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- PDB-5v0w: Crystal structure of glycylpeptide N-tetradecanoyltransferase fro... -

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Basic information

Entry
Database: PDB / ID: 5v0w
TitleCrystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001088
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
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-KFK / 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: 1.8 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-0001088
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)147,28125
Polymers141,7533
Non-polymers5,52822
Water30,1931676
1
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1028
Polymers47,2511
Non-polymers1,8517
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1389
Polymers47,2511
Non-polymers1,8878
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0418
Polymers47,2511
Non-polymers1,7917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.320, 119.130, 176.610
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: Eschericia 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, 1698 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-KFK / 1-[5-[3,4-bis(fluoranyl)-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-1-methyl-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine


Mass: 453.527 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H29F2N5O / Comment: inhibitor*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1676 / 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: 42.17 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 27% PEG 3350, 200 mM Ammonium Sulfate, 100 mM BisTris pH 6.0, 0.5mM IMP-0001088, 0.5mM myristoyl CoA; protein conc 12.53mg/mL; hdg0-9

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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: 1.8→50 Å / Num. obs: 112736 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.248 % / Biso Wilson estimate: 12.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.115 / Χ2: 1.04 / Net I/σ(I): 15.21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.856.2680.5153.7482130.9050.56299.4
1.85-1.97.3420.4285.0380030.9410.461100
1.9-1.957.3950.375.8478450.9560.398100
1.95-2.017.390.2917.2776020.970.313100
2.01-2.087.3730.2468.673340.9750.265100
2.08-2.157.3690.2061071690.9830.222100
2.15-2.237.3750.17811.4969070.9870.192100
2.23-2.327.3360.1541366500.9890.166100
2.32-2.437.3640.13814.1663780.9910.149100
2.43-2.557.3580.12715.0961100.9930.13799.9
2.55-2.687.3540.11516.7658080.9930.124100
2.68-2.857.3390.09819.1355460.9950.105100
2.85-3.047.3330.08621.1851960.9960.092100
3.04-3.297.2730.06925.2548270.9970.07499.9
3.29-3.67.2480.05928.8945100.9980.06499.9
3.6-4.027.2550.05132.0840860.9980.054100
4.02-4.657.2210.04435.1536010.9990.04799.9
4.65-5.697.2470.04334.3630990.9990.047100
5.69-8.057.1310.04631.2324370.9990.05100
8.05-506.6110.03637.6714150.9990.03999.4

