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- PDB-2wsa: Crystal Structure of Leishmania major N-myristoyltransferase (NMT... -

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Basic information

Entry
Database: PDB / ID: 2wsa
TitleCrystal Structure of Leishmania major N-myristoyltransferase (NMT) with bound myristoyl-CoA and a pyrazole sulphonamide ligand (DDD85646)
ComponentsGLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
KeywordsTRANSFERASE / ACYLTRANSFERASE / DRUG DISCOVERY
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm
Similarity search - Function
Aminopeptidase - #170 / 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 / Acyl-CoA N-acyltransferase ...Aminopeptidase - #170 / 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 / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-646 / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRobinson, D.A. / Brand, S. / Fairlamb, A.H. / Ferguson, M.A.J. / Frearson, J.A. / Wyatt, P.G. / Structural Genomics Consortium (SGC)
Citation
Journal: Nature / Year: 2010
Title: N-Myristoyltransferase Inhibitors as New Leads to Treat Sleeping Sickness.
Authors: Frearson, J.A. / Brand, S. / Cleghorn, L.A.T. / Mcelroy, S. / Smid, O. / Stojanovski, L. / Torrie, L. / Robinson, D.A. / Hallyburton, I. / Guther, M.L. / Price, H.P. / Mpamhanga, C.P. / ...Authors: Frearson, J.A. / Brand, S. / Cleghorn, L.A.T. / Mcelroy, S. / Smid, O. / Stojanovski, L. / Torrie, L. / Robinson, D.A. / Hallyburton, I. / Guther, M.L. / Price, H.P. / Mpamhanga, C.P. / Brannigan, J.A. / Hodgkinson, M. / Raimi, O. / Van Aalten, D.M.F. / Brenk, R. / Gilbert, I.H. / Read, K.D. / Fairlamb, A.H. / Ferguson, M.A.J. / Smith, D.F. / Wyatt, P.G.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Myristoyl-Coa:Protein N-Myristoyltransferase, an Essential Enzyme and Potential Drug Target in Kinetoplastid Parasites.
Authors: Price, H.P. / Menon, M.R. / Panethymitaki, C. / Goulding, D. / Mckean, P.G. / Smith, D.F.
History
DepositionSep 4, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Version format compliance
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

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Assembly

Deposited unit
A: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0013
Polymers50,5271
Non-polymers1,4732
Water10,016556
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.510, 90.317, 52.972
Angle α, β, γ (deg.)90.00, 112.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE / N-MYRISTOYL TRANSFERASE


Mass: 50527.238 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q4Q5S8, 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-646 / 2,6-dichloro-4-(2-piperazin-1-ylpyridin-4-yl)-N-(1,3,5-trimethyl-1H-pyrazol-4-yl)benzenesulfonamide


Mass: 495.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24Cl2N6O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.22 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 5.5 / Details: 25.9%PEG1500,0.2M NACL, 0.1M NACACODYLATE, PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 53906 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H5Z

3h5z


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.801 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES -16-10 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.21296 1678 3.1 %RANDOM
Rwork0.176 ---
obs0.17714 52161 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.248 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20.44 Å2
2---0.88 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 95 556 3997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.9844845
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2075412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96523.779172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05115559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6521522
X-RAY DIFFRACTIONr_chiral_restr0.1150.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212751
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_it0.9331.52070
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.62923366
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.59131481
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.894.51476
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: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 107 -
Rwork0.318 3739 -
obs--96.37 %

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