PDB-6du6: Crystal structure of the pyruvate kinase (PK1) from the mosquito ...

ID or keywords:

Entry

Database: PDB / ID: 6du6

Title

Crystal structure of the pyruvate kinase (PK1) from the mosquito Aedes aegypti

Components

Pyruvate kinase

Keywords

TRANSFERASE / Pyruvate kinase / mosquito / vector / glycolysis / carbon metabolism

Function / homology

Function and homology information

pyruvate kinase / pyruvate kinase activity / potassium ion binding / kinase activity / magnesium ion binding / ATP binding
Similarity search - Function

Biological species

Aedes aegypti (yellow fever mosquito)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.513 Å

Authors

Pizarro, J.C. / Scaraffia, P.Y. / Petchampai, N. / Murillo-Solano, C.

Funding support

United States, 1items

Citation

Journal: Insect Biochem. Mol. Biol. / Year: 2018
Title: Distinctive regulatory properties of pyruvate kinase 1 from Aedes aegypti mosquitoes.
Authors: Petchampai, N. / Murillo-Solano, C. / Isoe, J. / Pizarro, J.C. / Scaraffia, P.Y.

History

Deposition	Jun 19, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 30, 2019	Provider: repository / Type: Initial release
Revision 1.1	Feb 13, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6du6.cif.gz	783.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6du6.ent.gz	659.5 KB	Display	PDB format
PDBx/mmJSON format	6du6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6du6_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	6du6_full_validation.pdf.gz	1.5 MB	Display
Data in XML	6du6_validation.xml.gz	72.6 KB	Display
Data in CIF	6du6_validation.cif.gz	95.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/du/6du6 ftp://data.pdbj.org/pub/pdb/validation_reports/du/6du6	HTTPS FTP

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Related structure data

Related structure data	3n25S S: Starting model for refinement
Similar structure data	1aqf-1 3srh-d 3srf-1 4jpg-d 1zjh-1 3srf-3 6gg6-2 3srf-2 2vgf-d 1a5u-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (14) #102 - Jun 2008 Lactate Dehydrogenase similarity (1)

Deposited unit

A: Pyruvate kinase

B: Pyruvate kinase

C: Pyruvate kinase

D: Pyruvate kinase

hetero molecules

248 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	109.229, 113.654, 202.075
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁
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

#1: Protein

Pyruvate kinase

Mass: 61707.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Aedes aegypti (yellow fever mosquito) / Gene: 5565629, AAEL014913 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q16F38, pyruvate kinase

#2: Sugar

ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose

Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₁₂P₂

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.59 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M ammonium citrate tribasic pH 7, 20% w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 145 K
Diffraction source	Source: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38079 Å
Detector	Type: MAR CCD 130 mm / Detector: CCD / Date: Jun 9, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.38079 Å / Relative weight: 1
Reflection	Resolution: 3.51→49.53 Å / Num. obs: 60499 / % possible obs: 99.8 % / Observed criterion σ(I): -1 / Redundancy: 3.9 % / CC_1/2: 0.98 / R_merge(I) obs: 0.279 / R_rim(I) all: 0.323 / Net I/σ(I): 5.79
Reflection shell	Resolution: 3.51→3.73 Å / Redundancy: 3.8 % / R_merge(I) obs: 1.33 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 9668 / CC_1/2: 0.46 / R_rim(I) all: 1.55 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3N25

3n25

Resolution: 3.513→49.53 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3186	4826	7.99 %
R_work	0.2706	-	-
obs	0.2744	60418	99.73 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.513→49.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15287	0	80	0	15367

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	15589
X-RAY DIFFRACTION	f_angle_d	0.726	21109
X-RAY DIFFRACTION	f_dihedral_angle_d	10.99	9565
X-RAY DIFFRACTION	f_chiral_restr	0.049	2489
X-RAY DIFFRACTION	f_plane_restr	0.005	2717

