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Yorodumi- PDB-4b10: Plasmodium vivax N-myristoyltransferase with a non-hydrolysable c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b10 | ||||||
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Title | Plasmodium vivax N-myristoyltransferase with a non-hydrolysable co- factor | ||||||
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: 1.56 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 Anti-Malarial 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 | 4b10.cif.gz | 290.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b10.ent.gz | 234.5 KB | Display | PDB format |
PDBx/mmJSON format | 4b10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/4b10 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/4b10 | HTTPS FTP |
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-Related structure data
Related structure data | 4b11C 4b12C 4b13C 4b14C 2wuuS 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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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 / Plasmid: PET28 DERIVATIVE / 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, 1397 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence 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, 25% PEG 3350, 1 M BIS-TRIS PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→42 Å / Num. obs: 161442 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.56→1.6 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / % possible all: 82.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WUU Resolution: 1.56→41.83 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / SU B: 2.058 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.103 / 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: 13.769 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→41.83 Å
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Refine LS restraints |
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