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Yorodumi- PDB-3b7p: Crystal structure of spermidine synthase from Plasmodium falcipar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b7p | ||||||
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Title | Crystal structure of spermidine synthase from Plasmodium falciparum in complex with spermine | ||||||
Components | Spermidine synthase | ||||||
Keywords | TRANSFERASE / spermidine synthase / spermine / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information Metabolism of polyamines / spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Qiu, W. / Dong, A. / Ren, H. / Wu, H. / Zhao, Y. / Schapira, M. / Wasney, G. / Vedadi, M. / Lew, J. / Kozieradzki, I. ...Qiu, W. / Dong, A. / Ren, H. / Wu, H. / Zhao, Y. / Schapira, M. / Wasney, G. / Vedadi, M. / Lew, J. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Plotnikov, A.N. / Bochkarev, A. / Hui, R. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of spermidine synthase from Plasmodium falciparum in complex with spermine. Authors: Qiu, W. / Dong, A. / Ren, H. / Wu, H. / Zhao, Y. / Schapira, M. / Wasney, G. / Vedadi, M. / Lew, J. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / ...Authors: Qiu, W. / Dong, A. / Ren, H. / Wu, H. / Zhao, Y. / Schapira, M. / Wasney, G. / Vedadi, M. / Lew, J. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Plotnikov, A.N. / Bochkarev, A. / Hui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b7p.cif.gz | 193.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b7p.ent.gz | 153.8 KB | Display | PDB format |
PDBx/mmJSON format | 3b7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/3b7p ftp://data.pdbj.org/pub/pdb/validation_reports/b7/3b7p | HTTPS FTP |
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-Related structure data
Related structure data | 2pwpS S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 32221.150 Da / Num. of mol.: 3 / Fragment: Residues 40-321 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 #2: Chemical | #3: Chemical | #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: 3.34 Å3/Da / Density % sol: 63.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 5.5 Details: 25% w/v PEG 3350, 0.1M Ammonium sulfate, 0.1M Bis-tris, pH 5.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 27, 2007 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 84798 / Num. obs: 84798 / % possible obs: 98.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.4 Å2 / Rsym value: 0.068 / Net I/σ(I): 16.67 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.21 / Num. unique all: 7768 / Rsym value: 0.472 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PWP Resolution: 2→29.44 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.724 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.564 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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