PDB-9ef6: Crystal structure of Cryptosporidium parvum N-myristoyltransferas...

ID or keywords:

Entry

Database: PDB / ID: 9ef6

Title

Crystal structure of Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA and inhibitor 20045

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: 1.95 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 20045
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	9ef6.cif.gz	681.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9ef6.ent.gz		Display	PDB format
PDBx/mmJSON format	9ef6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ef6_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	9ef6_full_validation.pdf.gz	1.1 MB	Display
Data in XML	9ef6_validation.xml.gz	48.6 KB	Display
Data in CIF	9ef6_validation.cif.gz	67.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ef/9ef6 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/9ef6	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

105 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
52.9 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)	54.455, 88.259, 98.238
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 , 7 types, 709 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-A1BHP / (2M)-N-(4-methyl-1,3-thiazol-2-yl)-2-[2-(piperazin-1-yl)phenyl]-1H-1,3-benzimidazole-4-carboxamide Mass: 418.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₂H₂₂N₆OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#7: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.31 Å³/Da / Density % sol: 46.68 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 100 mM Bis-Tris, pH 6.05, 26.14% 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: 0.999987 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: 0.999987 Å / Relative weight: 1

Reflection

Resolution: 1.95→50 Å / Num. obs: 66407 / % possible obs: 98.9 % / Redundancy: 4.5 % / B_iso Wilson estimate: 25.06 Å² / CC_1/2: 0.981 / CC star: 0.995 / R_merge(I) obs: 0.164 / R_pim(I) all: 0.089 / R_rim(I) all: 0.188 / Χ²: 2.005 / Net I/σ(I): 9.9 / Num. measured all: 299986

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
1.95-1.98	4.5	1.261	3287	0.215	0.595	0.662	1.431	1.025	99.9
1.98-2.02	4.5	0.956	3351	0.528	0.831	0.495	1.081	1.07	99.6
2.02-2.06	4.5	0.861	3343	0.592	0.862	0.45	0.977	1.37	99.5
2.06-2.1	4.5	0.681	3304	0.711	0.912	0.358	0.774	1.577	99.3
2.1-2.15	4.6	0.538	3316	0.743	0.923	0.278	0.609	1.307	99.4
2.15-2.2	4.6	0.497	3335	0.802	0.943	0.255	0.561	1.382	99.2
2.2-2.25	4.5	0.51	3293	0.769	0.932	0.266	0.578	2.093	98.5
2.25-2.31	4.6	0.505	3307	0.846	0.957	0.259	0.57	1.638	98.7
2.31-2.38	4.6	0.365	3294	0.898	0.973	0.186	0.412	1.645	98.9
2.38-2.46	4.6	0.325	3334	0.914	0.977	0.166	0.367	1.624	98.3
2.46-2.54	4.6	0.283	3240	0.931	0.982	0.146	0.32	1.784	98.1
2.54-2.65	4.6	0.267	3323	0.934	0.983	0.138	0.302	1.994	98.5
2.65-2.77	4.6	0.231	3249	0.949	0.987	0.12	0.261	2.246	97.5
2.77-2.91	4.6	0.194	3291	0.961	0.99	0.101	0.22	2.362	98.2
2.91-3.1	4.4	0.156	3302	0.967	0.992	0.084	0.178	2.72	98.3
3.1-3.33	4.5	0.125	3341	0.971	0.993	0.068	0.143	2.662	98.8
3.33-3.67	4.4	0.116	3343	0.972	0.993	0.065	0.134	3.224	98.9
3.67-4.2	4.3	0.104	3358	0.972	0.993	0.06	0.121	2.999	99.3
4.2-5.29	4.4	0.095	3366	0.976	0.994	0.054	0.11	2.823	99.4
5.29-50	4.5	0.082	3430	0.982	0.995	0.047	0.096	2.708	99.2

