+Open data
-Basic information
Entry | Database: PDB / ID: 2wsq | ||||||
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Title | MonoTIM mutant RMM0-1, dimeric form. | ||||||
Components | TRIOSE PHOSPHATE ISOMERASE, GLYCOSOMAL | ||||||
Keywords | ISOMERASE / TEMPERATURE DEPENDANT EQUILIBRIUM / CATALYSIS / GLYCOSOME / GLYCOLYSIS / PENTOSE SHUNT / GLUCONEOGENESIS / LIPID SYNTHESIS / FATTY ACID BIOSYNTHESIS | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Rudino-Pinera, E. / Rojas-Trejo, S.P. / Arreola, R. / Saab-Rincon, G. / Soberon, X. / Horjales, E. | ||||||
Citation | Journal: To be Published Title: Space Group Transition Driven by Temperature and Related to Monomer-Dimer Transition in Solution: The Case of Monomeric Tim of Trypanosoma Brucei Brucei Authors: Rudino-Pinera, E. / Rojas-Trejo, S.P. / Arreola, R. / Saab-Rincon, G. / Soberon, X. / Horjales, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wsq.cif.gz | 228.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wsq.ent.gz | 184.4 KB | Display | PDB format |
PDBx/mmJSON format | 2wsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wsq_validation.pdf.gz | 469.6 KB | Display | wwPDB validaton report |
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Full document | 2wsq_full_validation.pdf.gz | 499 KB | Display | |
Data in XML | 2wsq_validation.xml.gz | 57.4 KB | Display | |
Data in CIF | 2wsq_validation.cif.gz | 87.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/2wsq ftp://data.pdbj.org/pub/pdb/validation_reports/ws/2wsq | HTTPS FTP |
-Related structure data
Related structure data | 2wsrC 1triS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25973.650 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-67,84-250 / 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(DE3) / References: UniProt: P04789, triose-phosphate isomerase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, SER 43 TO PRO ENGINEERED RESIDUE IN CHAIN A, THR 44 TO SER ...ENGINEERED | Sequence details | UNIPROT DEPOSITION | |
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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: 2.16 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | Temperature: 303 K / pH: 6.2 Details: 100 MM MES BUFFER PH 6.2, 180 MM LI2SO4, 26 PERCENT PEG 6000, 5 MM DITHIOTHREITOL, 1 MM EDTA AND 1 MM NAN3, AT 30 DEGREES CELSIUS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 16, 2006 Details: VERTICAL FOCUSING MIRROR, SINGLE CRYSTAL (SI111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING). |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.14 Å / Num. obs: 53956 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 37.86 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TRI Resolution: 2.1→71.25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.333 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.229 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.087 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→71.25 Å
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Refine LS restraints |
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