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

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Basic information

Entry
Database: PDB / ID: 8fbt
TitleCrystal structure of Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / NMT / inhibitor / Myristoyl-CoA / MyrCoA / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStaker, B.L. / Fenwick, M.K. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI155536 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 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 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Sep 4, 2024Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)103,7068
Polymers101,4282
Non-polymers2,2786
Water6,053336
1
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8604
Polymers50,7141
Non-polymers1,1463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8464
Polymers50,7141
Non-polymers1,1323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.433, 105.338, 71.120
Angle α, β, γ (deg.)90.00, 112.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 50714.125 Da / Num. of mol.: 2 / Mutation: K310A, E311A
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, glycylpeptide N-tetradecanoyltransferase

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Non-polymers , 5 types, 342 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: CrpaA.18219.a.A42.PS38366 32 mg/mL was incubated with final concentrations of 0.7 mM Myristoyl-CoA at 4C for 30 min, then 0.6 microliter was mixed with 1:1 BisTris-HCl, pH 5.5, 25% PEG 3350. ...Details: CrpaA.18219.a.A42.PS38366 32 mg/mL was incubated with final concentrations of 0.7 mM Myristoyl-CoA at 4C for 30 min, then 0.6 microliter was mixed with 1:1 BisTris-HCl, pH 5.5, 25% PEG 3350. Cryo solution contained crystallant plus 27% PEG-400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999989 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 45534 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.043 / Rrim(I) all: 0.083 / Χ2: 0.995 / Net I/σ(I): 19.11
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.06 / Num. unique obs: 2260 / CC1/2: 0.772 / CC star: 0.934 / Rpim(I) all: 0.359 / Rrim(I) all: 0.703 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.83 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 2251 4.95 %
Rwork0.1636 --
obs0.1663 45504 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.85 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6680 0 147 336 7163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137112
X-RAY DIFFRACTIONf_angle_d1.1779658
X-RAY DIFFRACTIONf_dihedral_angle_d18.6142582
X-RAY DIFFRACTIONf_chiral_restr0.0651070
X-RAY DIFFRACTIONf_plane_restr0.011215
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.240.269913350.2081227084
2.24-2.290.25961320.20522709100
2.29-2.340.26371460.20132732100
2.34-2.410.22681460.18822713100
2.41-2.480.30211500.18972696100
2.48-2.560.25241320.18482740100
2.56-2.650.23981420.17872736100
2.65-2.760.24271150.17092761100
2.76-2.880.24421280.17952704100
2.88-3.030.27431560.17972720100
3.03-3.220.21991550.1622726100
3.22-3.470.20611210.15832743100
3.47-3.820.19861510.15482739100
3.82-4.370.18691500.13552735100
4.38-5.510.171760.13572718100
5.51-49.830.25021180.18032811100
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)
12.0921-0.5283-2.19913.70132.182.4712-0.35040.4848-0.43850.5068-0.32511.30140.5543-0.49640.46750.5734-0.00590.04030.5132-0.12970.797420.588929.540341.9532
22.3592-1.0945-0.98275.07832.45114.2185-0.39780.0018-0.63011.02830.13260.5831.17540.07380.16270.65030.06050.07470.3041-0.01760.396331.246924.703344.0024
33.86710.125-1.194.5965-0.81622.21390.11040.05871.099-0.19710.1164-0.3374-0.40980.119-0.17020.3144-0.0623-0.0190.29040.00140.557512.67425.65514.7007
43.89210.6009-0.21782.6807-0.48221.7673-0.1521-0.0972-0.0794-0.29440.0459-0.53120.1160.14650.06220.2766-0.00420.06260.2349-0.00070.278620.28764.648910.6199
52.5003-1.9018-1.16045.35663.39184.5180.18290.05090.2969-0.76360.4918-1.0166-0.50660.7194-0.4710.4271-0.06950.09310.5147-0.13460.417344.145734.133729.5436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 213 through 289 )
2X-RAY DIFFRACTION2chain 'A' and (resid 290 through 466 )
3X-RAY DIFFRACTION3chain 'B' and (resid 42 through 212 )
4X-RAY DIFFRACTION4chain 'B' and (resid 213 through 466 )
5X-RAY DIFFRACTION5chain 'A' and (resid 38 through 212 )

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