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Yorodumi- PDB-2pt9: The structure of Plasmodium falciparum spermidine synthase in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pt9 | ||||||
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Title | The structure of Plasmodium falciparum spermidine synthase in complex with decarboxylated S-adenosylmethionine and the inhibitor cis-4-methylcyclohexylamine (4MCHA) | ||||||
Components | Spermidine synthase | ||||||
Keywords | TRANSFERASE / SPERMIDINE SYNTHASE / STRUCTURAL GENOMICS CONSORTIUM / SGC / INHIBITOR COMPLEX / Structural Biology of Malarial Parasites and Other Apicomplexans | ||||||
Function / homology | Function and homology information Metabolism of polyamines / spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dufe, V.T. / Qiu, W. / Muller, I.B. / Hui, R. / Walter, R.D. / Al-Karadaghi, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal structure of Plasmodium falciparum spermidine synthase in complex with the substrate decarboxylated S-adenosylmethionine and the potent inhibitors 4MCHA and AdoDATO. Authors: Dufe, V.T. / Qiu, W. / Muller, I.B. / Hui, R. / Walter, R.D. / Al-Karadaghi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pt9.cif.gz | 186.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pt9.ent.gz | 146.6 KB | Display | PDB format |
PDBx/mmJSON format | 2pt9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/2pt9 ftp://data.pdbj.org/pub/pdb/validation_reports/pt/2pt9 | HTTPS FTP |
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-Related structure data
Related structure data | 2i7cSC 2pssC 2pt6C 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 on special symmetry positions |
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Details | The biological unit is a dimer (chains B & C) |
-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 36640.465 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: PF11_0301 / Plasmid: PET28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-ROSETTA OXFORD / References: UniProt: Q8II73, spermidine synthase |
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-Non-polymers , 6 types, 185 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / | #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: 2.88 Å3/Da / Density % sol: 62.75 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG3350, 0.1 M Ammonium Sulphate and 0.1 M Bis-Tris pH5.5, 2.5 mM dcAdoMet, 2.5 mM 4MCHA, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.043 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 7, 2006 / Details: mirrors |
Radiation | Monochromator: Bent silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.043 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 62364 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 3.45 % / Biso Wilson estimate: 39.247 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.85 |
Reflection shell | Resolution: 2.2→2.5 Å / Redundancy: 3.45 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.8 / Num. measured obs: 68248 / Num. unique all: 19744 / % possible all: 98.8 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2I7C Resolution: 2.2→19.77 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.884 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): -3 / ESU R: 0.21 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.374 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→19.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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