PDB-5v0x: Crystal structure of glycylpeptide N-tetradecanoyltransferase fro...

ID or keywords:

Entry

Database: PDB / ID: 5v0x

Title

Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001114

Components

Glycylpeptide N-tetradecanoyltransferase

Keywords

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

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: 2.1 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-0001114
Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Feb 28, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 7, 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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Download

PDBx/mmCIF format	5v0x.cif.gz	503.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5v0x.ent.gz	408.9 KB	Display	PDB format
PDBx/mmJSON format	5v0x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5v0x_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	5v0x_full_validation.pdf.gz	2 MB	Display
Data in XML	5v0x_validation.xml.gz	52.5 KB	Display
Data in CIF	5v0x_validation.cif.gz	77.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v0/5v0x ftp://data.pdbj.org/pub/pdb/validation_reports/v0/5v0x	HTTPS FTP

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Related structure data

Related structure data	4b14S 5v0w S: Starting model for refinement
Similar structure data	2ynd-2 4ufx-2 3mz0-d 6nxg-2 3jtk-1 6nxg-1 6maz-1 6mb1-1 5o4v-2 4ufv-1 Search similar-shape structures by Omokage search (details) 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

C: Glycylpeptide N-tetradecanoyltransferase

hetero molecules

148 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycylpeptide N-tetradecanoyltransferase

hetero molecules

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

2

B: Glycylpeptide N-tetradecanoyltransferase

hetero molecules

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

3

C: Glycylpeptide N-tetradecanoyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	57.200, 118.010, 173.710
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 3 molecules ABC

#1: Protein	Glycylpeptide N-tetradecanoyltransferase Mass: 47250.945 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: PVC01_130042700, PVP01_1336100 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A1G4HIY1, UniProt: A5K1A2*PLUS, glycylpeptide N-tetradecanoyltransferase

#1: Protein

Glycylpeptide N-tetradecanoyltransferase

Mass: 47250.945 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Plasmodium vivax (malaria parasite P. vivax)
Gene: PVC01_130042700, PVP01_1336100 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A1G4HIY1, UniProt: A5K1A2*PLUS, glycylpeptide N-tetradecanoyltransferase

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Non-polymers , 5 types, 1017 molecules

#2: Chemical	ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA Mass: 977.890 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃₅H₆₂N₇O₁₇P₃S
#3: Chemical	ChemComp-8RD / {4-[2-(5-fluoro-2-{3-[(methylamino)methyl][1,2,4]triazolo[4,3-a]pyridin-6-yl}phenoxy)ethyl]-1,5-dimethyl-1H-pyrazol-3-yl}(morpholin-4-yl)methanone Mass: 507.560 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₆H₃₀FN₇O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 991 / 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: 2.07 Å³/Da / Density % sol: 41 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 22% PEG 3350, 200 mM Ammonium Sulfate, 100 mM BisTris pH 5.5, 0.5mM IMP-0001114, 0.5mM myristoyl CoA: protein conc 12.53mg/mL: hdg0-1

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.97949 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 27, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.97949 Å / Relative weight: 1

Reflection

Resolution: 2.1→48.808 Å / Num. obs: 69068 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.103 % / B_iso Wilson estimate: 16.83 Å² / CC_1/2: 0.992 / R_merge(I) obs: 0.128 / R_rim(I) all: 0.148 / Χ²: 1.017 / Net I/σ(I): 11.25

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.1-2.15	3.873	0.447	3.74	4904	0.824	0.519	97
2.15-2.21	4.18	0.423	4.31	4932	0.85	0.487	99.2
2.21-2.28	4.169	0.381	4.73	4806	0.881	0.439	99.8
2.28-2.35	4.18	0.337	5.31	4629	0.908	0.389	99.4
2.35-2.42	4.183	0.298	5.89	4524	0.926	0.343	99.4
2.42-2.51	4.179	0.277	6.2	4387	0.938	0.319	99.6
2.51-2.6	4.156	0.248	6.98	4235	0.946	0.286	99.6
2.6-2.71	4.166	0.219	7.75	4089	0.953	0.253	99.9
2.71-2.83	4.163	0.189	8.84	3918	0.962	0.218	99.7
2.83-2.97	4.15	0.162	10.18	3741	0.972	0.187	99.8
2.97-3.13	4.119	0.127	12.56	3576	0.982	0.147	99.7
3.13-3.32	4.088	0.097	15.54	3398	0.989	0.112	99.5
3.32-3.55	4.062	0.082	17.87	3205	0.991	0.095	99.4
3.55-3.83	4.039	0.069	20.44	2981	0.993	0.08	99.2
3.83-4.2	4.035	0.057	23.33	2724	0.995	0.067	99
4.2-4.7	4.046	0.047	26.27	2506	0.996	0.055	98.8
4.7-5.42	4.063	0.049	24.56	2205	0.996	0.057	99.1
5.42-6.64	4.028	0.063	18.91	1919	0.995	0.073	99.8
6.64-9.39	3.949	0.039	25.7	1517	0.998	0.046	99.8
9.39-50	3.665	0.029	31.36	872	0.999	0.034	97.5

