PDB-9ef7: Crystal structure of Cryptosporidium parvum N-myristoyltransferas...

ID or keywords:

Entry

Database: PDB / ID: 9ef7

Title

Crystal structure of Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA and inhibitor 20057

Components

Glycylpeptide N-tetradecanoyltransferase

Keywords

TRANSFERASE/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

Biological species

Cryptosporidium parvum Iowa II (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.8 Å

Authors

Fenwick, M.K. / Staker, B.L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
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

Citation

Journal: To Be Published
Title: Crystal structure of Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA and inhibitor 20057
Authors: Staker, B.L. / Fan, E.

History

Deposition	Nov 19, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 26, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ef7.cif.gz	694.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9ef7.ent.gz		Display	PDB format
PDBx/mmJSON format	9ef7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ef7_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	9ef7_full_validation.pdf.gz	1.1 MB	Display
Data in XML	9ef7_validation.xml.gz	47.8 KB	Display
Data in CIF	9ef7_validation.cif.gz	65.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ef/9ef7 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/9ef7	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CrpaA.18219.a.A10.PS38408

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Glycylpeptide N-tetradecanoyltransferase

B: Glycylpeptide N-tetradecanoyltransferase

hetero molecules

106 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycylpeptide N-tetradecanoyltransferase

hetero molecules

defined by author
Evidence: gel filtration
53.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glycylpeptide N-tetradecanoyltransferase

hetero molecules

defined by author
52.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.812, 88.162, 97.985
Angle α, β, γ (deg.)	90.000, 97.620, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 2 molecules AB

#1: Protein	Glycylpeptide N-tetradecanoyltransferase Mass: 50717.109 Da / Num. of mol.: 2 / 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, glycylpeptide N-tetradecanoyltransferase

#1: Protein

Glycylpeptide N-tetradecanoyltransferase

Mass: 50717.109 Da / Num. of mol.: 2 / 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, glycylpeptide N-tetradecanoyltransferase

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Non-polymers , 6 types, 629 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-A1BHQ / (2M)-2-[5-chloro-2-(piperazin-1-yl)phenyl]-N-(5-methyl-1,3-thiazol-2-yl)-1H-1,3-benzimidazole-4-carboxamide Mass: 452.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₂H₂₁ClN₆OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#6: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.84 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 100 mM Bis-Tris, pH 5.42, 25.68% w/v PEG3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.1 / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. obs: 80552 / % possible obs: 96.6 % / Redundancy: 4.3 % / B_iso Wilson estimate: 30.35 Å² / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.076 / R_pim(I) all: 0.041 / R_rim(I) all: 0.087 / Χ²: 1.379 / Net I/σ(I): 11.3 / Num. measured all: 349940

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.8-1.83	4.3	1.222	3924	0.44	0.782	0.675	1.404	0.687	94.8
1.83-1.86	4.4	1.066	3934	0.579	0.856	0.575	1.217	0.732	94.9
1.86-1.9	4.4	0.909	3942	0.648	0.887	0.487	1.036	0.854	94.6
1.9-1.94	4.4	0.685	3897	0.705	0.91	0.368	0.781	0.961	94.7
1.94-1.98	4.4	0.508	3967	0.846	0.957	0.271	0.578	0.845	94.7
1.98-2.03	4.4	0.394	3912	0.882	0.968	0.211	0.449	0.937	95.2
2.03-2.08	4.4	0.332	3937	0.891	0.971	0.178	0.378	1.2	94.5
2.08-2.13	4.4	0.265	3982	0.938	0.984	0.142	0.302	1.189	95.5
2.13-2.2	4.4	0.23	3939	0.957	0.989	0.123	0.262	1.32	95.4
2.2-2.27	4.4	0.23	4015	0.95	0.987	0.123	0.262	1.768	96.3
2.27-2.35	4.3	0.182	4014	0.972	0.993	0.098	0.207	1.541	96.5
2.35-2.44	4.3	0.156	4084	0.976	0.994	0.084	0.178	1.664	97
2.44-2.55	4.4	0.134	4046	0.982	0.995	0.072	0.153	1.728	98.1
2.55-2.69	4.3	0.117	4100	0.985	0.996	0.064	0.134	1.864	98.4
2.69-2.86	4.3	0.1	4119	0.989	0.997	0.055	0.115	2.042	98.7
2.86-3.08	4.4	0.082	4089	0.992	0.998	0.045	0.094	2.16	98.9
3.08-3.39	4.3	0.068	4146	0.993	0.998	0.037	0.077	1.857	98.5
3.39-3.88	4.3	0.059	4144	0.995	0.999	0.032	0.067	1.765	99
3.88-4.88	4.2	0.052	4199	0.995	0.999	0.029	0.059	1.222	99.3
4.88-50	4.2	0.04	4162	0.998	0.999	0.022	0.046	1.152	97.7

