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- PDB-6nxg: Crystal structure of glycylpeptide N-tetradecanoyltransferase fro... -

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Basic information

Entry
Database: PDB / ID: 6nxg
TitleCrystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor 303a
ComponentsGlycylpeptide N-tetradecanoyltransferase
Keywordstransferase/transferase inhibitor / TRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / 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
BETA-MERCAPTOETHANOL / Chem-L7Y / TETRADECANOYL-COA / OXAMIC ACID / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsStaker, B.L. / Mayclin, S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI137815 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Identification of Selective Inhibitors ofPlasmodiumN-Myristoyltransferase by High-Throughput Screening.
Authors: Harupa, A. / De Las Heras, L. / Colmenarejo, G. / Lyons-Abbott, S. / Reers, A. / Caballero Hernandez, I. / Chung, C.W. / Charter, D. / Myler, P.J. / Fernandez-Menendez, R.M. / Calderon, F. / ...Authors: Harupa, A. / De Las Heras, L. / Colmenarejo, G. / Lyons-Abbott, S. / Reers, A. / Caballero Hernandez, I. / Chung, C.W. / Charter, D. / Myler, P.J. / Fernandez-Menendez, R.M. / Calderon, F. / Palomo, S. / Rodriguez, B. / Berlanga, M. / Herreros-Aviles, E. / Staker, B.L. / Fernandez Alvaro, E. / Kaushansky, A.
History
DepositionFeb 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)146,09919
Polymers141,7533
Non-polymers4,34616
Water30,3911687
1
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8807
Polymers47,2511
Non-polymers1,6296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8537
Polymers47,2511
Non-polymers1,6026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3675
Polymers47,2511
Non-polymers1,1164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.420, 119.030, 175.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / PlviB.18219.a.FR2


Mass: 47250.945 Da / Num. of mol.: 3 / Mutation: 27-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (strain Salvador I) (eukaryote)
Strain: Salvador I / Gene: PVX_085815 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A5K1A2, glycylpeptide N-tetradecanoyltransferase

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Non-polymers , 8 types, 1703 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3NO3
#5: Chemical ChemComp-L7Y / 5-(4-chlorophenyl)-3-({[3-(morpholine-4-carbonyl)phenyl]amino}methyl)pyridin-2(1H)-one


Mass: 423.892 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22ClN3O3
#6: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#7: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1687 / 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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PlviB.18219.a.FR2.PS38192 at 13.5 mg/mL was incubated with final concentrations of 0.8 mM Myristoyl-CoA and 0.8 mM compound at 4C for 30 min, then mixed with 1:1 with 0.06M Magnesium ...Details: PlviB.18219.a.FR2.PS38192 at 13.5 mg/mL was incubated with final concentrations of 0.8 mM Myristoyl-CoA and 0.8 mM compound at 4C for 30 min, then mixed with 1:1 with 0.06M Magnesium chloride hexahydrate: 0.0.06M Calcium chloride dihydrate, 0.1M Tris (base): BICINE 49 % of Precipitant Mix 1 (40% (v/v) PEG 500-MME: 20 % (w/v) PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.6→49.29 Å / Num. obs: 158878 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 18.869 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.096 / Net I/σ(I): 14.82
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 11632 / CC1/2: 0.873 / Rrim(I) all: 0.589 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ynd

2ynd


Resolution: 1.6→49.29 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.75 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17409 7923 5 %RANDOM
Rwork0.14911 ---
obs0.15037 150955 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.489 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0 Å2-0 Å2
2---0.04 Å20 Å2
3---0.58 Å2
Refinement stepCycle: 1 / Resolution: 1.6→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9463 0 277 1687 11427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01310275
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179490
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.65713992
X-RAY DIFFRACTIONr_angle_other_deg1.3681.58222090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91651225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68923.006539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.178151792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4561545
X-RAY DIFFRACTIONr_chiral_restr0.0720.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022203
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6010.9144696
X-RAY DIFFRACTIONr_mcbond_other0.6010.9144695
X-RAY DIFFRACTIONr_mcangle_it1.0691.3685893
X-RAY DIFFRACTIONr_mcangle_other1.0691.3685894
X-RAY DIFFRACTIONr_scbond_it0.7661.0045579
X-RAY DIFFRACTIONr_scbond_other0.7661.0045580
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2341.478066
X-RAY DIFFRACTIONr_long_range_B_refined4.71212.35112228
X-RAY DIFFRACTIONr_long_range_B_other4.71212.35312229
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 558 -
Rwork0.205 11063 -
obs--99.89 %
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)
10.4755-0.0396-0.06550.2393-0.00330.18450.00330.0236-0.0304-0.0038-0.0017-0.00220.0102-0.0121-0.00160.0064-0.0013-0.00590.0041-0.00190.0084-25.898123.1157-18.8905
20.63350.13810.00210.19010.00040.1909-0.00160.0291-0.0137-0.00450.0022-0.01210.0110.0003-0.00050.00320.00420.00050.00870.0010.0049-13.559943.8619-52.1838
30.6725-0.0418-0.01550.26940.05990.1542-0.0163-0.0619-0.03250.01660.0151-0.0050.00860.01410.00110.00520.00130.00080.01360.00890.0079-4.988770.8411-8.6991
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 410
2X-RAY DIFFRACTION1A501 - 503
3X-RAY DIFFRACTION2B26 - 410
4X-RAY DIFFRACTION2B501 - 502
5X-RAY DIFFRACTION3C27 - 410

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