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
Coot		model building
PHENIX		refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4b14

4b14

Resolution: 2.1→48.808 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.56

	R_factor	Num. reflection	% reflection
R_free	0.2212	1977	2.86 %
R_work	0.1626	-	-
obs	0.1643	69063	99.3 %

Solvent computation

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

Displacement parameters

B_iso max: 89.66 Å² / B_iso mean: 19.8306 Å² / B_iso min: 0.75 Å²

Refinement step

Cycle: final / Resolution: 2.1→48.808 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9311	0	388	1002	10701
B_iso mean	-	-	24.44	27.26	-
Num. residues	-	-	-	-	1143

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9972
X-RAY DIFFRACTION	f_angle_d	0.909	13586
X-RAY DIFFRACTION	f_chiral_restr	0.055	1457
X-RAY DIFFRACTION	f_plane_restr	0.005	1670
X-RAY DIFFRACTION	f_dihedral_angle_d	14.868	5834

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1-2.1525	0.2624	138	0.2007	4601	4739	97
2.1525-2.2107	0.2566	155	0.1859	4703	4858	99
2.2107-2.2758	0.2319	121	0.1768	4778	4899	100
2.2758-2.3492	0.2325	144	0.1738	4719	4863	99
2.3492-2.4332	0.2474	143	0.1711	4727	4870	99
2.4332-2.5306	0.2896	160	0.1762	4771	4931	100
2.5306-2.6458	0.2454	131	0.177	4754	4885	100
2.6458-2.7853	0.2182	143	0.167	4796	4939	100
2.7853-2.9598	0.2898	157	0.1787	4780	4937	100
2.9598-3.1882	0.2064	128	0.1679	4836	4964	100
3.1882-3.509	0.2201	131	0.158	4802	4933	99
3.509-4.0166	0.1849	144	0.1356	4821	4965	99
4.0166-5.0596	0.1567	139	0.1247	4893	5032	99
5.0596-48.8207	0.2063	143	0.1761	5105	5248	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	1.1438	-0.0428	-0.4015	1.061	0.0318	0.7029	-0.0347	-0.0142	-0.0308	-0.0285	0.0024	0.1038	0.0234	-0.0998	0.0414	0.0902	-0.0063	-0.0065	0.1136	-0.0086	0.1023	-7.6227	-71.3194	-13.979
2	2.2001	0.6422	-0.178	0.7671	-0.2241	0.5026	-0.0326	-0.1537	0.085	0.035	0.0059	0.0207	-0.0275	-0.0775	0.0113	0.107	0.0158	-0.0025	0.1067	-0.0192	0.0713	-3.6075	-62.6273	-7.2695
3	3.4304	1.1546	1.0444	2.4177	1.889	1.9765	-0.0215	0.2306	-0.1855	-0.1833	0.1098	0.0888	0.079	0.2042	-0.121	0.0897	0.0186	0.0108	0.1573	-0.025	0.111	44.4105	-33.3154	-25.7602
4	0.8571	-0.2551	-0.1561	1.2396	0.2992	0.4911	0.0008	-0.0169	0.0872	0.0511	0.0217	-0.1134	-0.024	0.0353	-0.0306	0.0918	-0.0128	-0.0097	0.1139	-0.0011	0.0962	36.4503	-19.0293	-12.2471
5	0.724	0.0852	0.0614	0.4446	-0.0578	0.1772	-0.0171	0.1069	0.0405	-0.048	-0.0024	0.0916	-0.0269	0.0028	0.0114	0.1322	0.0002	-0.0025	0.1343	0.0138	0.108	12.0458	-16.8339	-27.983
6	1.8953	-0.1023	-0.1086	1.9253	0.222	1.8863	-0.0377	-0.1685	-0.2263	0.1421	0.0245	0.0787	0.1103	-0.0364	0.0137	0.0943	-0.0061	-0.0019	0.1009	0.0204	0.107	17.7632	-33.5277	-11.9891
7	1.5104	0.3285	-0.1332	1.5999	0.1306	1.0744	0.014	0.0422	0.0213	-0.0198	-0.0329	0.073	-0.01	-0.0421	-0.0017	0.0747	0.0093	-0.0041	0.0933	0.0127	0.0736	11.7528	-22.3499	-21.8352
8	3.1623	-0.3832	1.0112	0.9923	-0.6344	2.0254	0.0497	0.1033	-0.2206	-0.1205	-0.0309	0.1671	0.0005	0.0634	-0.0306	0.0961	-0.0134	-0.0018	0.0778	-0.026	0.0917	30.8727	-31.3508	-25.5628
9	2.988	1.0496	1.084	2.7049	1.4568	3.1016	-0.006	-0.2777	0.2484	0.0748	-0.1158	0.0602	-0.2227	0.0703	0.0836	0.0997	0.0047	0.0263	0.1715	-0.016	0.131	-5.1924	-41.6735	-39.3126
