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Yorodumi- PDB-4uoe: Crystal Structure of Plasmodium Falciparum Spermidine Synthase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uoe | |||||||||
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Title | Crystal Structure of Plasmodium Falciparum Spermidine Synthase in Complex with 5'-Deoxy-5'-Methylioadenosine and 4-Aminomethylaniline | |||||||||
Components | SPERMIDINE SYNTHASE | |||||||||
Keywords | TRANSFERASE / AMINOPROPYL TRANSFERASE / POLYAMINE PATHWAY / ROSSMANN-LIKE FOLD | |||||||||
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: 2.05 Å | |||||||||
Authors | Sprenger, J. / Halander, J.C. / Svensson, B. / Al-Karadaghi, S. / Person, L. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Three-Dimensional Structures of Plasmodium Falciparum Spermidine Synthase with Bound Inhibitors Suggest New Strategies for Drug Design. Authors: Sprenger, J. / Svensson, B. / Halander, J. / Carey, J. / Persson, L. / 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 | 4uoe.cif.gz | 188.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uoe.ent.gz | 149.9 KB | Display | PDB format |
PDBx/mmJSON format | 4uoe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/4uoe ftp://data.pdbj.org/pub/pdb/validation_reports/uo/4uoe | HTTPS FTP |
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-Related structure data
Related structure data | 4bp1C 4bp3C 4cwaC 4cxmC 2i7cS 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
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 32077.021 Da / Num. of mol.: 3 / Fragment: RESIDUES 41-321 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) Strain: 3D7 / Plasmid: P15-TEV-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8II73, spermidine synthase |
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-Non-polymers , 5 types, 435 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-1PG / | #6: 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: 63.19 % / Description: NONE |
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Crystal grow | Details: 27.5 % PEG 3350, 0.1 M MES PH 5.6, 0.1M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04122 |
Detector | Type: MARRESEARCH 165 MM / Detector: CCD / Date: Nov 28, 2012 / Details: MULTILAYER MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04122 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→29.54 Å / Num. obs: 76132 / % possible obs: 96 % / Observed criterion σ(I): 1 / Redundancy: 3.25 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.13 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 3.17 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.15 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2I7C Resolution: 2.05→29.53 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.461 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.164 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→29.53 Å
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