PDB-6b1l: Crystal structure of glycylpeptide N-tetradecanoyltransferase fro...

ID or keywords:

Entry

Database: PDB / ID: 6b1l

Title

Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001173

Components

Glycylpeptide N-tetradecanoyltransferase

Keywords

TRANSFERASE / SSGCID / glycylpeptide N-tetradecanoyltransferase / N-myristoyltransferase / NMT / Plasmodium vivax / Salvador I / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Plasmodium vivax (malaria parasite P. vivax)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.3 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001173
Authors: Dranow, D.M. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Sep 18, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 26, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6b1l.cif.gz	295 KB	Display	PDBx/mmCIF format
PDB format	pdb6b1l.ent.gz	234.4 KB	Display	PDB format
PDBx/mmJSON format	6b1l.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b1/6b1l ftp://data.pdbj.org/pub/pdb/validation_reports/b1/6b1l	HTTPS FTP

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Related structure data

Related structure data	5v0xS S: Starting model for refinement
Similar structure data	3kxy-2 3iu1-1 4b14-3 5g1z-3 4puj-d 4gcx-d 4fr6-d 4gmi-d 3veu-d 4ufw-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-PlviB.18219.a

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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

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

1

A: Glycylpeptide N-tetradecanoyltransferase

hetero molecules

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

2

B: Glycylpeptide N-tetradecanoyltransferase

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

Unit cell

Length a, b, c (Å)	80.030, 81.490, 119.440
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Glycylpeptide N-tetradecanoyltransferase / PlviB.18219.a.FR2 Mass: 47250.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (strain Salvador I) (eukaryote) Strain: Salvador I / Gene: PVX_085815 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A5K1A2, glycylpeptide N-tetradecanoyltransferase
#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-CJ4 / 1-(5-fluoro-2-{methyl[3-(methylamino)propyl]amino}pyrimidin-4-yl)-N-[(imidazo[1,2-a]pyridin-3-yl)methyl]azetidine-3-carboxamide Mass: 426.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₇FN₈O / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 41.87 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: PlviB.18219.a.FR2.PS38192 at 13.5 mg/mL was incubated with final concentrations of 0.4 mM Myristoyl-CoA and 0.4 mM IMP-0001173 at 4C for 30 min, then mixed with 1:1 with 0.06M Magnesium ...Details: PlviB.18219.a.FR2.PS38192 at 13.5 mg/mL was incubated with final concentrations of 0.4 mM Myristoyl-CoA and 0.4 mM IMP-0001173 at 4C for 30 min, then mixed with 1:1 with 0.06M Magnesium chloride hexahydrate: 0.0.06M Calcium chloride dihydrate, 0.1M Tris (base): BICINE pH = 8.5 and 49 % of Precipitant Mix 1 (40% (v/v) PEG 500-MME: 20 % (w/v) PEG 20000), Tray 101d6, puck hr00407-15

Crystal

Density Matthews: 2.12 Å³/Da / Density % sol: 41.87 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop
Details: PlviB.18219.a.FR2.PS38192 at 13.5 mg/mL was incubated with final concentrations of 0.4 mM Myristoyl-CoA and 0.4 mM IMP-0001173 at 4C for 30 min, then mixed with 1:1 with 0.06M Magnesium ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.2 / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2017

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.3→48.17 Å / Num. obs: 35084 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.413 % / B_iso Wilson estimate: 40.53 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.058 / R_rim(I) all: 0.065 / Χ²: 1.003 / Net I/σ(I): 19.19 / Num. measured all: 189923 / Scaling rejects: 6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.3-2.36	4.785	0.517	3.03	11451	2593	2393	0.896	0.577	92.3
2.36-2.42	5.457	0.458	3.81	13566	2498	2486	0.93	0.506	99.5
2.42-2.49	5.688	0.409	4.45	13908	2449	2445	0.941	0.449	99.8
2.49-2.57	5.636	0.32	5.43	13302	2370	2360	0.965	0.352	99.6
2.57-2.66	5.558	0.265	6.41	12833	2317	2309	0.975	0.292	99.7
2.66-2.75	5.272	0.212	7.7	11666	2222	2213	0.981	0.235	99.6
2.75-2.85	5.453	0.176	9.39	11861	2181	2175	0.986	0.195	99.7
2.85-2.97	5.691	0.143	11.79	11667	2054	2050	0.991	0.158	99.8
2.97-3.1	5.622	0.103	15.5	11216	1999	1995	0.995	0.114	99.8
3.1-3.25	5.466	0.08	19.27	10538	1930	1928	0.997	0.089	99.9
3.25-3.43	5.131	0.061	23.6	9375	1831	1827	0.998	0.068	99.8
3.43-3.64	5.539	0.05	29.11	9511	1729	1717	0.998	0.055	99.3
3.64-3.89	5.605	0.041	35.21	9114	1632	1626	0.999	0.045	99.6
3.89-4.2	5.452	0.035	39.47	8260	1522	1515	0.999	0.038	99.5
4.2-4.6	5.11	0.029	43.54	7230	1420	1415	0.999	0.033	99.6
4.6-5.14	5.636	0.028	47.77	7259	1289	1288	0.999	0.03	99.9
5.14-5.94	5.382	0.031	43.05	6066	1129	1127	0.999	0.034	99.8
5.94-7.27	4.933	0.032	40.76	4884	995	990	0.998	0.035	99.5
7.27-10.29	5.308	0.023	53.23	4119	779	776	0.999	0.025	99.6
10.29-48.17	4.67	0.022	55.28	2097	459	449	0.999	0.025	97.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
PHENIX	1.12_2829	refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5V0X