10	1.7981	0.2169	0.2467	0.7085	-0.3342	0.8561	-0.0226	0.2134	-0.0588	-0.1066	-0.0041	-0.0156	0.0373	-0.024	0.0296	0.1062	0.0133	0.0046	0.1341	-0.0155	0.0933	2.6077	-47.5346	-58.0761
11	0.4649	0.3686	0.3193	0.6545	-0.1492	0.2639	-0.0528	0.0257	0.1328	-0.0533	0.0205	-0.0739	-0.0726	0.0649	0.0079	0.1309	-0.0116	0.0101	0.1181	0.0097	0.1323	27.5535	-32.2202	-53.2042
12	1.9733	-0.1889	-0.0522	2.3549	0.0049	2.079	0.0596	0.0458	-0.3997	0.0191	-0.0953	-0.0979	0.0454	-0.045	0.0033	0.0776	-0.0181	-0.0131	0.1424	0.0186	0.1568	21.2599	-54.2127	-45.428
13	1.893	-0.0265	0.2775	0.5352	0.1834	0.9873	-0.0214	0.0095	-0.0441	-0.0787	0.0525	-0.091	0.0267	0.0255	-0.0383	0.0974	-0.0029	0.0196	0.1047	0.0049	0.1271	28.3469	-43.2081	-52.1952
14	3.8178	0.5002	-1.0464	0.2887	-0.2506	0.7409	0.0555	-0.1316	0.0856	-0.0041	-0.0907	0.0131	-0.0906	0.043	0.0064	0.1121	-0.0066	-0.0026	0.0825	-0.0074	0.0785	17.4935	-37.5533	-45.2577
15	2.0837	-1.3529	0.246	2.9462	-0.6223	0.4907	-0.1426	0.0858	0.2433	0.1895	-0.0019	-0.0892	-0.2376	-0.0556	0.1351	0.1214	-0.0461	-0.0326	0.1124	-0.0066	0.1842	23.7905	-58.2962	-12.4993
16	1.1401	0.0319	-0.1246	0.7718	-0.1179	0.7053	-0.009	-0.0605	-0.0911	0.0348	0.0065	0.0004	0.0877	-0.016	0.0057	0.0956	0.0061	-0.0091	0.1032	-0.0089	0.1043	15.4708	-77.608	-8.7559
17	0.5951	-0.3596	0.3006	0.3868	0.0653	0.4444	-0.1281	-0.1643	-0.1047	0.1221	0.0582	0.0424	0.0633	0.0011	0.0452	0.1969	0.0355	0.0427	0.1678	-0.0277	0.1349	-3.6479	-65.1728	3.6168

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 246 through 331 )	C	246 - 331
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 332 through 410 )	C	332 - 410
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 26 through 59 )	A	26 - 59
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 60 through 198 )	A	60 - 198
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 199 through 257 )	A	199 - 257
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 258 through 296 )	A	258 - 296
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 297 through 386 )	A	297 - 386
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 387 through 410 )	A	387 - 410
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 26 through 59 )	B	26 - 59
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 60 through 198 )	B	60 - 198
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 199 through 257 )	B	199 - 257
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 258 through 296 )	B	258 - 296
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 297 through 358 )	B	297 - 358
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 359 through 410 )	B	359 - 410
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 26 through 59 )	C	26 - 59
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 60 through 198 )	C	60 - 198
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 199 through 245 )	C	199 - 245

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Protein , 1 types, 3 molecules ABC

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Non-polymers , 5 types, 1017 molecules

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