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Yorodumi- PDB-4b13: Plasmodium vivax N-myristoyltransferase with a bound benzofuran i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b13 | ||||||
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Title | Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 25) | ||||||
Components | GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / MALARIA / DRUG DESIGN | ||||||
Function / homology | Function and homology information glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity Similarity search - Function | ||||||
Biological species | PLASMODIUM VIVAX (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Yu, Z. / Brannigan, J.A. / Moss, D.K. / Brzozowski, A.M. / Wilkinson, A.J. / Holder, A.A. / Tate, E.W. / Leatherbarrow, R.J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Design and Synthesis of Inhibitors of Plasmodium Falciparum N-Myristoyltransferase, a Promising Target for Antimalarial Drug Discovery. Authors: Yu, Z. / Brannigan, J.A. / Moss, D.K. / Brzozowski, A.M. / Wilkinson, A.J. / Holder, A.A. / Tate, E.W. / Leatherbarrow, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b13.cif.gz | 282.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b13.ent.gz | 227.4 KB | Display | PDB format |
PDBx/mmJSON format | 4b13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/4b13 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/4b13 | HTTPS FTP |
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-Related structure data
Related structure data | 4b10SC 4b11C 4b12C 4b14C 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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 45077.594 Da / Num. of mol.: 3 / Fragment: RESIDUES 27-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM VIVAX (malaria parasite P. vivax) Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: A5K1A2, glycylpeptide N-tetradecanoyltransferase |
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-Non-polymers , 6 types, 1166 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | 4-{[2-(3-BENZYL-1,2, 4-OXADIAZOL-5-YL)-3-METHYL-1- BENZOFURANSequence details | MET26 EQUIVALENT | |
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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: 2.22 Å3/Da / Density % sol: 44.5 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.2 M AMMONIUM SULPHATE, 24-26% PEG 3350, 0.1 M BISTRIS PH 6.0 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Jan 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→37 Å / Num. obs: 163266 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.58→1.62 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.9 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4B10 Resolution: 1.58→37.51 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.88 / SU B: 2.808 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 16.261 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→37.51 Å
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Refine LS restraints |
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