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- PDB-5v0x: Crystal structure of glycylpeptide N-tetradecanoyltransferase fro... -

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Basic information

Entry
Database: PDB / ID: 5v0x
TitleCrystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001114
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / SSGCID / glycylpeptide N-tetradecanoyltransferase / N-myristoyltransferase / NMT / Plasmodium vival / Salvador I / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / 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-8RD / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001114
Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)147,94929
Polymers141,7533
Non-polymers6,19626
Water17,853991
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A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,44411
Polymers47,2511
Non-polymers2,19310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2529
Polymers47,2511
Non-polymers2,0018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2529
Polymers47,2511
Non-polymers2,0018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.200, 118.010, 173.710
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: 47250.945 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVC01_130042700, PVP01_1336100 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A1G4HIY1, UniProt: A5K1A2*PLUS, glycylpeptide N-tetradecanoyltransferase

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Non-polymers , 5 types, 1017 molecules

#2: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#3: Chemical ChemComp-8RD / {4-[2-(5-fluoro-2-{3-[(methylamino)methyl][1,2,4]triazolo[4,3-a]pyridin-6-yl}phenoxy)ethyl]-1,5-dimethyl-1H-pyrazol-3-yl}(morpholin-4-yl)methanone


Mass: 507.560 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H30FN7O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 991 / 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: 2.07 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 22% PEG 3350, 200 mM Ammonium Sulfate, 100 mM BisTris pH 5.5, 0.5mM IMP-0001114, 0.5mM myristoyl CoA: protein conc 12.53mg/mL: hdg0-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→48.808 Å / Num. obs: 69068 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.103 % / Biso Wilson estimate: 16.83 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.148 / Χ2: 1.017 / Net I/σ(I): 11.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.153.8730.4473.7449040.8240.51997
2.15-2.214.180.4234.3149320.850.48799.2
2.21-2.284.1690.3814.7348060.8810.43999.8
2.28-2.354.180.3375.3146290.9080.38999.4
2.35-2.424.1830.2985.8945240.9260.34399.4
2.42-2.514.1790.2776.243870.9380.31999.6
2.51-2.64.1560.2486.9842350.9460.28699.6
2.6-2.714.1660.2197.7540890.9530.25399.9
2.71-2.834.1630.1898.8439180.9620.21899.7
2.83-2.974.150.16210.1837410.9720.18799.8
2.97-3.134.1190.12712.5635760.9820.14799.7
3.13-3.324.0880.09715.5433980.9890.11299.5
3.32-3.554.0620.08217.8732050.9910.09599.4
3.55-3.834.0390.06920.4429810.9930.0899.2
3.83-4.24.0350.05723.3327240.9950.06799
4.2-4.74.0460.04726.2725060.9960.05598.8
4.7-5.424.0630.04924.5622050.9960.05799.1
5.42-6.644.0280.06318.9119190.9950.07399.8
6.64-9.393.9490.03925.715170.9980.04699.8
9.39-503.6650.02931.368720.9990.03497.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4b14

