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- PDB-6mb0: Crystal structure of N-myristoyl transferase (NMT) G386E mutant f... -

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Basic information

Entry
Database: PDB / ID: 6mb0
TitleCrystal structure of N-myristoyl transferase (NMT) G386E mutant from Plasmodium vivax in complex with inhibitor IMP-1002
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / SSGCID / glycylpeptide N-tetradecanoyltransferase / N-myristoyltransferase / NMT / 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
Chem-JCY / 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: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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)146,62016
Polymers141,9693
Non-polymers4,65113
Water32,5531807
1
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8645
Polymers47,3231
Non-polymers1,5414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9266
Polymers47,3231
Non-polymers1,6035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8305
Polymers47,3231
Non-polymers1,5074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.440, 121.190, 178.250
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, 1820 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-JCY / 1-(5-{4-fluoro-2-[2-(1,3,5-trimethyl-1H-pyrazol-4-yl)ethoxy]phenyl}-1-methyl-1H-indazol-3-yl)-N,N-dimethylmethanamine


Mass: 435.537 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H30FN5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1807 / 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 6.5, 0.5mM IMP-0001088, 0.5mM myristoyl CoA: PlviB.18219.a.FR21.PS38348 conc 12.53mg/mL: 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: 1.55→50 Å / Num. obs: 176323 / % possible obs: 97.6 % / Redundancy: 6.036 % / Biso Wilson estimate: 19.091 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.102 / Χ2: 1.021 / Net I/σ(I): 12.78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.596.0260.5443.18127040.8380.59596.2
1.59-1.636.1750.4583.85124700.8850.50196.4
1.63-1.686.1560.3854.55120560.9180.42196.5
1.68-1.736.1550.335.35118110.9320.36196.5
1.73-1.796.1360.2726.38114340.9520.29896.7
1.79-1.856.0880.227.81111170.9690.24196.9
1.85-1.926.0630.1839.38107800.9780.297.4
1.92-26.0250.15510.69104020.9830.16997.7
2-2.096.0010.12912.799880.9870.14197.7
2.09-2.195.9830.11114.4795360.990.12197.5
2.19-2.315.980.09715.9791740.9930.10697.9
2.31-2.455.9540.08717.3587020.9940.09698.7
2.45-2.625.9740.08118.3581940.9940.08998
2.62-2.835.9750.07220.1876820.9950.07999.2
2.83-3.15.9890.06322.7870930.9960.06998.7
3.1-3.475.9920.05425.9464480.9970.05999.1
3.47-45.9990.0528.2357510.9970.05599.3
4-4.95.9420.04729.6748940.9970.05299.3
4.9-6.935.8620.04927.5638620.9970.05399.5
6.93-505.4430.04528.7222250.9970.0598.5