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 (%)
3.5131-3.553	0.4416	145	0.3881	1820	X-RAY DIFFRACTION	95
3.553-3.5947	0.3828	158	0.3651	1809	X-RAY DIFFRACTION	100
3.5947-3.6386	0.3898	161	0.3418	1885	X-RAY DIFFRACTION	100
3.6386-3.6846	0.3577	153	0.3621	1821	X-RAY DIFFRACTION	100
3.6846-3.7331	0.4484	151	0.3523	1872	X-RAY DIFFRACTION	100
3.7331-3.7842	0.4174	158	0.3417	1880	X-RAY DIFFRACTION	100
3.7842-3.8383	0.3279	140	0.3313	1889	X-RAY DIFFRACTION	100
3.8383-3.8955	0.3888	160	0.3437	1866	X-RAY DIFFRACTION	100
3.8955-3.9564	0.3564	179	0.2983	1818	X-RAY DIFFRACTION	100
3.9564-4.0212	0.3421	146	0.3197	1872	X-RAY DIFFRACTION	100
4.0212-4.0905	0.3238	172	0.3051	1847	X-RAY DIFFRACTION	100
4.0905-4.1649	0.351	168	0.298	1827	X-RAY DIFFRACTION	100
4.1649-4.2449	0.4018	166	0.3183	1873	X-RAY DIFFRACTION	100
4.2449-4.3315	0.3877	151	0.2958	1870	X-RAY DIFFRACTION	100
4.3315-4.4256	0.3379	167	0.2705	1868	X-RAY DIFFRACTION	100
4.4256-4.5285	0.3059	170	0.2532	1832	X-RAY DIFFRACTION	100
4.5285-4.6417	0.2932	165	0.2418	1847	X-RAY DIFFRACTION	100
4.6417-4.7671	0.3076	169	0.2708	1882	X-RAY DIFFRACTION	100
4.7671-4.9073	0.2813	166	0.2484	1827	X-RAY DIFFRACTION	100
4.9073-5.0655	0.3311	163	0.2682	1858	X-RAY DIFFRACTION	100
5.0655-5.2463	0.3386	159	0.2794	1864	X-RAY DIFFRACTION	100
5.2463-5.4562	0.3211	165	0.2641	1860	X-RAY DIFFRACTION	100
5.4562-5.7041	0.3576	164	0.2833	1842	X-RAY DIFFRACTION	100
5.7041-6.0044	0.3266	164	0.2889	1855	X-RAY DIFFRACTION	100
6.0044-6.3798	0.2928	162	0.2878	1865	X-RAY DIFFRACTION	100
6.3798-6.8713	0.3248	155	0.2618	1860	X-RAY DIFFRACTION	100
6.8713-7.5606	0.2545	164	0.2357	1851	X-RAY DIFFRACTION	100
7.5606-8.6496	0.2525	154	0.1937	1856	X-RAY DIFFRACTION	100
8.6496-10.8785	0.2042	170	0.1668	1852	X-RAY DIFFRACTION	100
10.8785-49.5353	0.2968	161	0.2394	1824	X-RAY DIFFRACTION	98

