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

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Basic information

Entry
Database: PDB / ID: 6maz
TitleCrystal structure of N-myristoyl transferase (NMT) G386E mutant from Plasmodium vivax in complex with inhibitor IMP-0366
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / SSGCID / glycylpeptide N-tetradecanoyltransferase / N-myristoyltransferase / NMT / 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
Chem-646 / TETRADEC-13-YNOIC ACID - COA THIOESTER / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 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)146,92418
Polymers141,9693
Non-polymers4,95515
Water34,2101899
1
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8905
Polymers47,3231
Non-polymers1,5674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0487
Polymers47,3231
Non-polymers1,7256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9866
Polymers47,3231
Non-polymers1,6635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.500, 121.250, 177.930
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 / 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 , 6 types, 1914 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-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.: 3 / Source method: obtained synthetically / Formula: C21H24Cl2N6O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


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


Mass: 18.015 Da / Num. of mol.: 1899 / 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: 27% PEG 3350, 200 mM Ammonium Sulfate, 100 mM BisTris pH 6.0, 0.5mM IMP-0366, 0.5mM myristoyl CoA: PlviB.18219.a.FR21.PS38348 conc 12.2mg/mL: 20eg: puck id zzu5-6

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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: 1.55→50 Å / Num. obs: 180669 / % possible obs: 100 % / Redundancy: 6.18 % / Biso Wilson estimate: 20.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.073 / Χ2: 1.03 / Net I/σ(I): 18.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.596.150.5373.4132160.8870.586100
1.59-1.636.1650.4454.13129170.920.486100
1.63-1.686.1710.374.94125330.9450.404100
1.68-1.736.1820.3135.86122250.9540.341100
1.73-1.796.1910.2527.22118160.9710.276100
1.79-1.856.1970.1999.13114620.9810.218100
1.85-1.926.2070.15911.31110800.9870.173100
1.92-26.2130.13113.49106400.9910.143100
2-2.096.2130.10317102310.9940.112100
2.09-2.196.2280.08619.9797640.9960.093100
2.19-2.316.2230.07322.7493730.9970.079100
2.31-2.456.2250.06525.5887960.9970.071100
2.45-2.626.2290.05927.6283720.9980.064100
2.62-2.836.2160.0531.7777320.9980.054100
2.83-3.16.2020.0436.9271760.9990.044100
3.1-3.476.1840.03244.4165240.9990.034100
3.47-46.1470.02749.9457800.9990.03100
4-4.96.1070.02454.3949190.9990.026100
4.9-6.935.990.02649.5238790.9990.02999.9
6.93-505.5470.02453.822340.9990.02699