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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: 1.8→49.575 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.16
RfactorNum. reflection% reflection
Rfree0.184 2031 1.8 %
Rwork0.1466 --
obs0.1473 112717 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.87 Å2 / Biso mean: 16.217 Å2 / Biso min: 0.91 Å2
Refinement stepCycle: final / Resolution: 1.8→49.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9405 0 348 1697 11450
Biso mean--16.28 27.54 -
Num. residues----1147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710204
X-RAY DIFFRACTIONf_angle_d0.93513929
X-RAY DIFFRACTIONf_chiral_restr0.0611497
X-RAY DIFFRACTIONf_plane_restr0.0061721
X-RAY DIFFRACTIONf_dihedral_angle_d15.5126079
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7999-1.84180.29181190.22687250736999
1.8418-1.88790.20991370.18872837420100
1.8879-1.93890.1921150.164272987413100
1.9389-1.9960.19431360.15272987434100
1.996-2.06040.19241250.146973537478100
2.0604-2.1340.17721460.144273067452100
2.134-2.21950.2221260.147173367462100
2.2195-2.32050.2011550.145673177472100
2.3205-2.44280.20121330.146673347467100
2.4428-2.59590.18091210.155573997520100
2.5959-2.79630.20011270.154973517478100
2.7963-3.07760.2121540.151373997553100
3.0776-3.52290.15861490.132374317580100
3.5229-4.4380.13691190.116775657684100
4.438-49.59410.16461690.142977667935100
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)
10.5550.0275-0.00560.6820.17990.4721-0.00130.01490.0390.0070.0305-0.06850.00250.0326-0.0260.073-0.0075-0.00590.08480.00370.071338.2447-21.9053-15.0752
20.8349-0.17410.12080.3365-0.03020.35210.0060.06180.066-0.00960.0010.0083-0.0267-0.0247-0.00550.0659-0.00480.0050.06730.00520.06514.8843-23.9799-22.3693
32.53770.05751.27411.72330.71723.1448-0.037-0.18480.22840.1617-0.1228-0.0143-0.197-0.14150.13830.07410.01060.01890.1121-0.02580.1009-5.0773-42.1739-39.7447
42.64330.9357-0.51380.8019-0.34921.0163-0.03920.3020.0356-0.07570.05540.0526-0.0093-0.0266-0.0010.09570.0139-0.00950.1154-0.00210.06335.021-46.2607-64.6034
51.04670.4022-0.21030.4473-0.07250.37690.0170.09950.054-0.0248-0.01010.0118-0.0175-0.045-0.00250.07730.0159-0.00090.08920.00180.07126.8337-43.0034-54.7994
61.0271-0.04310.13551.5889-0.69110.7734-0.00130.06130.0190.1354-0.0705-0.1946-0.08040.07230.07240.08260.01330.0160.11250.00610.085737.6749-38.9438-53.5891
72.1609-0.3986-0.30482.47780.66972.9058-0.0476-0.0179-0.22530.0907-0.0152-0.02920.21680.01250.0550.0461-0.0017-0.00560.08070.00980.081921.287-54.6644-46.4131
81.38750.3288-0.39130.40340.00690.65630.0210.01140.0549-0.0148-0.0049-0.0476-0.01560.0441-0.01560.0639-0.0017-0.00250.06880.00630.064523.3963-40.8959-50.0502
91.7344-0.92460.07882.8422-0.47041.2375-0.0769-0.05470.21240.0720.0433-0.1543-0.18020.01030.02460.068-0.0231-0.01860.0583-0.0060.119224.0876-58.8806-12.5618
101.4980.0569-0.54180.797-0.15080.9405-0.0414-0.0568-0.1370.02990.008-0.00920.07860.00680.02230.0755-0.0063-0.00940.06970.00180.074913.1727-82.3726-4.8767
110.7373-0.1271-0.18890.56240.12310.48140.0086-0.0228-0.0108-0.0213-0.0066-0.02960.01-0.00430.00970.0542-0.0117-0.00450.06710.00780.063815.4192-72.7704-9.8961
121.076-0.21260.02280.55070.16280.7541-0.1177-0.22070.07250.11720.0350.07540.0004-0.01370.04510.09720.0034-0.00160.15030.00250.125-15.827-70.4834-1.1677
132.9652.77380.51125.86931.24881.6143-0.11340.22120.0002-0.32620.041-0.015-0.096-0.0161-0.00560.07490.0016-0.01070.14090.01430.0882-6.175-66.987-24.0666
141.3720.36110.12951.80570.11331.0807-0.06260.1641-0.0659-0.14780.1219-0.01610.0629-0.0782-0.01540.0541-0.00070.00110.10410.0080.0608-0.5775-72.1799-18.9744
151.1407-0.00030.08431.0018-0.29871.57380.0107-0.0973-0.12440.01330.05840.05430.029-0.1322-0.03850.04150.00320.02170.06940.00660.0684-8.3938-74.2933-6.6752
161.31590.3032-0.08380.4511-0.03510.29790.04-0.08170.06710.0072-0.02910.0496-0.0241-0.0431-0.0060.07460.0055-0.00290.0825-0.00360.0829-3.5355-63.2202-7.3505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 198 )A26 - 198
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 410 )A199 - 410
3X-RAY DIFFRACTION3chain 'B' and (resid 26 through 59 )B26 - 59
4X-RAY DIFFRACTION4chain 'B' and (resid 60 through 116 )B60 - 116
5X-RAY DIFFRACTION5chain 'B' and (resid 117 through 234 )B117 - 234
6X-RAY DIFFRACTION6chain 'B' and (resid 235 through 257 )B235 - 257
7X-RAY DIFFRACTION7chain 'B' and (resid 258 through 296 )B258 - 296
8X-RAY DIFFRACTION8chain 'B' and (resid 297 through 410 )B297 - 410
9X-RAY DIFFRACTION9chain 'C' and (resid 25 through 59 )C25 - 59
10X-RAY DIFFRACTION10chain 'C' and (resid 60 through 116 )C60 - 116
11X-RAY DIFFRACTION11chain 'C' and (resid 117 through 215 )C117 - 215
12X-RAY DIFFRACTION12chain 'C' and (resid 216 through 257 )C216 - 257
13X-RAY DIFFRACTION13chain 'C' and (resid 258 through 274 )C258 - 274
14X-RAY DIFFRACTION14chain 'C' and (resid 275 through 296 )C275 - 296
15X-RAY DIFFRACTION15chain 'C' and (resid 297 through 331 )C297 - 331
16X-RAY DIFFRACTION16chain 'C' and (resid 332 through 410 )C332 - 410

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