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- PDB-6may: Crystal structure of N-myristoyl transferase (NMT) G386E mutant f... -

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Basic information

Entry
Database: PDB / ID: 6may
TitleCrystal structure of N-myristoyl transferase (NMT) G386E mutant from Plasmodium vivax
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / SSGCID / glycylpeptide N-tetradecanoyltransferase / N-myristoyltransferase / NMT / Plasmodium vivax / Salvador I / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / 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
TETRADEC-13-YNOIC ACID - COA THIOESTER / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Cell Chem Biol / Year: 2019
Title: Structure-Guided Identification of Resistance Breaking Antimalarial N‐Myristoyltransferase Inhibitors.
Authors: Schlott, A.C. / Mayclin, S. / Reers, A.R. / Coburn-Flynn, O. / Bell, A.S. / Green, J. / Knuepfer, E. / Charter, D. / Bonnert, R. / Campo, B. / Burrows, J. / Lyons-Abbott, S. / Staker, B.L. / ...Authors: Schlott, A.C. / Mayclin, S. / Reers, A.R. / Coburn-Flynn, O. / Bell, A.S. / Green, J. / Knuepfer, E. / Charter, D. / Bonnert, R. / Campo, B. / Burrows, J. / Lyons-Abbott, S. / Staker, B.L. / Chung, C.W. / Myler, P.J. / Fidock, D.A. / Tate, E.W. / Holder, A.A.
History
DepositionAug 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase
B: Glycylpeptide N-tetradecanoyltransferase
C: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,43715
Polymers141,9693
Non-polymers3,46812
Water21,4021188
1
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4905
Polymers47,3231
Non-polymers1,1674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3944
Polymers47,3231
Non-polymers1,0713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5536
Polymers47,3231
Non-polymers1,2305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.810, 120.810, 179.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 47323.008 Da / Num. of mol.: 3 / Fragment: PlviB.18219.a.FR21 / Mutation: G386E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVC01_130042700, PVP01_1336100 / Plasmid: PlviB.18219.a.FR21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A1G4HIY1, glycylpeptide N-tetradecanoyltransferase

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Non-polymers , 5 types, 1200 molecules