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX		phasing
Coot		model building
PHENIX	1.20.1-4487	refinement

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.8→38.54 Å / SU ML: 0.2002 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1377
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1978	4084	5.08 %
R_work	0.1682	76360	-
obs	0.1697	80444	96.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 39.74 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→38.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7036	0	262	614	7912

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0082	8040
X-RAY DIFFRACTION	f_angle_d	0.8366	10913
X-RAY DIFFRACTION	f_chiral_restr	0.0538	1150
X-RAY DIFFRACTION	f_plane_restr	0.0067	1396
X-RAY DIFFRACTION	f_dihedral_angle_d	17.4512	3060

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8-1.82	0.3387	118	0.2969	2390	X-RAY DIFFRACTION	88.87
1.82-1.85	0.2778	135	0.2703	2592	X-RAY DIFFRACTION	94.1
1.85-1.87	0.3007	128	0.2686	2577	X-RAY DIFFRACTION	94.51
1.87-1.89	0.3536	126	0.2668	2560	X-RAY DIFFRACTION	94.71
1.89-1.92	0.28	162	0.2485	2567	X-RAY DIFFRACTION	93.62
1.92-1.95	0.2322	134	0.2326	2557	X-RAY DIFFRACTION	95.02
1.95-1.98	0.2608	139	0.217	2575	X-RAY DIFFRACTION	94.7
1.98-2.01	0.269	147	0.2089	2560	X-RAY DIFFRACTION	94.16
2.01-2.04	0.2643	147	0.1973	2607	X-RAY DIFFRACTION	95.29
2.04-2.08	0.2242	150	0.1997	2562	X-RAY DIFFRACTION	94.17
2.08-2.11	0.2096	167	0.184	2576	X-RAY DIFFRACTION	95.88
2.11-2.15	0.2072	136	0.1873	2616	X-RAY DIFFRACTION	94.8
2.15-2.2	0.2144	122	0.183	2598	X-RAY DIFFRACTION	95.81
2.2-2.25	0.2334	155	0.1911	2615	X-RAY DIFFRACTION	95.45
2.25-2.3	0.2481	157	0.1819	2589	X-RAY DIFFRACTION	96.93
2.3-2.36	0.2254	134	0.1799	2647	X-RAY DIFFRACTION	96.3
2.36-2.42	0.2061	116	0.1661	2669	X-RAY DIFFRACTION	97.17
2.42-2.49	0.224	140	0.1652	2671	X-RAY DIFFRACTION	97.71
2.49-2.57	0.2185	145	0.161	2676	X-RAY DIFFRACTION	97.54
2.57-2.66	0.1747	133	0.1592	2682	X-RAY DIFFRACTION	98.22
2.66-2.77	0.1985	155	0.1568	2675	X-RAY DIFFRACTION	98.64
2.77-2.9	0.1835	154	0.1715	2680	X-RAY DIFFRACTION	98.85
2.9-3.05	0.1864	143	0.1629	2720	X-RAY DIFFRACTION	98.38
3.05-3.24	0.2079	135	0.1505	2706	X-RAY DIFFRACTION	98.78
3.24-3.49	0.1876	127	0.152	2727	X-RAY DIFFRACTION	98.86
3.49-3.84	0.1778	161	0.1427	2727	X-RAY DIFFRACTION	98.84
3.84-4.4	0.1488	144	0.1341	2733	X-RAY DIFFRACTION	99.24
4.4-5.53	0.1555	141	0.142	2750	X-RAY DIFFRACTION	99.48
5.54-38.54	0.216	133	0.1971	2756	X-RAY DIFFRACTION	97.4