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.14_3228: ???)refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementResolution: 1.55→50 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.94
RfactorNum. reflection% reflection
Rfree0.1664 2028 1.12 %
Rwork0.1448 --
obs0.145 180664 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.11 Å2 / Biso mean: 17.8017 Å2 / Biso min: 5.63 Å2
Refinement stepCycle: final / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9397 0 314 1920 11631
Biso mean--19.58 30.3 -
Num. residues----1143
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
1.55-1.58870.22561450.18491261012755
1.5887-1.63170.22091340.1781262712761
1.6317-1.67970.19641360.16781265512791
1.6797-1.73390.21031420.16241265112793
1.7339-1.79590.19631380.15971269612834
1.7959-1.86780.16741400.15531262912769
1.8678-1.95280.19971520.14951267812830
1.9528-2.05580.16731780.1471269012868
2.0558-2.18460.18461490.14541268712836
2.1846-2.35320.16691340.14231277112905
2.3532-2.590.17961500.15021278012930
2.59-2.96480.16281450.14691283412979
2.9648-3.7350.12261400.12861296013100
3.735-44.88290.14311450.12931336813513
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)
12.4541.66230.74672.70961.38371.7383-0.14310.2313-0.0834-0.35320.2293-0.03330.01560.0857-0.05080.08970.00430.01950.1057-0.02660.102844.2828-33.1367-26.6055
21.2357-0.1753-0.00940.5309-0.08490.31020.00470.01540.1143-0.0096-0.00180.0018-0.05270.0083-0.01050.1093-0.0109-0.00950.08480.00010.087634.0985-12.9022-11.7105
30.64-0.02880.08780.1664-0.03340.285-0.00330.02370.0278-0.02070.00920.0029-0.01670.0087-0.00860.0832-0.0102-0.00580.05860.00380.075132.3094-20.2039-19.0626
40.7280.1655-0.18621.064-0.29980.281-0.03460.05760.1162-0.07860.04530.1273-0.017-0.0787-0.02970.0881-0.0105-0.01470.10270.02890.10571.346-19.2151-23.6361
51.3321-0.00410.09730.8290.00360.6736-0.0238-0.0350.02610.01850.01450.0271-0.0094-0.0285-0.00530.0711-0.0093-0.01080.06840.00950.069713.8852-25.092-17.1937
63.5486-1.7007-0.03591.3745-0.19370.10830.02040.16750.0088-0.0488-0.00230.03260.00170.0038-0.02580.095-0.0173-0.0090.08280.00860.062622.1275-25.7855-27.9733
72.2390.28951.79721.56650.89343.1767-0.0695-0.13630.1680.167-0.0768-0.0023-0.2412-0.11620.11540.06870.02030.02190.1144-0.03070.0906-4.8115-42.386-40.6671
81.98960.1379-0.32380.6004-0.18360.7415-0.04630.22750.0681-0.07820.0237-0.0039-0.013-0.01270.0190.09480.0085-0.01960.1178-0.01030.07415.2634-46.8607-65.4217
91.30810.0120.64060.8235-0.131.6890.02610.1542-0.0798-0.12780.00210.0380.034-0.0048-0.01240.08240.0018-0.0080.11-0.01550.09863.1981-52.3254-60.0918
100.730.0256-0.140.5351-0.08260.6909-0.00180.0670.0456-0.0009-0.01380.0314-0.00530.01090.00390.06620-0.01240.0802-0.00850.07280.2199-47.1885-52.6978
110.7040.2228-0.12830.305-0.08850.3302-0.00050.08270.1583-0.01570.011-0.033-0.08040.0222-0.02270.1158-0.0066-0.01360.11560.00570.111927.9209-33.2452-54.8043
121.2497-0.0818-0.22380.93180.46741.1395-0.0088-0.0162-0.10440.04040.0309-0.00040.06970.00260.0180.07790.0032-0.00860.09070.00460.090321.5274-54.5159-46.3833
131.29620.4136-0.05650.9126-0.27761.014-0.03640.08290.0369-0.01650.0158-0.0354-0.00320.06130.01590.0643-0.0044-0.00640.0883-0.00620.081228.8969-43.7281-53.6953
143.53270.8222-1.55460.423-0.61950.97930.0345-0.00190.14570.0124-0.02830.0135-0.05160.025-0.01050.08440.0018-0.0180.0622-0.00840.07717.5616-37.7962-46.6648
152.1511-1.40590.29613.62790.1841.1482-0.0907-0.01610.28230.01840.0512-0.0555-0.28220.01190.04740.0828-0.0395-0.0070.08580.00440.184123.3846-60.4236-12.8078
162.06910.1035-0.48350.6719-0.23880.6439-0.0515-0.0972-0.07320.05310.043-0.00060.0179-0.0051-0.00190.09840.0038-0.00880.086-0.00730.081612.9088-83.8971-4.7454
170.91490.07630.07580.6888-0.11660.7693-0.0197-0.0049-0.0064-0.01880.02320.00150.0051-0.0107-0.00210.0610.00210.00160.0726-0.0080.079116.9373-76.7078-11.5358
181.84850.30380.27380.39570.00410.0613-0.1217-0.36140.07350.05830.05160.02890.0266-0.05790.05690.140.03710.00810.1817-0.02950.1305-4.4825-67.34773.1
192.37490.3533-0.4131.16770.03350.9996-0.03370.1879-0.0089-0.08220.00320.0426-0.0117-0.06980.02570.07990.0048-0.03660.10650.00420.0807-12.0823-70.3786-20.2596
201.68870.36320.00822.2565-0.19321.3315-0.07460.1017-0.0025-0.15630.0699-0.0390.0197-0.04890.0030.05210.0076-0.00930.0882-0.00150.0666-0.9117-73.3221-18.9866
211.66090.07380.04141.0613-0.1011.17-0.0429-0.16030.08250.05920.00250.0615-0.0175-0.06550.0390.05690.00980.00480.093-0.01490.0871-9.3696-69.8677-5.9899
223.5613-0.1784-0.85760.67270.31251.4573-0.0302-0.05430.2197-0.00550.0422-0.0213-0.0258-0.0264-0.0080.0816-0.0006-0.02220.0617-0.01050.10359.6482-61.9183-11.1431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 59 )A26 - 59
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 116 )A60 - 116
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 234 )A117 - 234
4X-RAY DIFFRACTION4chain 'A' and (resid 235 through 257 )A235 - 257
5X-RAY DIFFRACTION5chain 'A' and (resid 258 through 359 )A258 - 359
6X-RAY DIFFRACTION6chain 'A' and (resid 360 through 410 )A360 - 410
7X-RAY DIFFRACTION7chain 'B' and (resid 26 through 59 )B26 - 59
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 116 )B60 - 116
9X-RAY DIFFRACTION9chain 'B' and (resid 117 through 150 )B117 - 150
10X-RAY DIFFRACTION10chain 'B' and (resid 151 through 198 )B151 - 198
11X-RAY DIFFRACTION11chain 'B' and (resid 199 through 257 )B199 - 257
12X-RAY DIFFRACTION12chain 'B' and (resid 258 through 296 )B258 - 296
13X-RAY DIFFRACTION13chain 'B' and (resid 297 through 358 )B297 - 358
14X-RAY DIFFRACTION14chain 'B' and (resid 359 through 410 )B359 - 410
15X-RAY DIFFRACTION15chain 'C' and (resid 26 through 59 )C26 - 59
16X-RAY DIFFRACTION16chain 'C' and (resid 60 through 116 )C60 - 116
17X-RAY DIFFRACTION17chain 'C' and (resid 117 through 198 )C117 - 198
18X-RAY DIFFRACTION18chain 'C' and (resid 199 through 246 )C199 - 246
19X-RAY DIFFRACTION19chain 'C' and (resid 247 through 274 )C247 - 274
20X-RAY DIFFRACTION20chain 'C' and (resid 275 through 296 )C275 - 296
21X-RAY DIFFRACTION21chain 'C' and (resid 297 through 386 )C297 - 386
22X-RAY DIFFRACTION22chain 'C' and (resid 387 through 410 )C387 - 410

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