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Yorodumi- PDB-2j24: The functional role of the conserved active site proline of trios... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j24 | ||||||
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Title | The functional role of the conserved active site proline of triosephosphate isomerase | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL | ||||||
Keywords | ISOMERASE / PROTEIN ENGINEERING / FATTY ACID BIOSYNTHESIS / GLUCONEOGENESIS / LIPID SYNTHESIS / PENTOSE SHUNT / POINT MUTATION / LOOP7 / GLYCOSOME / TIM-BARREL | ||||||
Function / homology | Function and homology information glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | TRYPANOSOMA BRUCEI BRUCEI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Casteleijn, M.G. / Alahuhta, M. / Groebel, K. / El-Sayed, I. / Augustyns, K. / Lambeir, A.M. / Neubauer, P. / Wierenga, R.K. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Functional Role of the Conserved Active Site Proline of Triosephosphate Isomerase. Authors: Casteleijn, M.G. / Alahuhta, M. / Groebel, K. / El-Sayed, I. / Augustyns, K. / Lambeir, A.M. / Neubauer, P. / Wierenga, R.K. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 | 2j24.cif.gz | 115.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j24.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 2j24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j24_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 2j24_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 2j24_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 2j24_validation.cif.gz | 35.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/2j24 ftp://data.pdbj.org/pub/pdb/validation_reports/j2/2j24 | HTTPS FTP |
-Related structure data
Related structure data | 2j27C 5timS 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 5 / Auth seq-ID: 2 - 250 / Label seq-ID: 2 - 250
NCS oper: (Code: given Matrix: (-1, -0.000139, 0.001548), Vector: |
-Components
#1: Protein | Mass: 26839.795 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P04789, triose-phosphate isomerase #2: Water | ChemComp-HOH / | Compound details | 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: 2.07 Å3/Da / Density % sol: 40.54 % |
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Crystal grow | pH: 7 Details: WELL SOLUTION: 0.1 M TEA PH 7.0, 27% PEG 2K MME AND 0.2 M KSCN PROTEIN SOLUTION: 11 MG/ML PROTEIN, 0.02 M TRIS/HCL PH 7.0, 0.1 M NACL, 1 MM DTT, 1 MM EDTA AND 1 MM NAN3. |
-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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 16, 2004 / Details: MONTEL MIRRORS |
Radiation | Monochromator: MONTEL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. obs: 22102 / % possible obs: 94.5 % / Redundancy: 2.65 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 2.63 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 8.67 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5TIM Resolution: 2.1→19.21 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.883 / SU B: 10.282 / SU ML: 0.15 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.11 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.21 Å
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Refine LS restraints |
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