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	2.9896	-0.0541	-1.2796	1.4108	0.4578	1.2337	-0.0756	0.2725	0.2414	-0.9638	0.1618	-0.2441	-0.3292	0.0622	-0.2393	1.2366	-0.2776	0.0793	1.0112	0.2499	0.6427	20.0254	24.3146	13.193
2	3.6874	2.5304	0.2195	3.8227	0.8443	3.1634	-0.018	-0.2749	-0.5003	-0.0538	-0.0732	0.2335	0.3734	-0.0727	0.0311	0.5983	-0.0521	0.0355	0.3447	0.0216	0.4623	8.3009	-11.2795	17.8801
3	2.3312	0.868	0.9555	2.9052	0.6035	1.2452	-0.0844	0.2303	-0.0237	-0.279	-0.0339	-0.5279	-0.3266	0.3534	0.1853	0.5545	-0.1134	0.1674	0.4695	0.0571	0.4631	23.7877	5.7731	21.3913
4	2.9809	1.4035	-0.292	1.7922	-0.4076	0.5104	-0.1092	0.224	0.3565	-0.3736	0.0831	-0.1007	-0.4693	0.3897	-0.0387	1.0315	-0.2545	0.1262	0.7985	0.0739	0.5895	30.1014	28.8233	23.5734
5	0.9668	-0.0783	-0.485	2.1332	-0.2457	4.6466	-0.0466	-0.1446	0.4298	0.0509	0.006	0.2121	-0.4647	-0.1387	0.0069	0.8295	-0.0001	-0.1042	0.4509	-0.1179	0.6593	31.0254	25.5676	88.3397
6	0.074	0.3077	-0.401	1.4221	-1.611	2.4763	-0.0974	-0.2754	1.0497	0.2596	-0.1962	-0.7772	-0.5573	1.608	-0.0722	0.4619	-0.2499	-0.1475	1.2222	-0.0373	0.8656	51.5871	16.997	89.617
7	3.4102	0.3829	-0.9115	2.3248	-0.8439	1.0154	-0.0455	-1.4026	-0.2158	0.5489	-1.0555	-0.601	0.39	2.0417	1.0705	0.6849	0.1589	-0.0971	1.5558	0.3075	1.035	65.1636	10.0973	82.226
8	2.3603	1.0501	0.0418	2.4704	-0.7698	3.8495	0.0064	0.2799	-0.0147	-0.1068	0.0963	-0.0407	0.0732	0.2659	-0.0413	0.2428	0.0977	-0.0716	0.4672	-0.0412	0.4628	38.9809	16.8856	80.6244
9	4.1367	1.3026	0.1875	5.4663	-1.2513	3.1213	-0.1903	-0.0968	0.1498	0.21	0.1221	-0.2222	-0.542	-0.1066	-0.0275	0.5917	0.0623	-0.0171	0.3317	0.0672	0.5813	14.5677	18.0727	77.7476
10	3.8091	-0.5221	-1.6136	8.0342	3.8403	3.8755	-0.1917	0.1178	0.5229	0.9466	0.4711	1.2462	0.0784	-0.2019	-0.2674	0.4686	-0.038	0.1136	0.5585	0.0533	0.4831	5.9821	19.4899	77.3896
11	4.5439	2.2272	-0.7989	1.8828	1.3218	3.8772	-0.5943	-0.7234	-0.1656	-0.5589	-0.0151	0.4446	0.3912	-0.7402	0.5012	0.692	0.0719	-0.0866	0.569	-0.0331	0.7228	-7.9915	11.5945	40.1661
12	2.1331	-1.2258	-2.7256	2.9677	2.0385	3.5484	0.7727	0.859	0.6992	-2.3687	-0.16	0.5974	-0.8029	-1.5498	-0.0259	1.5074	0.1261	-0.5098	0.8596	0.3653	1.4004	-12.9321	38.9666	16.7256
13	3.4742	0.9263	-1.481	4.518	0.3799	1.1273	-0.4792	0.4011	0.9212	-1.6565	0.5073	0.7141	-0.6112	-1.283	-0.1904	0.5307	0.4513	-0.5901	0.7367	-0.0844	0.8862	-13.3956	37.3678	28.7803
14	2.7856	-0.5096	-0.0505	0.9973	0.52	3.1803	-0.446	0.1673	0.4118	-0.2616	-0.1051	0.5753	-0.3115	-0.6702	0.4824	0.5154	0.0721	-0.2241	0.4716	-0.0497	0.6459	-2.6081	24.0655	36.7039
15	4.0228	0.0655	0.3098	3.5793	0.2348	3.1465	0.2056	0.2012	0.3932	-0.8743	0.1476	-0.3202	-0.3878	0.2134	-0.3737	0.4457	0.0778	0.0022	0.6658	-0.1809	0.5492	2.196	18.9504	56.6066
16	1.9745	0.248	0.0105	2.9033	-0.9039	1.2793	-0.1249	-0.0217	-0.007	-0.1158	0.1147	0.2435	0.2264	-0.8133	0.1193	0.2063	0.0311	0.0672	0.7431	-0.0912	0.5895	-6.1617	9.327	63.7907
17	3.2408	-0.0139	-0.0153	1.4371	-1.1371	1.0338	0.0749	-0.3328	0.4548	0.5436	-0.1573	-0.1316	-0.5086	0.5534	0.0347	0.9524	-0.5004	0.0405	1.1712	-0.0943	1.0136	56.9458	42.8414	65.9766
18	1.4613	0.8521	-0.615	1.8286	0.3495	1.7903	1.4422	-1.4136	0.7804	0.6662	-0.293	0.69	0.1427	1.288	-0.6535	1.9982	-0.7187	0.1944	1.3805	-0.498	1.4292	37.5048	60.3742	90.6215
19	1.8745	0.6275	0.0618	3.9768	-1.4282	1.0863	-0.1511	0.2447	0.5095	-0.0111	0.2046	0.0161	-1.1881	0.5154	-0.0522	1.032	-0.4191	-0.0303	0.7428	0.009	0.8666	43.8705	45.7722	65.2134
20	1.7575	0.2207	-0.6096	1.3651	-0.7312	1.1782	-0.0918	0.2958	-0.3839	-0.4528	0.2039	-0.375	-0.2026	1.0389	0.1013	0.9454	-0.8721	0.2614	1.2718	0.1244	0.7773	53.3576	38.0959	42.1127

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 21:106 )	A	21 - 106
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 107:202 )	A	107 - 202
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 203:332 )	A	203 - 332
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 333:527 )	A	333 - 527
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 21:96 )	B	21 - 96
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 97:141 )	B	97 - 141
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 142:207 )	B	142 - 207
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 208:385 )	B	208 - 385
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 386:498 )	B	386 - 498
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 499:529 )	B	499 - 529
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 18:106 )	C	18 - 106
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 107:183 )	C	107 - 183
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 184:245 )	C	184 - 245
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 246:386 )	C	246 - 386
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 387:463 )	C	387 - 463
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 464:529 )	C	464 - 529
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 21:126 )	D	21 - 126
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 127:204 )	D	127 - 204
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 205:405 )	D	205 - 405
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 406:529 )	D	406 - 529

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