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

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Basic information

Entry
Database: PDB / ID: 8fbu
TitleCrystal structure of Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA and Compound-2
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 / TRIETHYLENE GLYCOL / Chem-XOL / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStaker, B.L. / Fenwick, M. / 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: To Be Published
Title: Crystal structure of Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA
Authors: Staker, B.L. / Fenwick, M.
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

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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)104,96913
Polymers101,4342
Non-polymers3,53511
Water10,395577
1
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 52.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)52,7447
Polymers50,7171
Non-polymers2,0276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


  • defined by author
  • 52.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)52,2256
Polymers50,7171
Non-polymers1,5085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.777, 88.228, 98.060
Angle α, β, γ (deg.)90.00, 97.83, 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 Iowa II (eukaryote)
Gene: cgd3_320
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5CV46

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Non-polymers , 8 types, 588 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-XOL / (2M)-2-[2-(piperazin-1-yl)phenyl]-N-(1,3-thiazol-2-yl)-1H-benzimidazole-4-carboxamide


Mass: 404.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N6OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: CrpaA.18219.a.A10.PS38408 at 17.5 mg/mL was incubated with final concentrations of 0.8 mM Myristoyl-CoA and 1.0 mM compound at 4C for 30 min, then mixed with 1:1 with 100 mM BisTris-HCl pH 6. ...Details: CrpaA.18219.a.A10.PS38408 at 17.5 mg/mL was incubated with final concentrations of 0.8 mM Myristoyl-CoA and 1.0 mM compound at 4C for 30 min, then mixed with 1:1 with 100 mM BisTris-HCl pH 6.5 and 27.5% PEG 3350. Protein buffer is 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol, 2 mM DTT, 0.025% Azide. Crystals are harvested using crystallant plus 25% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 59810 / % possible obs: 97.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 26.23 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rpim(I) all: 0.058 / Rrim(I) all: 0.109 / Χ2: 1.44 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.46 / Num. unique obs: 2994 / CC1/2: 0.504 / CC star: 0.819 / Rpim(I) all: 0.506 / Rrim(I) all: 0.927 / Χ2: 0.778 / % possible all: 99

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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→35.37 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 2926 4.9 %
Rwork0.1552 --
obs0.1577 59728 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→35.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7013 0 232 577 7822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127751
X-RAY DIFFRACTIONf_angle_d1.12210519
X-RAY DIFFRACTIONf_dihedral_angle_d18.7712912
X-RAY DIFFRACTIONf_chiral_restr0.061122
X-RAY DIFFRACTIONf_plane_restr0.0091338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.2762800.20821539X-RAY DIFFRACTION55
2.02-2.050.24131450.1952744X-RAY DIFFRACTION98
2.05-2.090.26921470.19352738X-RAY DIFFRACTION97
2.09-2.130.25081320.1932761X-RAY DIFFRACTION98
2.13-2.170.23681490.19182747X-RAY DIFFRACTION97
2.17-2.220.26051240.18362757X-RAY DIFFRACTION97
2.22-2.270.2521390.18822749X-RAY DIFFRACTION96
2.27-2.330.21641330.17222701X-RAY DIFFRACTION96
2.33-2.390.23361310.16992755X-RAY DIFFRACTION97
2.39-2.460.26441550.16832675X-RAY DIFFRACTION95
2.46-2.540.24711510.16132698X-RAY DIFFRACTION96
2.54-2.630.25151350.16122712X-RAY DIFFRACTION96
2.63-2.740.21581220.15712713X-RAY DIFFRACTION95
2.74-2.860.21951190.16432767X-RAY DIFFRACTION96
2.86-3.010.23361480.16452748X-RAY DIFFRACTION97
3.01-3.20.19811470.15512780X-RAY DIFFRACTION99
3.2-3.450.18951360.14032826X-RAY DIFFRACTION99
3.45-3.80.18051610.13842843X-RAY DIFFRACTION100
3.8-4.350.16631720.12282795X-RAY DIFFRACTION99
4.35-5.470.17121450.12542865X-RAY DIFFRACTION99
5.47-35.370.20331550.17012889X-RAY DIFFRACTION99
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)
11.6267-0.194-0.61382.1349-0.39372.4019-0.05330.0162-0.12080.06040.0542-0.03170.10630.08130.00650.1521-0.0267-0.0160.1385-0.02820.1513.4719-2.259740.5788
21.7275-0.24610.35231.49230.29513.3274-0.0047-0.07750.2567-0.01870.00590.1219-0.321-0.44280.02770.16850.01140.00540.1520.00630.22922.544724.530246.3747
31.6615-0.4914-0.15211.80360.53061.54640.04330.10690.1318-0.2197-0.01430.0147-0.2638-0.0498-0.02510.1978-0.024-0.00690.16030.02710.14049.412917.218436.0485
42.2763-0.37370.09991.6814-0.33961.6817-0.02210.12540.1018-0.28310.0235-0.02060.04450.1512-0.00610.2296-0.0582-0.00190.1713-0.02170.134711-13.8866-2.8043
52.9523-0.2131.88880.0447-0.03262.01020.0406-0.1548-0.01950.2849-0.0999-0.20920.03810.05140.05880.2417-0.0030.05130.2066-0.01090.120415.7295-22.7924.8562
61.2789-0.66410.4571.8681-0.53121.3992-0.041-0.1118-0.00170.06310.05780.24050.0648-0.0867-0.01930.1994-0.03440.03480.1648-0.02230.16930.4472-20.714614.5636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 220 )
2X-RAY DIFFRACTION2chain 'A' and (resid 221 through 288 )
3X-RAY DIFFRACTION3chain 'A' and (resid 289 through 466 )
4X-RAY DIFFRACTION4chain 'B' and (resid 41 through 212 )
5X-RAY DIFFRACTION5chain 'B' and (resid 213 through 271 )
6X-RAY DIFFRACTION6chain 'B' and (resid 272 through 466 )

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