5v0x

Resolution: 2.3→48.17 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.43

	R_factor	Num. reflection	% reflection
R_free	0.271	1884	5.37 %
R_work	0.2317	-	-
obs	0.2339	35070	99.01 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 140.58 Å² / B_iso mean: 57.1567 Å² / B_iso min: 13.16 Å²

Refinement step

Cycle: final / Resolution: 2.3→48.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5264	0	94	188	5546
B_iso mean	-	-	42.91	45.82	-
Num. residues	-	-	-	-	693

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	5510
X-RAY DIFFRACTION	f_angle_d	0.543	7529
X-RAY DIFFRACTION	f_chiral_restr	0.045	843
X-RAY DIFFRACTION	f_plane_restr	0.004	953
X-RAY DIFFRACTION	f_dihedral_angle_d	12.578	3207

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 13

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.3-2.3622	0.3152	144	0.2723	2327	2471	92
2.3622-2.4317	0.2976	151	0.2564	2518	2669	99
2.4317-2.5102	0.3294	150	0.2561	2498	2648	100
2.5102-2.5999	0.2873	119	0.2557	2573	2692	100
2.5999-2.7039	0.3127	144	0.2479	2537	2681	100
2.7039-2.827	0.2975	121	0.2526	2566	2687	100
2.827-2.976	0.2819	148	0.2604	2547	2695	100
2.976-3.1624	0.3411	143	0.244	2556	2699	100
3.1624-3.4066	0.2974	159	0.2367	2554	2713	100
3.4066-3.7493	0.2539	142	0.2168	2570	2712	99
3.7493-4.2915	0.2217	185	0.2129	2558	2743	100
4.2915-5.4057	0.2495	145	0.1983	2626	2771	100
5.4057-48.1801	0.2761	133	0.2444	2756	2889	99

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	2.0606	0.2758	1.2659	2.5598	0.2493	2.2037	-0.0105	0.0288	0.3094	0.0973	-0.0685	0.1704	-0.0763	-0.0704	0.0732	0.231	0.0028	0.0274	0.2167	0.0168	0.3322	-14.2513	23.1475	-52.6278
2	1.9153	-0.7271	0.4227	2.2199	-0.9843	1.6893	0.0493	-0.3953	-0.4448	0.2574	0.1812	0.475	0.202	-0.2946	-0.1674	0.3244	-0.05	-0.0031	0.3177	0.0585	0.4339	-20.6403	4.298	-39.6115
3	5.3522	0.5735	-0.6098	3.0038	-0.3857	0.6017	-0.5932	-0.4386	-1.0702	0.4671	0.3177	0.2024	0.719	0.3413	0.1604	0.8709	0.2038	0.0934	0.379	0.0279	0.4965	-0.4533	7.4822	-19.9453
4	0.1909	-0.2643	-0.4221	0.4648	0.5293	1.2414	-0.4441	-1.2467	-0.001	0.5681	0.6924	-0.4465	-0.1909	0.6254	0.149	0.6969	0.3196	-0.1743	1.2681	-0.1128	0.5183	10.1591	22.0522	-2.8594
5	0.1564	0.234	-0.4008	0.7629	-0.9337	1.2961	-0.5358	-0.7635	-0.367	0.9426	0.5325	-0.0802	0.4706	0.1566	-0.2424	0.8199	0.3276	-0.0022	0.7391	0.0768	0.3147	2.3887	15.86	-10.8615
6	1.2843	-1.6458	1.106	2.1467	-1.349	1.1111	-0.1513	-0.2928	-0.1957	-0.1028	0.1315	-0.2505	0.1566	0.9572	0.0223	0.4417	0.166	-0.061	0.9227	-0.2802	0.5694	21.8211	16.1409	-22.3124
7	0.0502	0.224	-0.0987	1.0823	-0.0285	1.919	-0.3604	0.006	0.314	-0.1225	0.1108	-0.2776	-0.0005	-0.1185	0.0238	0.5204	-0.0956	-0.0125	0.9357	-0.69	1.4354	26.7976	40.5278	-21.6443
8	0.9748	1.0399	-0.6735	1.2021	-0.4986	1.2673	0.0336	-0.3604	0.7709	0.2077	0.9292	-0.871	-0.1493	0.5514	1.4623	0.5226	-0.0076	0.0187	0.7412	-0.6579	0.9441	10.76	36.4839	-18.3527
9	1.0025	-0.3365	-0.6041	1.0536	0.7954	0.7258	-0.2472	-0.5927	0.8833	0.1403	0.4788	-1.1089	-0.0684	0.7659	-0.3124	0.6708	-0.0337	-0.0723	1.211	-0.5459	1.2191	25.5265	30.6854	-18.7418
10	1.9063	-0.3256	0.28	2.7202	0.1905	0.8275	-0.3077	-0.5319	0.3742	0.0867	0.4163	-0.8211	-0.1889	0.7555	-0.2556	0.5154	-0.0951	0.0529	0.7349	-0.2332	0.6641	15.9212	20.9562	-24.4579

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 27 through 198 )	A	27 - 198
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 199 through 410 )	A	199 - 410
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 27 through 59 )	B	27 - 59
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 60 through 150 )	B	60 - 150
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 151 through 198 )	B	151 - 198
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 199 through 222 )	B	199 - 222
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 223 through 257 )	B	223 - 257
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 258 through 316 )	B	258 - 316
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 317 through 359 )	B	317 - 359
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 360 through 410 )	B	360 - 410

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