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Yorodumi- PDB-6ooi: Crystal structure of triosephosphate isomerase from Schistosoma m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ooi | ||||||
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Title | Crystal structure of triosephosphate isomerase from Schistosoma mansoni in complex with 2PG | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE | ||||||
Function / homology | Function and homology information triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | Schistosoma mansoni (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Jimenez-Sandoval, P. / Brieba, L. | ||||||
Funding support | Mexico, 1items
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Citation | Journal: Plos Negl Trop Dis / Year: 2020 Title: Crystal structures of Triosephosphate Isomerases from Taenia solium and Schistosoma mansoni provide insights for vaccine rationale and drug design against helminth parasites. Authors: Jimenez-Sandoval, P. / Castro-Torres, E. / Gonzalez-Gonzalez, R. / Diaz-Quezada, C. / Gurrola, M. / Camacho-Manriquez, L.D. / Leyva-Navarro, L. / Brieba, L.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ooi.cif.gz | 407.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ooi.ent.gz | 327.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ooi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ooi_validation.pdf.gz | 284.5 KB | Display | wwPDB validaton report |
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Full document | 6ooi_full_validation.pdf.gz | 285.8 KB | Display | |
Data in XML | 6ooi_validation.xml.gz | 2.1 KB | Display | |
Data in CIF | 6ooi_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/6ooi ftp://data.pdbj.org/pub/pdb/validation_reports/oo/6ooi | HTTPS FTP |
-Related structure data
Related structure data | 6oogC 5zfxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 28456.465 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: TPI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P48501, triose-phosphate isomerase |
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-Non-polymers , 5 types, 1099 molecules
#2: Chemical | ChemComp-PGA / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.4 Å3/Da / Density % sol: 48.79 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05M Cesium chloride 0.1M MES monohydrate 6.5 30% v/v Jeffamine M-600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5419 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→58.61 Å / Num. obs: 115018 / % possible obs: 100 % / Redundancy: 4.5 % / CC1/2: 0.984 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.081 / Rrim(I) all: 0.173 / Net I/σ(I): 5.6 / Num. measured all: 517652 / Scaling rejects: 76 |
Reflection shell | Resolution: 2.14→2.18 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.804 / Num. measured all: 24134 / Num. unique obs: 5688 / CC1/2: 0.639 / Rpim(I) all: 0.436 / Rrim(I) all: 0.917 / Net I/σ(I) obs: 1.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZFX Resolution: 2.14→58.609 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.04 Å2 / Biso mean: 24.1252 Å2 / Biso min: 7.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.14→58.609 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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