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- PDB-8fbq: Crystal structure of Plasmodium vivax glycylpeptide N-tetradecano... -

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Basic information

Entry
Database: PDB / ID: 8fbq
TitleCrystal structure of Plasmodium vivax glycylpeptide N-tetradecanoyltransferase (N-myristoyltransferase, NMT) bound to myristoyl-CoA and inhibitor 12b
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE/INHIBITOR / Enzyme / Inhibitor / Complex / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / 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 / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETATE ION / TETRADECANOYL-COA / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-XOQ / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFenwick, M.K. / Staker, B.L. / Lovell, S.W. / Phan, I.Q. / Early, J. / Myler, P.J. / 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)R01AI155536 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: Nat Commun / Year: 2023
Title: Identification of potent and selective N-myristoyltransferase inhibitors of Plasmodium vivax liver stage hypnozoites and schizonts.
Authors: Rodriguez-Hernandez, D. / Vijayan, K. / Zigweid, R. / Fenwick, M.K. / Sankaran, B. / Roobsoong, W. / Sattabongkot, J. / Glennon, E.K.K. / Myler, P.J. / Sunnerhagen, P. / Staker, B.L. / ...Authors: Rodriguez-Hernandez, D. / Vijayan, K. / Zigweid, R. / Fenwick, M.K. / Sankaran, B. / Roobsoong, W. / Sattabongkot, J. / Glennon, E.K.K. / Myler, P.J. / Sunnerhagen, P. / Staker, B.L. / Kaushansky, A. / Grotli, M.
History
DepositionNov 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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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)48,45522
Polymers45,1011
Non-polymers3,35421
Water7,837435
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.930, 91.930, 101.286
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-955-

HOH

21A-998-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 45100.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Strain: Salvador I / Gene: PVX_085815 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5K1A2

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Non-polymers , 11 types, 456 molecules

#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: Chemical ChemComp-XOQ / 1-[(3M)-3-{3-[2-(1,3,5-trimethyl-1H-pyrazol-4-yl)ethoxy]pyridin-2-yl}phenyl]piperazine


Mass: 391.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#10: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#11: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: JCSG+ condition A1: 0.2 M lithium sulfate, 0.1 M sodium acetate, 50% PEG 400, pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 52868 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.032 / Rrim(I) all: 0.12 / Χ2: 0.737 / Net I/σ(I): 5.3 / Num. measured all: 751443
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.65-1.6813.40.88925770.9030.2460.9240.418
1.68-1.71140.82626280.9140.2250.8570.432
1.71-1.7414.20.68325660.9420.1860.7080.443
1.74-1.7814.20.60126250.9450.1640.6230.46
1.78-1.8214.30.52925870.9660.1440.5480.484
1.82-1.8614.30.43426020.9710.1180.450.499
1.86-1.914.30.37126050.9760.1010.3840.534
1.9-1.9614.30.30826300.9850.0840.3190.562
1.96-2.0114.40.24426010.9890.0660.2530.585
2.01-2.0814.40.20826270.9930.0560.2160.624
2.08-2.1514.50.17826100.9940.0480.1850.703
2.15-2.2414.50.15926320.9950.0430.1650.742
2.24-2.3414.50.14526330.9960.0390.1510.84
2.34-2.4614.50.13426320.9960.0360.1390.918
2.46-2.6214.40.12626580.9960.0340.1311.042
2.62-2.8214.40.11126470.9970.030.1161.219
2.82-3.1114.20.08926860.9980.0250.0931.292
3.11-3.55140.06526790.9990.0180.0671.188
3.55-4.4813.80.04127400.9990.0110.0430.932
4.48-5013.60.03229030.9990.0090.0330.746

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.19.1-4122-000refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NXG

