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Yorodumi- PDB-2jgq: Kinetics and structural properties of triosephosphate isomerase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jgq | ||||||
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Title | Kinetics and structural properties of triosephosphate isomerase from Helicobacter pylori | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE | ||||||
Keywords | ISOMERASE / GLYCOLYSIS / PENTOSE SHUNT / GLUCONEOGENESIS / LIPID SYNTHESIS / HELICOBACTER PYLORI / FATTY ACID BIOSYNTHESIS / TRIOSEPHOSPHATE ISOMERASE | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | ||||||
Biological species | HELICOBACTER PYLORI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Chu, C.-H. / Lai, Y.-J. / Sun, Y.-J. | ||||||
Citation | Journal: Proteins: Struct., Funct., Bioinf. / Year: 2008 Title: Kinetics and Structural Properties of Triosephosphate Isomerase from Helicobacter Pylori Authors: Chu, C.-H. / Lai, Y.-J. / Sun, Y.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jgq.cif.gz | 110.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jgq.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 2jgq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/2jgq ftp://data.pdbj.org/pub/pdb/validation_reports/jg/2jgq | HTTPS FTP |
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-Related structure data
Related structure data | 1mo0S 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: 26611.730 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-234 Source method: isolated from a genetically manipulated source Details: MISSING RESIDUES, LYS 167 AND LYS 168 / Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG13009 / References: UniProt: P56076, triose-phosphate isomerase #2: Chemical | ChemComp-QGA / | #3: Chemical | #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: 2.14 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | pH: 8 / Details: pH 8 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: CONFOCAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 22125 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 12 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 7.1 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MO0 Resolution: 2.3→29.73 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 232396.76 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.4624 Å2 / ksol: 0.387442 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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