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Yorodumi- PDB-1kv5: Structure of Trypanosoma brucei brucei TIM with the salt-bridge-f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kv5 | ||||||
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Title | Structure of Trypanosoma brucei brucei TIM with the salt-bridge-forming residue Arg191 mutated to Ser | ||||||
Components | triosephosphate isomerase, glycosomal | ||||||
Keywords | ISOMERASE / TIM barrel / mutant / salt bridge | ||||||
Function / homology | Function and homology information glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Kursula, I. / Partanen, S. / Lambeir, A.-M. / Wierenga, R.K. | ||||||
Citation | Journal: FEBS Lett. / Year: 2002 Title: The importance of the conserved Arg191-Asp227 salt bridge of triosephosphate isomerase for folding, stability, and catalysis Authors: Kursula, I. / Partanen, S. / Lambeir, A.-M. / Wierenga, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kv5.cif.gz | 128.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kv5.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/1kv5 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/1kv5 | HTTPS FTP |
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-Related structure data
Related structure data | 5timS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 26795.717 Da / Num. of mol.: 2 / Mutation: R191S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Species: Trypanosoma brucei / Strain: brucei / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04789, triose-phosphate isomerase |
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-Non-polymers , 5 types, 787 molecules
#2: Chemical | #3: Chemical | ChemComp-DTT / | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / | #6: 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: 46.69 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: ammonium sulfate, sodium chloride, citric acid, pH 5.5, VAPOR DIFFUSION, HANGING DROP at 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.85 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 27, 2001 |
Radiation | Monochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→15 Å / Num. all: 115031 / Num. obs: 115031 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 37.7 |
Reflection shell | Resolution: 1.65→1.68 Å / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5.4 / % possible all: 99.3 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. obs: 60451 / Num. measured all: 245458 |
Reflection shell | *PLUS % possible obs: 99.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5TIM Resolution: 1.65→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: BABINET MODEL WITH MASK PARAMETERS FOR MASK CALCULATION | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.469 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→15 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.65 Å / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.172 / Total num. of bins used: 20 | ||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / Rfactor obs: 0.143 / Rfactor Rfree: 0.175 / Rfactor Rwork: 0.143 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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