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- PDB-9ef8: Crystal structure of Cryptosporidium parvum N-myristoyltransferas... -

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Basic information

Entry
Database: PDB / ID: 9ef8
TitleCrystal structure of Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA and inhibitor 20084
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE/INHIBITOR / N-myristoyltransferase / NMT / glycylpeptide N-tetradecanoyltransferase / inhibitor / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / 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 / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsFenwick, M.K. / Staker, B.L. / 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)R01 AI155536 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)6R21 AI137815-02 United States
CitationJournal: To Be Published
Title: Crystal structure of Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA and inhibitor 20084
Authors: Staker, B.L. / Fan, E.
History
DepositionNov 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3487
Polymers50,7171
Non-polymers1,6316
Water6,377354
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.961, 68.664, 149.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 50717.109 Da / Num. of mol.: 1 / Mutation: del(1-39)
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
#2: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1BHR / 2-[1-(1,4-diazepan-1-yl)naphthalen-2-yl]-N-(4,5-dimethyl-1,3-thiazol-2-yl)-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide


Mass: 511.638 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H29N5O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 100 mM Bis-Tris, pH 6.05, 24.77% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999977 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999977 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23935 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.33 Å2 / CC1/2: 0.968 / CC star: 0.992 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.107 / Rrim(I) all: 0.207 / Χ2: 1.142 / Net I/σ(I): 5.2 / Num. measured all: 90999
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.70.57511270.5360.8350.350.6780.69296.2
2.24-2.283.60.63611800.4920.8120.4030.7580.65798.7
2.28-2.323.80.59611400.5850.8590.3640.7020.64799.2
2.32-2.373.90.54912020.5630.8490.340.6490.71199.8
2.37-2.423.90.53211610.6220.8760.3290.6280.741100
2.42-2.4840.49712090.7020.9080.3030.5850.758100
2.48-2.543.90.43911760.7730.9340.2690.5180.784100
2.54-2.6140.40811940.7510.9260.2460.4790.866100
2.61-2.693.90.38111780.7760.9350.2350.450.821100
2.69-2.773.90.34611930.8140.9470.210.4070.99999.8
2.77-2.873.90.30511990.8440.9570.1860.3591.07499.9
2.87-2.993.90.25612090.8910.9710.1550.3011.191100
2.99-3.123.80.21311960.9240.980.1320.2521.30299.8
3.12-3.293.80.16211920.9470.9860.0980.1911.39199.8
3.29-3.493.70.13812140.9590.9890.0840.1621.61899.8
3.49-3.763.70.11811970.9690.9920.0730.141.80398.5
3.76-4.143.70.09612120.9860.9970.0580.1131.87799.4
4.14-4.743.80.07212060.990.9980.0430.0841.7398.4
4.74-5.973.70.06612490.9920.9980.0390.0771.42299.2
5.97-503.50.06513010.9920.9980.0410.0781.79695.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→43.07 Å / SU ML: 0.2291 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.0104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2311 1183 4.95 %
Rwork0.18 22702 -
obs0.1825 23885 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.9 Å2
Refinement stepCycle: LAST / Resolution: 2.21→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3523 0 104 354 3981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333854
X-RAY DIFFRACTIONf_angle_d0.76385235
X-RAY DIFFRACTIONf_chiral_restr0.0464555
X-RAY DIFFRACTIONf_plane_restr0.0035663
X-RAY DIFFRACTIONf_dihedral_angle_d17.12131438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.310.26441260.2072644X-RAY DIFFRACTION93.61
2.31-2.430.25391490.19922807X-RAY DIFFRACTION99.7
2.43-2.580.28651810.19972802X-RAY DIFFRACTION99.97
2.58-2.780.27781330.19352858X-RAY DIFFRACTION99.97
2.78-3.060.25271450.19142857X-RAY DIFFRACTION99.9
3.06-3.50.21231400.17062876X-RAY DIFFRACTION99.87
3.5-4.410.19811550.15082861X-RAY DIFFRACTION98.95
4.41-43.070.20671540.1812997X-RAY DIFFRACTION97.8
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)
11.209820612190.09518438326170.1554831339081.603851301310.1296663653062.05620955339-0.000234257361615-0.024728297018-0.108408707864-0.0168630114280.009912541822450.08748062090840.204688975954-0.0905707297928-0.01002272314620.124659163745-0.007597792262770.01301672035210.2243657124810.008968321152080.146984838257-17.27295669-13.394334617720.0432347375
20.605225353283-0.06665811279230.2290734549680.848786110536-0.659776548271.3646024491-0.0215017756688-0.07969101867080.01978817648610.07229877865810.0232103567316-0.0144605195006-0.0614147856559-0.00287585070365-0.008202807906170.1244322361170.00348567770480.008308755404420.274984690122-0.01998994039480.137240332915-10.93034946418.5085634415120.7390846641
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 40 through 220 )40 - 2201 - 181
22chain 'A' and (resid 221 through 466 )221 - 466182 - 427

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