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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: 1.95→46.05 Å / SU ML: 0.1683 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.0697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1915	3234	4.87 %
R_work	0.1672	63112	-
obs	0.1684	66346	98.36 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.94 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→46.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7032	0	233	695	7960

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0089	7860
X-RAY DIFFRACTION	f_angle_d	0.7614	10666
X-RAY DIFFRACTION	f_chiral_restr	0.0543	1130
X-RAY DIFFRACTION	f_plane_restr	0.0063	1360
X-RAY DIFFRACTION	f_dihedral_angle_d	18.2228	2977

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 (%)
1.95-1.98	0.266	145	0.2337	2431	X-RAY DIFFRACTION	88.83
1.98-2.01	0.2327	130	0.2163	2789	X-RAY DIFFRACTION	99.76
2.01-2.04	0.257	119	0.2169	2762	X-RAY DIFFRACTION	99.48
2.04-2.08	0.2858	134	0.2247	2743	X-RAY DIFFRACTION	98.36
2.08-2.11	0.2558	136	0.2009	2763	X-RAY DIFFRACTION	99.38
2.11-2.15	0.2506	139	0.1935	2785	X-RAY DIFFRACTION	99.35
2.15-2.2	0.2094	154	0.1866	2752	X-RAY DIFFRACTION	99.35
2.2-2.25	0.1967	142	0.1951	2712	X-RAY DIFFRACTION	98.35
2.25-2.3	0.2322	149	0.1877	2745	X-RAY DIFFRACTION	98.7
2.3-2.35	0.2275	140	0.1798	2744	X-RAY DIFFRACTION	98.77
2.35-2.42	0.1992	157	0.174	2723	X-RAY DIFFRACTION	98.73
2.42-2.49	0.2324	135	0.1722	2734	X-RAY DIFFRACTION	98.12
2.49-2.57	0.1794	143	0.167	2711	X-RAY DIFFRACTION	98.14
2.57-2.66	0.2306	145	0.1683	2754	X-RAY DIFFRACTION	98.01
2.66-2.77	0.1703	136	0.1664	2709	X-RAY DIFFRACTION	97.63
2.77-2.89	0.2044	135	0.1709	2764	X-RAY DIFFRACTION	98.24
2.89-3.05	0.2185	142	0.1749	2744	X-RAY DIFFRACTION	98.13
3.05-3.24	0.1969	137	0.1564	2750	X-RAY DIFFRACTION	98.87
3.24-3.49	0.1807	144	0.1418	2773	X-RAY DIFFRACTION	99.05
3.49-3.84	0.1519	129	0.1427	2797	X-RAY DIFFRACTION	99.09
3.84-4.39	0.1529	163	0.1343	2768	X-RAY DIFFRACTION	99.42
4.39-5.53	0.1572	142	0.1398	2804	X-RAY DIFFRACTION	99.33
5.53-46.05	0.1768	138	0.1925	2855	X-RAY DIFFRACTION	99.17