4b14


Resolution: 2.1→48.808 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.56
RfactorNum. reflection% reflection
Rfree0.2212 1977 2.86 %
Rwork0.1626 --
obs0.1643 69063 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.66 Å2 / Biso mean: 19.8306 Å2 / Biso min: 0.75 Å2
Refinement stepCycle: final / Resolution: 2.1→48.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9311 0 388 1002 10701
Biso mean--24.44 27.26 -
Num. residues----1143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079972
X-RAY DIFFRACTIONf_angle_d0.90913586
X-RAY DIFFRACTIONf_chiral_restr0.0551457
X-RAY DIFFRACTIONf_plane_restr0.0051670
X-RAY DIFFRACTIONf_dihedral_angle_d14.8685834
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 (%)
2.1-2.15250.26241380.20074601473997
2.1525-2.21070.25661550.18594703485899
2.2107-2.27580.23191210.176847784899100
2.2758-2.34920.23251440.17384719486399
2.3492-2.43320.24741430.17114727487099
2.4332-2.53060.28961600.176247714931100
2.5306-2.64580.24541310.17747544885100
2.6458-2.78530.21821430.16747964939100
2.7853-2.95980.28981570.178747804937100
2.9598-3.18820.20641280.167948364964100
3.1882-3.5090.22011310.1584802493399
3.509-4.01660.18491440.13564821496599
4.0166-5.05960.15671390.12474893503299
5.0596-48.82070.20631430.17615105524899
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)
11.1438-0.0428-0.40151.0610.03180.7029-0.0347-0.0142-0.0308-0.02850.00240.10380.0234-0.09980.04140.0902-0.0063-0.00650.1136-0.00860.1023-7.6227-71.3194-13.979
22.20010.6422-0.1780.7671-0.22410.5026-0.0326-0.15370.0850.0350.00590.0207-0.0275-0.07750.01130.1070.0158-0.00250.1067-0.01920.0713-3.6075-62.6273-7.2695
33.43041.15461.04442.41771.8891.9765-0.02150.2306-0.1855-0.18330.10980.08880.0790.2042-0.1210.08970.01860.01080.1573-0.0250.11144.4105-33.3154-25.7602
40.8571-0.2551-0.15611.23960.29920.49110.0008-0.01690.08720.05110.0217-0.1134-0.0240.0353-0.03060.0918-0.0128-0.00970.1139-0.00110.096236.4503-19.0293-12.2471
50.7240.08520.06140.4446-0.05780.1772-0.01710.10690.0405-0.048-0.00240.0916-0.02690.00280.01140.13220.0002-0.00250.13430.01380.10812.0458-16.8339-27.983
61.8953-0.1023-0.10861.92530.2221.8863-0.0377-0.1685-0.22630.14210.02450.07870.1103-0.03640.01370.0943-0.0061-0.00190.10090.02040.10717.7632-33.5277-11.9891
71.51040.3285-0.13321.59990.13061.07440.0140.04220.0213-0.0198-0.03290.073-0.01-0.0421-0.00170.07470.0093-0.00410.09330.01270.073611.7528-22.3499-21.8352
83.1623-0.38321.01120.9923-0.63442.02540.04970.1033-0.2206-0.1205-0.03090.16710.00050.0634-0.03060.0961-0.0134-0.00180.0778-0.0260.091730.8727-31.3508-25.5628
92.9881.04961.0842.70491.45683.1016-0.006-0.27770.24840.0748-0.11580.0602-0.22270.07030.08360.09970.00470.02630.1715-0.0160.131-5.1924-41.6735-39.3126
101.79810.21690.24670.7085-0.33420.8561-0.02260.2134-0.0588-0.1066-0.0041-0.01560.0373-0.0240.02960.10620.01330.00460.1341-0.01550.09332.6077-47.5346-58.0761
110.46490.36860.31930.6545-0.14920.2639-0.05280.02570.1328-0.05330.0205-0.0739-0.07260.06490.00790.1309-0.01160.01010.11810.00970.132327.5535-32.2202-53.2042
121.9733-0.1889-0.05222.35490.00492.0790.05960.0458-0.39970.0191-0.0953-0.09790.0454-0.0450.00330.0776-0.0181-0.01310.14240.01860.156821.2599-54.2127-45.428
131.893-0.02650.27750.53520.18340.9873-0.02140.0095-0.0441-0.07870.0525-0.0910.02670.0255-0.03830.0974-0.00290.01960.10470.00490.127128.3469-43.2081-52.1952
143.81780.5002-1.04640.2887-0.25060.74090.0555-0.13160.0856-0.0041-0.09070.0131-0.09060.0430.00640.1121-0.0066-0.00260.0825-0.00740.078517.4935-37.5533-45.2577
152.0837-1.35290.2462.9462-0.62230.4907-0.14260.08580.24330.1895-0.0019-0.0892-0.2376-0.05560.13510.1214-0.0461-0.03260.1124-0.00660.184223.7905-58.2962-12.4993
161.14010.0319-0.12460.7718-0.11790.7053-0.009-0.0605-0.09110.03480.00650.00040.0877-0.0160.00570.09560.0061-0.00910.1032-0.00890.104315.4708-77.608-8.7559
170.5951-0.35960.30060.38680.06530.4444-0.1281-0.1643-0.10470.12210.05820.04240.06330.00110.04520.19690.03550.04270.1678-0.02770.1349-3.6479-65.17283.6168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 246 through 331 )C246 - 331
2X-RAY DIFFRACTION2chain 'C' and (resid 332 through 410 )C332 - 410
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 59 )A26 - 59
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 198 )A60 - 198
5X-RAY DIFFRACTION5chain 'A' and (resid 199 through 257 )A199 - 257
6X-RAY DIFFRACTION6chain 'A' and (resid 258 through 296 )A258 - 296
7X-RAY DIFFRACTION7chain 'A' and (resid 297 through 386 )A297 - 386
8X-RAY DIFFRACTION8chain 'A' and (resid 387 through 410 )A387 - 410
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 59 )B26 - 59
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 198 )B60 - 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 198 )C60 - 198
17X-RAY DIFFRACTION17chain 'C' and (resid 199 through 245 )C199 - 245

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