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Yorodumi- PDB-7rpn: Crystal structure of triosephosphate isomerase from Bacteroides t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rpn | ||||||
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Title | Crystal structure of triosephosphate isomerase from Bacteroides thetaiotaomicron | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / TIM / triosephosphate isomerase / glycolysis / gluconeogenesis | ||||||
Function / homology | Function and homology information triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | ||||||
Authors | Vickers, C.J. / Fraga, D. / Patrick, W.M. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: To be published Title: Structure of BthTPI - Bacteroides thetaiotaomicron triosephoshate isomerase Authors: Vickers, C.J. / Fraga, D. / Patrick, W.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rpn.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rpn.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 7rpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rpn_validation.pdf.gz | 411.9 KB | Display | wwPDB validaton report |
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Full document | 7rpn_full_validation.pdf.gz | 411.9 KB | Display | |
Data in XML | 7rpn_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 7rpn_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/7rpn ftp://data.pdbj.org/pub/pdb/validation_reports/rp/7rpn | HTTPS FTP |
-Related structure data
Related structure data | 6neeS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26828.510 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: tpiA, BatF92_04170, BSIG_2740, Btheta7330_00522, DW011_22160, DW780_28020, DWY18_05535, DXA83_01600, ERS852511_01061, ERS852557_00096, FE838_09570, GA053_13175, GAN59_07295, GAN75_16360, GAN91_ ...Gene: tpiA, BatF92_04170, BSIG_2740, Btheta7330_00522, DW011_22160, DW780_28020, DWY18_05535, DXA83_01600, ERS852511_01061, ERS852557_00096, FE838_09570, GA053_13175, GAN59_07295, GAN75_16360, GAN91_01280, GAO00_10320, GAO51_28160, HMPREF2534_01356 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0FGJ1, triose-phosphate isomerase |
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#2: 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: 2.97 Å3/Da / Density % sol: 58.63 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citrate, pH 5.0, 20% w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 A |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→44.73 Å / Num. obs: 68732 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 10.61 Å2 / CC1/2: 1 / Net I/σ(I): 43.91 |
Reflection shell | Resolution: 1.37→1.45 Å / Num. unique obs: 10909 / CC1/2: 0.995 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NEE Resolution: 1.37→44.73 Å / SU ML: 0.0874 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.6154 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 13.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→44.73 Å
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Refine LS restraints |
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LS refinement shell |
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