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Yorodumi- PDB-3m0n: Plasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS), E37A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m0n | ||||||
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Title | Plasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS), E37A catalytic residue mutant | ||||||
Components | Putative 6-pyruvoyl tetrahydrobiopterin synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / PTS / PTP SYNTHASE / PTPS / METAL-BINDING / TETRAHYDROBIOPTERIN BIOSYNTHESIS / FOLATE BIOSYNTHESIS / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP | ||||||
Function / homology | Function and homology information 6-pyruvoyltetrahydropterin synthase / 6-pyruvoyltetrahydropterin synthase activity / 6-carboxy-5,6,7,8-tetrahydropterin synthase activity / tetrahydrobiopterin biosynthetic process / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Larson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP) | ||||||
Citation | Journal: to be published Title: Structural analysis of the dual-functional 6-pyruvoyltetrahydropterin synthase from Malaria parasites. Authors: Larson, E.T. / Bosch, J. / Kim, J.E. / Kelley, A. / Castaneda, L. / Napuli, A. / Mueller, N. / Verlinde, C.L.M.J. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Hol, W.G.J. / Merritt, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m0n.cif.gz | 87.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m0n.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 3m0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m0n_validation.pdf.gz | 444.2 KB | Display | wwPDB validaton report |
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Full document | 3m0n_full_validation.pdf.gz | 445 KB | Display | |
Data in XML | 3m0n_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 3m0n_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/3m0n ftp://data.pdbj.org/pub/pdb/validation_reports/m0/3m0n | HTTPS FTP |
-Related structure data
Related structure data | 3lx3SC 3lzeC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20934.863 Da / Num. of mol.: 1 / Mutation: E37A Source method: isolated from a genetically manipulated source Details: E37A mutation confirmed from plasmid DNA sequence Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: PVX_114505 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A5K2B2, 6-pyruvoyltetrahydropterin synthase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-PE0 / |
#4: Water | ChemComp-HOH / |
Sequence details | E37A MUTATION CONFIRMED FROM PLASMID DNA SEQUENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 2 ul 25 mg/ml protein (in SGPP buffer) mixed with 2 ul 0.1 M sodium acetate (pH 5.2), 28% PEG 3350, 5 mM DTT; cryoprotected by 5 sec dip in 96 mM sodium acetate (pH 5.2), 24% PEG 3350, 134 ...Details: 2 ul 25 mg/ml protein (in SGPP buffer) mixed with 2 ul 0.1 M sodium acetate (pH 5.2), 28% PEG 3350, 5 mM DTT; cryoprotected by 5 sec dip in 96 mM sodium acetate (pH 5.2), 24% PEG 3350, 134 mM NaCl, 20% glycerol, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2010 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 19474 / % possible obs: 99.8 % / Observed criterion σ(I): 5 / Redundancy: 9.3 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1.064 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1947 / Χ2: 0.98 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3lx3, ligand removed and with E37 mutated to A Resolution: 1.9→35.3 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.565 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED. Identity of ligand in active site unknown but clear density for pterine ring of substrate or product present so modeled as such
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.34 Å2 / Biso mean: 49.913 Å2 / Biso min: 23.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→35.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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