+Open data
-Basic information
Entry | Database: PDB / ID: 5gzp | ||||||
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Title | Y74COX MUTANT OF PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / TIM BARREL / BETA-ALPHA BARRELS / GLYCOLYSIS / COVALENT DIMER | ||||||
Function / homology | Function and homology information triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Pareek, V. / Balaram, P. / Murthy, M.R.N. | ||||||
Citation | Journal: To Be Published Title: Y74COX MUTANT OF PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE Authors: Pareek, V. / Balaram, P. / Murthy, M.R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gzp.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gzp.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 5gzp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gzp_validation.pdf.gz | 464 KB | Display | wwPDB validaton report |
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Full document | 5gzp_full_validation.pdf.gz | 467.5 KB | Display | |
Data in XML | 5gzp_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 5gzp_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/5gzp ftp://data.pdbj.org/pub/pdb/validation_reports/gz/5gzp | HTTPS FTP |
-Related structure data
Related structure data | 5gv4C 1lyxS 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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-Components
#1: Protein | Mass: 27937.707 Da / Num. of mol.: 2 / Mutation: Y74C,A163V Source method: isolated from a genetically manipulated source Details: MUTATION OF A163V PRESENT IN THE WILD TYPE TIM CONSIDERED AS TEMPLATE Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: TPI / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AA200 / References: UniProt: Q07412, triose-phosphate isomerase #2: Chemical | #3: Chemical | ChemComp-EDO / #4: 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: 2.78 Å3/Da / Density % sol: 55.76 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: HEPES 100mM pH7, PEG 8000, EDTA 10mM, CaCl2 10mM, Sodium Azide 0.006% Protein 10mg/mL PH range: 5.5-7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→48.75 Å / Num. all: 40623 / Num. obs: 37957 / % possible obs: 98.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.034→2.087 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LYX Resolution: 2.03→48.75 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.819 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.161 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.988 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→48.75 Å
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Refine LS restraints |
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