#2: Chemical ChemComp-YNC / TETRADEC-13-YNOIC ACID - COA THIOESTER


Mass: 973.858 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H58N7O17P3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1188 / 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: 2.13 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 24% PEG 3350, 200 mM Ammonium Sulfate, 100 mM BisTris pH 6.0, 0.5mM myristoyl CoA: PlviB.18219.a.FR21.PS38348 conc 12.2mg/mL: 20eg: puck id zzu5-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 15, 2018
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 79557 / % possible obs: 99.9 % / Redundancy: 6.175 % / Biso Wilson estimate: 29.956 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.105 / Χ2: 1.039 / Net I/σ(I): 15.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.16.2480.5723.1557770.8750.624100
2.1-2.166.2420.4693.857060.9080.512100
2.16-2.226.2660.4533.9955320.9250.495100
2.22-2.296.2420.3684.9353190.9280.402100
2.29-2.376.2430.297651870.9620.324100
2.37-2.456.2590.2457.2750380.9720.267100
2.45-2.546.2470.2148.2448730.9810.234100
2.54-2.656.2430.1829.5546730.9860.199100
2.65-2.766.2460.14611.945210.9890.159100
2.76-2.96.2170.12413.9843190.9910.136100
2.9-3.066.2030.09717.5140970.9950.105100
3.06-3.246.1470.07422.0838870.9970.08199.9
3.24-3.476.1120.05926.6636650.9970.06599.9
3.47-3.746.1320.05726.9134250.9980.062100
3.74-4.16.0780.04632.331670.9980.05100
4.1-4.585.9970.03837.4528880.9990.041100
4.58-5.2960.03538.2325700.9990.038100
5.29-6.485.9720.04133.3621850.9990.045100
6.48-9.175.8310.03138.3917230.9990.03499.9
9.17-505.2360.02443.7410050.9990.02797.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.14_3228: ???)refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementResolution: 2.05→50 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.04
RfactorNum. reflection% reflection
Rfree0.2187 2024 2.54 %
Rwork0.1568 --
obs0.1583 79550 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.59 Å2 / Biso mean: 29.0538 Å2 / Biso min: 3.76 Å2
Refinement stepCycle: final / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9313 0 230 1190 10733
Biso mean--50.57 35.63 -
Num. residues----1136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.05-2.10130.24291130.191754485561
2.1013-2.15810.23421560.183254975653
2.1581-2.22160.25321540.188254555609
2.2216-2.29330.30451340.199754735607
2.2933-2.37520.24761350.172154985633
2.3752-2.47030.24481500.17154505600
2.4703-2.58270.22741430.172954975640
2.5827-2.71890.24781540.168954995653
2.7189-2.88920.22861510.177455555706
2.8892-3.11220.24321430.167355125655
3.1122-3.42530.21951500.150755495699
3.4253-3.92070.19881440.141855815725
3.9207-4.93880.17521580.114256385796
4.9388-45.07170.18331390.150558746013
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)
11.71920.02340.23490.8756-0.01752.2058-0.02050.25410.0253-0.0451-0.010.0488-0.1176-0.01570.03590.13570.0009-0.00650.1574-0.03710.18550.98-46.8406-56.1575
21.35630.3968-0.40780.63360.08840.5724-0.01830.12770.005-0.01280.032-0.0349-0.03020.0656-0.02110.12610.0081-0.01480.1639-0.00680.106424.2778-41.1856-51.1639
32.46910.2242-0.10412.4432-0.74811.355-0.1370.03220.2130.02430.0999-0.0642-0.08260.04650.03630.1204-0.0101-0.03710.1955-0.0310.181321.0538-73.95-10.3706
42.433-1.15-1.61162.462-0.64114.81350.0542-0.67440.7110.47410.4066-0.0447-0.48970.2746-0.38430.25290.01630.03890.4123-0.09090.33054.919-79.0062-1.0832
52.3777-0.15780.53853.1015-1.23932.204-0.1062-0.0176-0.06730.03020.024-0.1004-0.03230.01820.08140.0942-0.01270.00560.1668-0.02390.152517.3346-76.6775-11.6495
61.30940.08050.61260.67280.23560.6639-0.1632-0.7610.35250.16760.03190.10120.0003-0.10980.10680.25910.0527-0.00680.3832-0.0980.2438-5.0116-67.52322.4451
73.22320.3092-0.1821.22650.01780.9591-0.0975-0.06230.19560.00660.01560.1168-0.0517-0.08320.08330.1351-0.0024-0.03690.1511-0.020.1912-5.352-69.1925-10.9544
81.35380.1827-0.09131.72720.22781.0707-0.01850.08890.1391-0.13530.05060.0068-0.10450.0414-0.03490.15410.00530.00150.13520.02430.096339.0386-21.1136-15.5324
91.5113-0.53240.26560.7766-0.06980.6117-0.02580.00870.0271-0.04220.01560.0461-0.0126-0.0240.01820.1363-0.0199-0.00540.10890.01920.102415.8278-22.9386-23.0674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 198 )A27 - 198
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 410 )A199 - 410
3X-RAY DIFFRACTION3chain 'B' and (resid 27 through 94 )B27 - 94
4X-RAY DIFFRACTION4chain 'B' and (resid 95 through 116 )B95 - 116
5X-RAY DIFFRACTION5chain 'B' and (resid 117 through 198 )B117 - 198
6X-RAY DIFFRACTION6chain 'B' and (resid 199 through 248 )B199 - 248
7X-RAY DIFFRACTION7chain 'B' and (resid 249 through 410 )B249 - 410
8X-RAY DIFFRACTION8chain 'C' and (resid 27 through 198 )C27 - 198
9X-RAY DIFFRACTION9chain 'C' and (resid 199 through 410 )C199 - 410

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