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- PDB-4cxm: Crystal Structure of Plasmodium Falciparum Spermidine Synthase in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cxm | ||||||
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Title | Crystal Structure of Plasmodium Falciparum Spermidine Synthase in Complex with METHYLTHIOADENOSIN AND SPERMIDINE after catalysis in crystal | ||||||
![]() | SPERMIDINE SYNTHASE | ||||||
![]() | TRANSFERASE / ANINOPROPYL TRANSFERASE / POLYAMINE PATHWAY. ROSSMANN-LIKE FOLD | ||||||
Function / homology | ![]() Metabolism of polyamines / spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sprenger, J. / Svensson, B. / Al-Karadaghi, S. / Persson, L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.9 KB | Display | ![]() |
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PDB format | ![]() | 150.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 37.2 KB | Display | |
Data in CIF | ![]() | 53.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bp1C ![]() 4bp3C ![]() 4cwaC ![]() 4uoeC ![]() 2i7cS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 41-321 (ACCORDING TO UNIPROT SEQUENCE Q8II73) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 3D7 / Plasmid: P15-TEV-LIC / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT USED FOR CRYSTALLIZATION IS MISSES 40 RESIDUES FROM NATIVE SEQUENCE. RESIDUE LYS 41 ...THE CONSTRUCT USED FOR CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.66 % / Description: NONE |
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Crystal grow | Details: 27 % PEG 3350, 0.1 M MES PH 5.5, 0.1 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH 65 MM / Detector: CCD / Date: Dec 13, 2013 / 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: 1.75→50 Å / Num. obs: 124715 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.98 |
Reflection shell | Resolution: 1.75→1.86 Å / Redundancy: 3.04 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.29 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2I7C Resolution: 1.75→44.94 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.3 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.096 / 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: 25.319 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→44.94 Å
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Refine LS restraints |
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