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.88338182295	-0.156113376907	-0.465001809369	2.25462748631	0.310619798841	2.49872984974	-0.10770890561	0.0761783098198	-0.174515391078	0.109201712988	0.0641871264176	0.0345147959448	0.179092262722	0.0323484489306	0.0317331496132	0.226712798948	-0.0585155839962	-0.0123870928452	0.147529720656	-0.0272785654053	0.203928461804	13.2526887199	-2.24084781509	41.0366776979
2	2.43148155906	-0.245572044999	0.290108438514	1.76519793876	0.0350407600118	2.45628901431	-0.0369682134181	-0.233872180986	0.48563367674	0.015092472021	0.0543865179813	0.33376767884	-0.52099906752	-0.483236311202	0.00881008722718	0.297668179435	0.0679720368767	-4.47424972553E-5	0.219967988218	-0.023415300837	0.341912115495	2.28425358721	26.0128298045	53.7527871087
3	1.80293664156	-0.616868204149	-0.254890425118	2.05458539789	0.750913057649	1.87081321674	-0.000274129021504	0.267331816382	0.141506796487	-0.395931553344	-0.0348459152833	0.0932596782899	-0.433435826056	-0.237013283705	0.0300263475755	0.332113776522	-0.0262129676844	-0.0488980413005	0.238052926958	0.0224298473444	0.198875806951	8.38407745271	16.8589562369	36.2066669574
4	2.80005452178	-0.113020065303	-0.231375795106	2.0908588558	-0.577980127221	2.21958855563	-0.0600859053436	0.239968177027	0.139238752553	-0.409920148487	0.0342058629814	0.0484763299919	0.0223023048535	0.243863435897	0.0279216436978	0.263950511579	-0.0853689590425	-0.0217201857596	0.249677788391	-0.0189493266079	0.189049356789	11.3657287653	-13.9480081056	-3.17460540673
5	2.97699435714	-0.261868311211	2.20319253542	0.182133817247	-0.074846637958	2.70754017208	0.173168546562	-0.0189647182856	-0.0326828995548	0.211999898314	-0.156974519491	-0.150561941056	0.165039562213	0.19652959897	-0.0254822535959	0.219086742638	-0.0112228992555	0.0414422721902	0.191606065743	-0.0317981682511	0.144127686309	16.6599989861	-22.824307272	25.6910560191
6	1.41327510918	-0.174526027068	0.597404994649	2.55243219931	-0.707734503829	2.23970052309	0.00792727372954	-0.0496788051356	0.0408876952176	0.0466329292935	0.0817396691077	0.366646772155	0.0971966268098	-0.139250872382	-0.0766487068493	0.185451260818	-0.0476808335664	0.0359393877091	0.179139905496	-0.0288661461899	0.222859408513	0.64735738378	-20.5652126826	14.4232059007

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 41 through 220 )	A	A	41 - 220	1 - 180
2	2	chain 'A' and (resid 221 through 271 )	A	A	221 - 271	181 - 231
3	3	chain 'A' and (resid 272 through 466 )	A	A	272 - 466	232 - 426
4	4	chain 'B' and (resid 41 through 212 )	B	B	41 - 212	1 - 172
5	5	chain 'B' and (resid 213 through 271 )	B	B	213 - 271	173 - 231
6	6	chain 'B' and (resid 272 through 466 )	B	B	272 - 466	232 - 426

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