolution: 2.25→28.47 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2.14 / Phase error: 20.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→28.47 Å
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Refine LS restraints |
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LS refinement shell |
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