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Yorodumi- PDB-2x1u: Crystallographic binding studies with an engineered monomeric var... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x1u | ||||||
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Title | Crystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL | ||||||
Keywords | ISOMERASE / GLUCONEOGENESIS / LIPID SYNTHESIS / FATTY ACID BIOSYNTHESIS / TIM BARREL / PEROXISOME / GLYCOLYSIS / GLYCOSOME | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Salin, M. / Kapetaniou, E.G. / Vaismaa, M. / Lajunen, M. / Casteleijn, M.G. / Neubauer, P. / Salmon, L. / Wierenga, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Crystallographic Binding Studies with an Engineered Monomeric Variant of Triosephosphate Isomerase Authors: Salin, M. / Kapetaniou, E.G. / Vaismaa, M. / Lajunen, M. / Casteleijn, M.G. / Neubauer, P. / Salmon, L. / Wierenga, R. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x1u.cif.gz | 112.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x1u.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 2x1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/2x1u ftp://data.pdbj.org/pub/pdb/validation_reports/x1/2x1u | HTTPS FTP |
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-Related structure data
Related structure data | 2x16C 2x1rC 2x1sC 2x1tC 2x2gC 2vekS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25659.289 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-13,15-72,80-234,238-250 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P04789, triose-phosphate isomerase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 15 TO SER ENGINEERED RESIDUE IN CHAIN A, GLN 18 TO PRO ...ENGINEERED | |
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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: 2.24 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 20% PEG6000, 0.1M CITRATE, PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 10, 2008 / Details: MONTEL MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→16.23 Å / Num. obs: 36565 / % possible obs: 97.9 % / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.84→1.89 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VEK Resolution: 1.84→8.22 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 23.42 / Stereochemistry target values: ML / Details: RESIDUES 12-19 IN MOLECULE A ARE DISORDERED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.45 Å2 / ksol: 0.49 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→8.22 Å
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Refine LS restraints |
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LS refinement shell |
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