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	1.45946075917	-0.395577757238	-0.696310816639	1.77500847565	0.0227600582589	2.22347686462	-0.0364912183425	0.0586015767401	-0.170051825106	0.0981857022061	-0.00735847891286	0.0280907419959	0.137830371996	0.0141254549166	0.0322576386751	0.119387593256	-0.0255046910802	-0.0205676360009	0.105106429826	-0.028888777039	0.173612107371	13.7737018366	-2.267267017	40.5607035064
2	1.24331078219	-0.481263654743	-0.1329471645	1.26267810302	0.373027662891	1.63986383791	0.0388041061216	0.116169944922	0.10297262249	-0.153734938205	-0.0343038025222	0.0279475360811	-0.182706737532	-0.156961448559	-0.0103150691816	0.132989669676	-0.00332633696506	-0.00853263099579	0.142907537257	0.0130502363911	0.169277613757	8.14938068841	19.0144917788	38.2360507717
3	5.82389103617	0.11989122938	-2.04710051684	1.28170295202	-1.23874719308	2.63754762891	0.118565673758	0.0636449139266	0.813267076831	-0.159314090833	0.0381326062318	0.129464190075	-0.52838127348	-0.184743303407	-0.114556186151	0.286261451009	-0.0290059760995	-0.0588369608809	0.139107653873	0.0342742179819	0.344215252251	2.93119942928	0.244450628632	-2.27454591143
4	2.69908240485	-0.314863462536	-0.367834366157	1.42980206489	-0.516384100553	1.44405304175	-0.0681536976729	0.198206564804	-0.00220802094427	-0.278430872671	0.027330236144	-0.0478255476471	0.164006325857	0.196243393163	0.0400002344227	0.203765824624	-0.0194087622476	-0.0112060362746	0.142881268345	-0.0162914238778	0.116665019318	13.4875123955	-17.3642794937	-3.50387268024
5	4.06450705299	-1.25065808504	2.7516788107	1.30967226655	-1.48868890753	2.94720442795	0.0439244257456	0.200833940635	0.218631089311	-0.0555480213095	-0.244981138349	-0.192994825659	-0.00584309744164	0.27081955002	0.21641350772	0.160817192016	-0.00367506323228	0.0233523401479	0.193931650438	-0.00889090256799	0.135111186924	18.8408667886	-16.8119313943	21.9163926735
6	4.53388115431	1.48342801905	2.05332563478	1.3433093242	0.163242843051	1.26256390156	0.230456675137	-0.281752415894	-0.334526003504	-0.0684740520331	0.0217681828829	0.0672779922791	0.388745920364	-0.246909972134	-0.286943193952	0.235599270326	-0.0148495941159	0.0075195231259	0.157041377144	0.00921896918064	0.150186463447	2.3588994109	-30.6712285531	21.9860122278
7	1.7604283265	-0.976768392396	0.449094591558	2.21903170403	-1.10243943054	1.90667305033	-0.0322187632855	-0.0604838976611	0.074996789976	-0.0438650160395	0.116439317324	0.250348673337	0.0870386716794	-0.395624025007	-0.06666745742	0.166191185109	-0.0675664690123	-0.0312441771398	0.221967070138	-0.0186912882309	0.232015241111	-7.52882671398	-17.774677521	10.0501454049
8	3.50244654106	0.0169796970605	0.223233185824	2.05091795455	-0.59538564905	2.34726620621	-0.094275901625	-0.10324008266	0.0389022966963	0.0517493405961	0.00956461572814	-0.0103276911871	0.115322721506	0.0727966122348	0.0751318822326	0.155186204839	0.0171887737349	-0.0120073589903	0.117457871866	-0.00455106525992	0.0994433374794	11.0866931634	-25.2139597516	20.334619815
9	3.67686594343	1.69462454524	-0.15295170963	0.862580189601	-0.793726236063	6.61066718421	-0.0166210783931	-0.356421292066	0.0795588164222	0.0137642281746	0.0233295041135	0.0851874289875	-0.153055611911	0.433254701497	-0.0272343688765	0.149831676441	0.023077759745	-0.00088631930333	0.117158850284	-0.0231455610523	0.194612417926	3.8186876165	-9.27674944034	11.4707175572

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 466 )	A	A	221 - 466	181 - 426
3	3	chain 'B' and (resid 41 through 77 )	B	B	41 - 77	1 - 37
4	4	chain 'B' and (resid 78 through 212 )	B	B	78 - 212	38 - 172
5	5	chain 'B' and (resid 213 through 248 )	B	B	213 - 248	173 - 208
6	6	chain 'B' and (resid 249 through 288 )	B	B	249 - 288	209 - 248
7	7	chain 'B' and (resid 289 through 363 )	B	B	289 - 363	249 - 323
8	8	chain 'B' and (resid 364 through 442 )	B	B	364 - 442	324 - 402
9	9	chain 'B' and (resid 443 through 466 )	B	B	443 - 466	403 - 426

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