+Open data
-Basic information
Entry | Database: PDB / ID: 5yg2 | ||||||
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Title | Plasmodium vivax SHMT bound with PLP-glycine and GS705 | ||||||
Components | Serine hydroxymethyltransferase | ||||||
Keywords | TRANSFERASE/INHIBITOR / alpha and beta protein / Transferase / methyltransferase activity / Inhibitor / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Model details | Plasmodium vivax SHMT bound with PLP-glycine and GS834 | ||||||
Authors | Chitnumsub, P. / Jaruwat, A. / Leartsakulpanich, U. / Schwertz, G. / Diederich, F. | ||||||
Citation | Journal: ChemMedChem / Year: 2018 Title: Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold Authors: Schwertz, G. / Witschel, M.C. / Rottmann, M. / Leartsakulpanich, U. / Chitnumsub, P. / Jaruwat, A. / Amornwatcharapong, W. / Ittarat, W. / Schafer, A. / Aponte, R.A. / Trapp, N. / Chaiyen, P. / Diederich, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yg2.cif.gz | 269.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yg2.ent.gz | 219.2 KB | Display | PDB format |
PDBx/mmJSON format | 5yg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/5yg2 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/5yg2 | HTTPS FTP |
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-Related structure data
Related structure data | 5yfzC 5yg3C 5yg4C 4tmrS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49249.160 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: PVC01_140059500, PVP01_1453700, PVT01_140059000 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A1G4H5I1, glycine hydroxymethyltransferase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.37 Å3/Da / Density % sol: 48.09 % / Mosaicity: 0.474 ° |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 8.5 / Details: PEG 4000, 0.06-0.12 M NaCl, 0.1 M Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→30 Å / Num. obs: 70254 / % possible obs: 99.1 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.015 / Rrim(I) all: 0.034 / Χ2: 0.828 / Net I/σ(I): 20 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TMR Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.872 / SU B: 9.746 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.43 / ESU R Free: 0.293 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.82 Å2 / Biso mean: 33.124 Å2 / Biso min: 12.32 Å2
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Refinement step | Cycle: final / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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