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- PDB-8fbm: Crystal structure of Cryptosporidium parvum N-myristoyltransferas... -

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Basic information

Entry
Database: PDB / ID: 8fbm
TitleCrystal structure of Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA and inhibitor 1
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE/INHIBITOR / NMT / inhibitor / Myristoyl-CoA / MyrCoA / 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 / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
TETRADECANOYL-COA / DI(HYDROXYETHYL)ETHER / Chem-XOF / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStaker, B.L. / Fenwick, M.K. / 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)R01AI155536 United States
CitationJournal: Acs Infect Dis. / Year: 2023
Title: Identification of and Structural Insights into Hit Compounds Targeting N -Myristoyltransferase for Cryptosporidium Drug Development.
Authors: Fenwick, M.K. / Reers, A.R. / Liu, Y. / Zigweid, R. / Sankaran, B. / Shin, J. / Hulverson, M.A. / Hammerson, B. / Fernandez Alvaro, E. / Myler, P.J. / Kaushansky, A. / Van Voorhis, W.C. / Fan, E. / Staker, B.L.
History
DepositionNov 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type
Revision 1.2Sep 4, 2024Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_bond ...audit_author / chem_comp_bond / citation / citation_author
Item: _audit_author.name / _chem_comp_bond.pdbx_aromatic_flag ..._audit_author.name / _chem_comp_bond.pdbx_aromatic_flag / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,66319
Polymers101,4342
Non-polymers4,22817
Water16,736929
1
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7769
Polymers50,7171
Non-polymers2,0598
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,88610
Polymers50,7171
Non-polymers2,1699
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.036, 88.332, 98.322
Angle α, β, γ (deg.)90.00, 97.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 50717.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd3_320
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5CV46

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Non-polymers , 7 types, 946 molecules

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


Mass: 977.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H62N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XOF / 2-chloro-5-[ethyl(phenyl)sulfamoyl]-N-[2-(2-oxopyrrolidin-1-yl)phenyl]benzamide


Mass: 497.994 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H24ClN3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 929 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: CrpaA.18219.a.A10.PS38408 at 17.5 mg/mL was incubated with final concentrations of 0.8 mM Myristoyl-CoA and 0.8 mM compound at RT for 30 min, then mixed with 1:1 with 0.06M Magnesium ...Details: CrpaA.18219.a.A10.PS38408 at 17.5 mg/mL was incubated with final concentrations of 0.8 mM Myristoyl-CoA and 0.8 mM compound at RT for 30 min, then mixed with 1:1 with 0.06M Magnesium chloride hexahydrate: 100 mM BisTris-HCl pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 71801 / % possible obs: 99.8 % / Redundancy: 4.4 % / CC1/2: 0.988 / CC star: 0.997 / Rpim(I) all: 0.068 / Rrim(I) all: 0.142 / Χ2: 0.775 / Net I/σ(I): 24.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3602 / CC1/2: 0.614 / CC star: 0.872 / Rpim(I) all: 0.54 / Rrim(I) all: 1.094 / Χ2: 0.728 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4887refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.79 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 3593 5.01 %Random selection
Rwork0.1476 ---
obs0.1497 71760 99.58 %-
Displacement parametersBiso mean: 22.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7028 0 272 929 8229
LS refinement shellResolution: 1.9→1.93 Å
RfactorNum. reflection% reflection
Rfree0.3591 134 5 %
Rwork0.292 2497 -
obs--100 %

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