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- PDB-5t6c: Crystal structure of Aspergillus fumigatus N-myristoyl transferas... -

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Basic information

Entry
Database: PDB / ID: 5t6c
TitleCrystal structure of Aspergillus fumigatus N-myristoyl transferase in complex with myristoyl CoA and a dichloro-methylpyridinyl-methoxy-phenyl-pyridine piperazine ligand
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / ACYLTRANSFERASE / DRUG DISCOVERY
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / cytosol / cytoplasm
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-75S / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRobinson, D.A. / Wyatt, P.G.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome TrustWT077705 United Kingdom
Wellcome TrustWT094090 United Kingdom
CitationJournal: J. Med. Chem. / Year: 2017
Title: Design and Synthesis of Brain Penetrant Trypanocidal N-Myristoyltransferase Inhibitors.
Authors: Bayliss, T. / Robinson, D.A. / Smith, V.C. / Brand, S. / McElroy, S.P. / Torrie, L.S. / Mpamhanga, C. / Norval, S. / Stojanovski, L. / Brenk, R. / Frearson, J.A. / Read, K.D. / Gilbert, I.H. / Wyatt, P.G.
History
DepositionSep 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8503
Polymers47,4431
Non-polymers1,4072
Water9,044502
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-13 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.143, 58.599, 152.146
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: nmt1, AFUA_4G08070 / Plasmid: PGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): pLysS
References: UniProt: Q9UVX3, glycylpeptide N-tetradecanoyltransferase
#2: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#3: Chemical ChemComp-75S / 1-(4-{3,5-dichloro-4-[(2-methylpyridin-3-yl)methoxy]phenyl}pyridin-2-yl)piperazine


Mass: 429.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22Cl2N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25%PEG3350,0.2M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→38.5 Å / Num. obs: 36493 / % possible obs: 99 % / Redundancy: 4.4 % / Biso Wilson estimate: 9.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 4.3 / CC1/2: 0.94 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CAX

4cax


Resolution: 1.9→38 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.881 / SU B: 4.111 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.166 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25629 1802 5 %RANDOM
Rwork0.22323 ---
obs0.22491 34332 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.483 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.9→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 92 502 3779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193369
X-RAY DIFFRACTIONr_bond_other_d0.0010.023199
X-RAY DIFFRACTIONr_angle_refined_deg2.0911.9884585
X-RAY DIFFRACTIONr_angle_other_deg1.6193.0017334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8325391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06823.51151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80315556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1561520
X-RAY DIFFRACTIONr_chiral_restr0.1520.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213700
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02776
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_it1.4341.4951567
X-RAY DIFFRACTIONr_mcbond_other1.4341.4951566
X-RAY DIFFRACTIONr_mcangle_it2.1482.2371957
X-RAY DIFFRACTIONr_mcangle_other2.1482.2371958
X-RAY DIFFRACTIONr_scbond_it1.961.6441802
X-RAY DIFFRACTIONr_scbond_other1.961.6441803
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9242.4042629
X-RAY DIFFRACTIONr_long_range_B_refined5.81313.7454342
X-RAY DIFFRACTIONr_long_range_B_other5.55413.1744103
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.576 123 -
Rwork0.583 2397 -
obs--94.24 %

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