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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: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.41
RfactorNum. reflection% reflection
Rfree0.1778 1978 1.12 %
Rwork0.1522 --
obs0.1525 176241 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.81 Å2 / Biso mean: 16.0235 Å2 / Biso min: 5.01 Å2
Refinement stepCycle: final / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9384 0 314 1852 11550
Biso mean--11.67 28.56 -
Num. residues----1144
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5499-1.58870.28731450.2296120961224196
1.5887-1.63170.25781320.2043121771230996
1.6317-1.67970.21961430.1882121891233296
1.6797-1.73390.19611160.1789122251234196
1.7339-1.79590.19561370.1705122591239697
1.7959-1.86780.19321530.163122701242397
1.8678-1.95280.16731390.1651123361247597
1.9528-2.05570.19261440.1558123651250997
2.0557-2.18450.20071430.153124311257498
2.1845-2.35320.171280.1466125551268398
2.3532-2.590.17371680.1507125561272498
2.59-2.96480.16591470.1499126761282399
2.9648-3.73510.14981410.13128331297499
3.7351-48.30490.1511420.1298132951343799
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)
11.4345-0.00380.08330.44030.08330.2335-0.0268-0.09680.0380.05580.01220.0507-0.0167-0.0345-0.00910.08790.01490.00580.0808-0.00560.0871-7.9968-68.7197-6.5679
21.1624-0.0025-0.16091.0255-0.18230.9334-0.0302-0.0286-0.0070.00550.0020.0641-0.0172-0.0450.01710.05460.00410.00170.0833-0.00390.0644-7.8046-72.6989-10.6886
32.99740.6952-0.97510.4194-0.16880.74460.0038-0.18370.20480.01580.02240.0354-0.01480.0017-0.02870.0860.0163-0.01030.0822-0.01610.08220.8962-63.3692-5.9173
42.37921.47670.68042.58321.20491.9073-0.14360.2516-0.0734-0.31710.1929-0.10170.05490.0796-0.04170.0871-0.00110.01630.1196-0.0230.078944.5031-33.0294-26.7525
50.5002-0.057-0.02530.3639-0.05620.3244-0.0111-0.01930.03850.00440.0031-0.0112-0.03320.00710.00560.0926-0.0118-0.01420.08440.00410.085535.2412-16.8122-12.4954
61.13-0.55110.31490.5492-0.1890.362-0.00180.05630.0327-0.04170.01350.0396-0.031-0.0149-0.01250.0834-0.0179-0.01160.07730.01490.0725.6157-17.8577-26.0627
71.3135-0.0078-0.02590.5986-0.1180.4659-0.0198-0.0455-0.02190.01470.04320.06670.0166-0.0608-0.02580.0755-0.0118-0.01330.07540.01340.067211.8014-25.9432-17.1871
82.5777-1.20030.05450.9451-0.10240.12620.00850.16590.0256-0.0434-0.01060.02890.02150.004-0.0040.0805-0.0196-0.01260.080.01740.054222.0646-25.2579-28.042
92.07780.37091.37981.86210.70772.7193-0.0393-0.11980.16250.1883-0.0798-0.0146-0.2072-0.11570.09750.0690.01740.01430.1104-0.02250.0711-5.1961-42.7932-41.128
101.64280.5246-0.35090.4254-0.10950.6918-0.02390.2173-0.0031-0.07030.03690.0324-0.0321-0.0087-0.00370.08670.0084-0.02020.11520.0020.0655.4827-46.6056-65.4014
110.78620.2352-0.12870.43040.020.23020.00530.08090.0426-0.0118-0.0010.0088-0.0314-0.00920.00270.07410.0022-0.01770.08860.00770.0577.3996-42.8564-55.5287
120.4449-0.95860.42143.5407-1.94961.3445-0.05120.09820.10010.2078-0.1118-0.3688-0.14330.10390.1710.0659-0.0051-0.00210.10590.00330.095237.9804-39.1123-54.4419
130.91150.0702-0.02980.6959-0.28130.6916-0.02220.0404-0.026-0.00140.0047-0.06080.01450.0550.01580.0607-0.0028-0.01330.0879-0.00090.066526.0535-47.9807-51.0312
143.05750.5816-1.24590.3721-0.53620.86390.0242-0.05230.1490.0218-0.0316-0.0049-0.02810.0483-0.00090.0746-0.0001-0.01990.0583-0.00350.073517.4607-37.6223-46.9942
152.4263-1.67580.13143.79690.52691.304-0.0346-0.0190.2866-0.03990.0515-0.1246-0.27870.05710.00420.0712-0.04580.00390.07530.00570.153823.7411-60.8455-13.1283
160.83910.1289-0.15560.5783-0.09230.5882-0.0091-0.0317-0.0640.03370.0013-0.0240.0268-0.00450.00490.06330.00420.00050.0684-0.00740.067615.1246-79.7279-8.7504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 199 through 274 )C199 - 274
2X-RAY DIFFRACTION2chain 'C' and (resid 275 through 358 )C275 - 358
3X-RAY DIFFRACTION3chain 'C' and (resid 359 through 410 )C359 - 410
4X-RAY DIFFRACTION4chain 'A' and (resid 26 through 59 )A26 - 59
5X-RAY DIFFRACTION5chain 'A' and (resid 60 through 173 )A60 - 173
6X-RAY DIFFRACTION6chain 'A' and (resid 174 through 241 )A174 - 241
7X-RAY DIFFRACTION7chain 'A' and (resid 242 through 358 )A242 - 358
8X-RAY DIFFRACTION8chain 'A' and (resid 359 through 410 )A359 - 410
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 59 )B26 - 59
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 116 )B60 - 116
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 234 )B117 - 234
12X-RAY DIFFRACTION12chain 'B' and (resid 235 through 257 )B235 - 257
13X-RAY DIFFRACTION13chain 'B' and (resid 258 through 358 )B258 - 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 198 )C60 - 198

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