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- PDB-8fi6: Crystal Structure of Glycylpeptide N-tetradecanoyltransferase (N-... -

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Basic information

Entry
Database: PDB / ID: 8fi6
TitleCrystal Structure of Glycylpeptide N-tetradecanoyltransferase (N-myristoyl transferase) (NMT) from Leishmania major Friedlin bound to tetradecanoyl-CoA (Orthorhombic P Form 3)
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homologyTETRADECANOYL-COA / :
Function and homology information
Biological speciesLeishmania major strain Friedlin (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorOD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Glycylpeptide N-tetradecanoyltransferase (N-myristoyl transferase) (NMT) from Leishmania major Friedlin bound to tetradecanoyl-CoA (Orthorhombic P Form 3)
Authors: Lovell, S. / Battaile, K.P. / Staker, B.L. / Liu, L.
History
DepositionDec 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn / Item: _diffrn.ambient_temp

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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)50,1532
Polymers49,1751
Non-polymers9781
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.809, 88.620, 92.490
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


Mass: 49174.914 Da / Num. of mol.: 1 / Mutation: K148R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major strain Friedlin (eukaryote)
Gene: LMJFC_320006100 / Plasmid: LemaA.18219.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8J9XEH4
#2: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Bicine, 20% PEG 6000, LemaA.18219.a.B2.PS38707 at 11.17 mg/mL. Tray: Tray 383B3/1 mM Perez-1, Puck: HR00406_03, Cryo: 20% MPD. MYA ligand was acquired from the expression host and not ...Details: 0.1 M Bicine, 20% PEG 6000, LemaA.18219.a.B2.PS38707 at 11.17 mg/mL. Tray: Tray 383B3/1 mM Perez-1, Puck: HR00406_03, Cryo: 20% MPD. MYA ligand was acquired from the expression host and not added prior to crystallization.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 10, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.8→47.78 Å / Num. obs: 43124 / % possible obs: 99.7 % / Redundancy: 9.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.028 / Rrim(I) all: 0.085 / Χ2: 1.01 / Net I/σ(I): 14.9 / Num. measured all: 393008
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 99.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 1.323 / Num. measured all: 24005 / Num. unique obs: 2515 / CC1/2: 0.65 / Rpim(I) all: 0.447 / Rrim(I) all: 1.399 / Χ2: 0.98 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.22 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 20.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 2155 5.01 %
Rwork0.1648 --
obs0.1671 43038 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 63 246 3633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013496
X-RAY DIFFRACTIONf_angle_d1.0174772
X-RAY DIFFRACTIONf_dihedral_angle_d13.3651310
X-RAY DIFFRACTIONf_chiral_restr0.06510
X-RAY DIFFRACTIONf_plane_restr0.009614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.29091150.25072680X-RAY DIFFRACTION100
1.84-1.890.26661430.22512695X-RAY DIFFRACTION99
1.89-1.940.22541580.20912650X-RAY DIFFRACTION99
1.94-20.24771380.1842697X-RAY DIFFRACTION99
2-2.060.26171280.18262699X-RAY DIFFRACTION100
2.06-2.130.18991390.17522685X-RAY DIFFRACTION100
2.13-2.220.22171440.16872696X-RAY DIFFRACTION100
2.22-2.320.22071350.17212725X-RAY DIFFRACTION100
2.32-2.440.20471490.17142706X-RAY DIFFRACTION100
2.44-2.60.23551510.1752716X-RAY DIFFRACTION100
2.6-2.80.21811600.17512731X-RAY DIFFRACTION100
2.8-3.080.22491820.17882714X-RAY DIFFRACTION100
3.08-3.520.21491210.15922783X-RAY DIFFRACTION100
3.52-4.440.2041190.13412816X-RAY DIFFRACTION100
4.44-47.220.17981730.15732890X-RAY DIFFRACTION99

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