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- PDB-4cav: Crystal structure of Aspergillus fumigatus N-myristoyl transferas... -

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Basic information

Entry
Database: PDB / ID: 4cav
TitleCrystal structure of Aspergillus fumigatus N-myristoyl transferase in complex with myristoyl CoA and a benzofuran ligand R0-09-4879
ComponentsGLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
KeywordsTRANSFERASE / DRUG DISCOVERY
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane / cytosol
Similarity search - Function
Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase ...Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2XQ / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsRobinson, 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.
CitationJournal: 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
DepositionOct 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9134
Polymers47,4431
Non-polymers1,4703
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.430, 57.011, 143.388
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE / MYRISTOYL-COA\:PROTEIN N-MYRISTOYLTRANSFERASE / NMT / PEPTIDE N-MYRISTOYLTRANSFERASE


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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-2XQ / 3-[[3-methyl-2-[[2,3,4-tris(fluoranyl)phenoxy]methyl]-1-benzofuran-4-yl]oxy]-N-(pyridin-3-ylmethyl)propan-1-amine


Mass: 456.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H23F3N2O3
#4: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.5 / Details: 25% PEG3350, 0.2M NACL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.9→1.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.6 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IYK

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.24835 1766 5 %RANDOM
Rwork0.18579 ---
obs0.1889 33387 94.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.788 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.89→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 97 412 3697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223384
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.181.9864608
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0855393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49523.51151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04615560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1821520
X-RAY DIFFRACTIONr_chiral_restr0.170.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212545
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1721.51969
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91723201
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.25631415
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8394.51405
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.887→1.936 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 105 -
Rwork0.219 1997 -
obs--78.29 %
Refinement TLS params.Method: refined / Origin x: 5.9489 Å / Origin y: -5.577 Å / Origin z: -18.8724 Å
111213212223313233
T0.0124 Å20.0052 Å20.0036 Å2-0.0056 Å20.0092 Å2--0.0225 Å2
L0.7206 °20.0149 °2-0.2488 °2-0.6502 °20.3751 °2--1.2494 °2
S-0.0324 Å °-0.0283 Å °-0.0907 Å °0.0064 Å °-0.003 Å °-0.0071 Å °0.0873 Å °0.0353 Å °0.0354 Å °

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