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Yorodumi- PDB-2yne: Plasmodium vivax N-myristoyltransferase in complex with a benzoth... -
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-Basic information
Entry | Database: PDB / ID: 2yne | ||||||
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Title | Plasmodium vivax N-myristoyltransferase in complex with a benzothiophene inhibitor | ||||||
Components | GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / MYRISTOYLATION / MALARIA | ||||||
Function / homology | Function and homology information glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | PLASMODIUM VIVAX (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.72 Å | ||||||
Authors | Wright, M.H. / Clough, B. / Rackham, M.D. / Brannigan, J.A. / Grainger, M. / Bottrill, A.R. / Heal, W.P. / Broncel, M. / Serwa, R.A. / Mann, D. ...Wright, M.H. / Clough, B. / Rackham, M.D. / Brannigan, J.A. / Grainger, M. / Bottrill, A.R. / Heal, W.P. / Broncel, M. / Serwa, R.A. / Mann, D. / Leatherbarrow, R.J. / Wilkinson, A.J. / Holder, A.A. / Tate, E.W. | ||||||
Citation | Journal: Nat.Chem. / Year: 2014 Title: Validation of N-Myristoyltransferase as an Antimalarial Drug Target Using an Integrated Chemical Biology Approach. Authors: Wright, M.H. / Clough, B. / Rackham, M.D. / Rangachari, K. / Brannigan, J.A. / Grainger, M. / Moss, D.K. / Bottrill, A.R. / Heal, W.P. / Broncel, M. / Serwa, R.A. / Brady, D. / Mann, D. / ...Authors: Wright, M.H. / Clough, B. / Rackham, M.D. / Rangachari, K. / Brannigan, J.A. / Grainger, M. / Moss, D.K. / Bottrill, A.R. / Heal, W.P. / Broncel, M. / Serwa, R.A. / Brady, D. / Mann, D. / Leatherbarrow, R.J. / Tewari, R. / Wilkinson, A.J. / Holder, A.A. / Tate, E.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yne.cif.gz | 288.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yne.ent.gz | 233.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/2yne ftp://data.pdbj.org/pub/pdb/validation_reports/yn/2yne | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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: 44946.402 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM VIVAX (malaria parasite P. vivax) 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 , 7 types, 1392 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Chemical | #7: Chemical | ChemComp-CL / #8: 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: 2.22 Å3/Da / Density % sol: 44.5 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 0.2 M AS, 25% PEG 3350, 0.1 M BIS-TRIS PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: PILATUS / Detector: PIXEL / Date: May 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→45 Å / Num. obs: 134040 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.72→1.81 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.72→44.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.28 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.114 / 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: 17.805 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→44.83 Å
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