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Yorodumi- PDB-4oyt: Crystal structure of ternary complex of Plasmodium vivax SHMT wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oyt | ||||||||||||||||||
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Title | Crystal structure of ternary complex of Plasmodium vivax SHMT with D-serine and folinic acid | ||||||||||||||||||
Components | Serine hydroxymethyltransferase, putative | ||||||||||||||||||
Keywords | TRANSFERASE / alpha and beta protein / methyltransferase activity | ||||||||||||||||||
Function / homology | Function and homology information purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity ...purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / protein homodimerization activity / zinc ion binding / nucleus / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||||||||||||||
Authors | Chitnumsub, P. / Jaruwat, A. / Leartsakulpanich, U. | ||||||||||||||||||
Funding support | Thailand, 5items
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Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structures of Plasmodium vivax serine hydroxymethyltransferase: implications for ligand-binding specificity and functional control. Authors: Chitnumsub, P. / Jaruwat, A. / Riangrungroj, P. / Ittarat, W. / Noytanom, K. / Oonanant, W. / Vanichthanankul, J. / Chuankhayan, P. / Maenpuen, S. / Chen, C.J. / Chaiyen, P. / Yuthavong, Y. ...Authors: Chitnumsub, P. / Jaruwat, A. / Riangrungroj, P. / Ittarat, W. / Noytanom, K. / Oonanant, W. / Vanichthanankul, J. / Chuankhayan, P. / Maenpuen, S. / Chen, C.J. / Chaiyen, P. / Yuthavong, Y. / Leartsakulpanich, U. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oyt.cif.gz | 274.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oyt.ent.gz | 222.5 KB | Display | PDB format |
PDBx/mmJSON format | 4oyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oyt_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 4oyt_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 4oyt_validation.xml.gz | 53 KB | Display | |
Data in CIF | 4oyt_validation.cif.gz | 71.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/4oyt ftp://data.pdbj.org/pub/pdb/validation_reports/oy/4oyt | HTTPS FTP |
-Related structure data
Related structure data | 4pffC 4pfnC 4o6zS 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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Details | gel filtration |
-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 49249.160 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: D-serine and folinic acid at the pockets Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Strain: Salvador I / Gene: PVX_100730 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5K8L9 |
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-Non-polymers , 6 types, 279 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-TRS / | #6: Chemical | ChemComp-ETF / | #7: 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: 2.34 Å3/Da / Density % sol: 47.46 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion / pH: 8.5 Details: PEG4000, 0.06-0.12 M sodium chloride, 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 315r / Detector: CCD / Date: Nov 3, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→30 Å / Num. obs: 51056 / % possible obs: 94.6 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.047 / Χ2: 1.426 / Net I/av σ(I): 20.384 / Net I/σ(I): 30.3 / Num. measured all: 126391 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4O6Z Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.919 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.045 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.69 Å2 / Biso mean: 43.375 Å2 / Biso min: 21.24 Å2
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Refinement step | Cycle: final / Resolution: 2.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.395→2.457 Å / Total num. of bins used: 20
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