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Yorodumi- PDB-4cav: Crystal structure of Aspergillus fumigatus N-myristoyl transferas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cav | ||||||
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Title | Crystal structure of Aspergillus fumigatus N-myristoyl transferase in complex with myristoyl CoA and a benzofuran ligand R0-09-4879 | ||||||
Components | GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / DRUG DISCOVERY | ||||||
Function / homology | Function and homology information glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ASPERGILLUS FUMIGATUS (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Robinson, D.A. / Fang, W. / Raimi, O.G. / Blair, D.E. / Harrison, J. / Ruda, G.F. / Lockhart, D.E.A. / Torrie, L.S. / Wyatt, P.G. / Gilbert, I.H. / Van Aalten, D.M.F. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2015 Title: N-Myristoyltransferase is a Cell Wall Target in Aspergillus Fumigatus. Authors: Fang, W. / Robinson, D.A. / Raimi, O.G. / Blair, D.E. / Harrison, J.R. / Lockhart, D.E.A. / Torrie, L.S. / Ruda, G.F. / Wyatt, P.G. / Gilbert, I.H. / Van Aalten, D.M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cav.cif.gz | 184.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cav.ent.gz | 143.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/4cav ftp://data.pdbj.org/pub/pdb/validation_reports/ca/4cav | HTTPS FTP |
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-Related structure data
Related structure data | 4cawC 4caxC 1iykS 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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Unit cell |
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-Components
#1: Protein | Mass: 47443.250 Da / Num. of mol.: 1 / Fragment: RESIDUES 86-492 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): PLYSS References: UniProt: Q9UVX3, glycylpeptide N-tetradecanoyltransferase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-2XQ / |
#4: Chemical | ChemComp-MYA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 25% PEG3350, 0.2M NACL, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. obs: 33389 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.6 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IYK Resolution: 1.89→19.93 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.62 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.162 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.788 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→19.93 Å
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Refine LS restraints |
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