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Yorodumi- PDB-4bp1: Crystal Structure of Plasmodium Falciparum Spermidine Synthase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bp1 | ||||||
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Title | Crystal Structure of Plasmodium Falciparum Spermidine Synthase in Complex with 5'-Methylthioadenosine and Putrescine | ||||||
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: 2.17 Å | ||||||
Authors | Sprenger, J. / Halander, J.C. / Svensson, B. / Al-Karadaghi, S. / Persson, 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 | 4bp1.cif.gz | 188.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bp1.ent.gz | 149.6 KB | Display | PDB format |
PDBx/mmJSON format | 4bp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bp1_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4bp1_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4bp1_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 4bp1_validation.cif.gz | 51.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/4bp1 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/4bp1 | HTTPS FTP |
-Related structure data
Related structure data | 4bp3C 4cwaC 4cxmC 4uoeC 2i7cS C: citing same article (ref.) 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
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 32221.150 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, 418 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #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: 3.39 Å3/Da / Density % sol: 63.75 % / Description: NONE |
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Crystal grow | Details: 27.5% PEG 3350, 0.1 M MES, 0.1 M 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: 2.17→28.65 Å / Num. obs: 67848 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 3.42 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.99 |
Reflection shell | Resolution: 2.18→2.31 Å / Redundancy: 3.38 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.18 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2I7C Resolution: 2.17→28.65 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.289 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.173 / 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: 28.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.17→28.65 Å
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Refine LS restraints |
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