6nxg


Resolution: 1.65→45.97 Å / SU ML: 0.144 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.9011
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1648 2749 5.21 %
Rwork0.1361 50038 -
obs0.1375 52787 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.7 Å2
Refinement stepCycle: LAST / Resolution: 1.65→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3176 0 209 435 3820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01033763
X-RAY DIFFRACTIONf_angle_d1.08515118
X-RAY DIFFRACTIONf_chiral_restr0.0603535
X-RAY DIFFRACTIONf_plane_restr0.0096635
X-RAY DIFFRACTIONf_dihedral_angle_d19.39281421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.23121160.21532430X-RAY DIFFRACTION98.95
1.68-1.710.22811540.18742468X-RAY DIFFRACTION100
1.71-1.740.21461350.1662443X-RAY DIFFRACTION99.96
1.74-1.780.20031420.14882471X-RAY DIFFRACTION99.96
1.78-1.820.17991430.14952440X-RAY DIFFRACTION100
1.82-1.860.18441570.14392446X-RAY DIFFRACTION99.92
1.86-1.90.16991410.14182472X-RAY DIFFRACTION100
1.9-1.960.14591230.14162501X-RAY DIFFRACTION100
1.96-2.010.17121450.12322462X-RAY DIFFRACTION100
2.01-2.080.161360.1222486X-RAY DIFFRACTION100
2.08-2.150.15571660.11372442X-RAY DIFFRACTION100
2.15-2.240.16171170.11212519X-RAY DIFFRACTION100
2.24-2.340.12321200.1132500X-RAY DIFFRACTION100
2.34-2.460.16031370.11682507X-RAY DIFFRACTION100
2.46-2.620.16531350.12042521X-RAY DIFFRACTION100
2.62-2.820.17911320.12482509X-RAY DIFFRACTION100
2.82-3.10.1521310.1282552X-RAY DIFFRACTION100
3.1-3.550.13951340.13152544X-RAY DIFFRACTION100
3.55-4.470.14391370.12342600X-RAY DIFFRACTION100
4.48-45.970.18771480.1792725X-RAY DIFFRACTION99.79
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7944045184630.135230435009-0.2182786805950.3648625624040.00826661641360.668097074525-0.0271847861556-0.01407376799610.0466348204152-0.01678982726880.01953245548090.0044085453066-0.04254774486880.02578571398990.007245921591570.0823452120331-0.000388774507641-0.008068147382470.0557977430272-0.008416518726880.064562555020424.7774195668-11.1788564232-7.9606892817
22.798344442561.21021269440.1774629709131.062666386520.1932186980410.944495131362-0.04960622528460.117103980974-0.0968897226483-0.03836079598310.0374803426578-0.03079277315020.029347094416-0.02488613570690.01551694778340.07939174948110.008404917223440.004902931495060.0461830102806-0.008740786931810.069259253073521.6486909649-18.3685706946-13.7578560696
31.173336367820.08519760031080.4136268655050.3459828275920.02835266961851.217782006290.0388347347033-0.12595845093-0.09785856493470.0713474660366-0.02191109271590.06523042191390.15167061183-0.163861115419-0.0100532108570.132863350118-0.01556551905430.02663392874270.09728908902760.003691527243130.1085182358510.1660200217-24.17796805133.35638920513
41.890862025270.18726672882-0.213412349992.525182656-0.4656434616383.05668162118-0.0215516631197-0.3541478747050.03817542778490.3662650329310.01207613095330.0814312594122-0.0638235215832-0.158880694249-0.009108837053660.0808493270122-0.003031273870250.0290131722760.138822943108-0.01690534115210.09905878125929.03827609295-17.28381477548.56170183959
53.19186628907-1.56541041422.42870894723.46982113596-2.442040575015.19587197554-0.1205413146570.0843293607367-0.05685664761110.130435914294-0.01421071922810.00674088481151-0.000463105072587-0.02949993740030.1028543329430.0619750410301-0.02103463900480.07180463571590.0899597902946-0.02884436648080.064298095967610.5948350472-23.61103365760.734055681565
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 174 through 359 )174 - 359149 - 334
22chain 'A' and (resid 360 through 410 )360 - 410335 - 385
33chain 'A' and (resid 26 through 116 )26 - 1161 - 91
44chain 'A' and (resid 117 through 150 )117 - 15092 - 125
55chain 'A' and (resid 151 through 173 )151 - 173126 - 148

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