PDB-3e0v: Crystal structure of pyruvate kinase from Leishmania mexicana in ...

ID or keywords:

Entry

Database: PDB / ID: 3e0v

Title

Crystal structure of pyruvate kinase from Leishmania mexicana in complex with sulphate ions

Components

Pyruvate kinase

Keywords

TRANSFERASE / PYRUVATE / KINASE / NAD+ NADH / ADP / PHOSPHOENOLPYRUVATE / PEP / GLYCOLYSIS / TRYPANOSOMATID / LEISHMANIA / MEXICANA / Allosteric enzyme / Magnesium / Metal-binding

Function / homology

Function and homology information

pyruvate kinase / pyruvate kinase activity / potassium ion binding / cellular response to insulin stimulus / kinase activity / phosphorylation / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function

Biological species

Leishmania mexicana (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.3 Å

Authors

Tulloch, L.B. / Gillmore, L.A. / Walkinshaw, M.D.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: Sulphate removal induces a major conformational change in Leishmania mexicana pyruvate kinase in the crystalline state.
Authors: Tulloch, L.B. / Morgan, H.P. / Hannaert, V. / Michels, P.A. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.

History

Deposition	Aug 1, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 19, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 20, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3e0v.cif.gz	568.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3e0v.ent.gz	468.2 KB	Display	PDB format
PDBx/mmJSON format	3e0v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3e0v_validation.pdf.gz	550.1 KB	Display	wwPDB validaton report
Full document	3e0v_full_validation.pdf.gz	613.3 KB	Display
Data in XML	3e0v_validation.xml.gz	106.9 KB	Display
Data in CIF	3e0v_validation.cif.gz	146.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e0/3e0v ftp://data.pdbj.org/pub/pdb/validation_reports/e0/3e0v	HTTPS FTP

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Related structure data

Related structure data	3e0wC 1pklS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1a3x-1 4drs-1 3gg8-d 3ktx-1 1pkl-1 1ea0-d 1pkl-2 1pky-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (13)

Deposited unit

A: Pyruvate kinase

B: Pyruvate kinase

C: Pyruvate kinase

D: Pyruvate kinase

E: Pyruvate kinase

F: Pyruvate kinase

hetero molecules

357 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pyruvate kinase

B: Pyruvate kinase

C: Pyruvate kinase

D: Pyruvate kinase

hetero molecules

defined by author&software
238 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Pyruvate kinase

F: Pyruvate kinase

hetero molecules

E: Pyruvate kinase

F: Pyruvate kinase

hetero molecules

defined by author&software
238 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	261.955, 261.955, 185.541
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-1052- HOH

#1: Protein	Pyruvate kinase / PK Mass: 58867.770 Da / Num. of mol.: 6 / Mutation: E452W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania mexicana (eukaryote) / Gene: PYK / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q27686, pyruvate kinase
#2: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 314 / 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: 4.51 Å³/Da / Density % sol: 72.7 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 20% Saturated ammonium sulphate, 100mM Na citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2003 / Details: Mirrors
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 3.3→99.06 Å / Num. obs: 86237 / % possible obs: 89.4 % / Redundancy: 3.1 % / R_merge(I) obs: 0.075 / R_sym value: 0.075 / Net I/σ(I): 8.9
Reflection shell	Resolution: 3.3→3.48 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.496 / Mean I/σ(I) obs: 1.6 / % possible all: 89.4

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
ADSC	Quantum	data collection
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1PKL, chain G

1pkl

Resolution: 3.3→99.06 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.895 / SU B: 51.049 / SU ML: 0.4 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.549 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28958	4286	5.1 %	RANDOM
R_work	0.22663	-	-	-
obs	0.22987	80266	87.18 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 74.381 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.98 Å²	0 Å²	0 Å²
2-	-	0.98 Å²	0 Å²
3-	-	-	-1.95 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→99.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22676	0	218	314	23208

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	23336
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.244	1.959	31641
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.152	5	2987
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.357	24.688	1041
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.562	15	4006
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.177	15	147
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	3631
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	17447
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	11574
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	15857
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.138	0.2	901
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.192	0.2	84
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.125	0.2	9
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.523	2	15093
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.001	3	23908
X-RAY DIFFRACTION	r_scbond_it	1.373	4.5	8994
X-RAY DIFFRACTION	r_scangle_it	2.297	6	7723
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.3→3.386 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.386	301	-
R_work	0.318	5511	-
obs	-	-	82.07 %

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	2.5422	0.8013	0.1618	3.8955	0.2626	2.2905	-0.0956	0.1211	0.1023	0.0347	0.2367	-0.0858	0.0588	-0.2676	-0.1411	-0.2824	-0.0799	0.2223	-0.091	-0.228	-0.1517	89.4227	260.0198	107.876
2	12.469	3.2817	0.3436	6.4486	0.3085	9.1009	-0.1593	0.0537	0.3092	-0.2831	0.2329	-0.3569	-0.1097	-0.1848	-0.0736	-0.3499	-0.0378	0.1274	0.0171	-0.0284	-0.1336	61.5343	269.3409	107.41
3	5.2691	-1.3436	1.5764	6.7907	3.5847	5.0009	-0.0106	0.2647	0.4194	-0.3944	0.0736	-0.6928	-0.1166	0.3333	-0.063	-0.2192	-0.1434	0.3046	-0.1442	-0.3035	0.1402	110.4974	253.0084	99.7505
4	3.9376	0.7076	-0.9586	2.6936	-0.4916	2.2114	-0.08	0.0443	-0.0564	0.1167	0.0811	-0.2679	0.0415	-0.196	-0.0011	-0.1778	-0.0772	0.1496	-0.1798	-0.2673	-0.1847	75.6619	230.0028	119.2794
5	10.1971	0.61	0.2439	8.6872	2.892	7.2951	-0.2103	0.0584	-0.2474	0.3066	0.1144	-0.1925	0.225	-0.1547	0.0959	-0.0928	-0.0612	-0.0398	-0.1956	-0.2042	-0.1169	85.2432	238.7944	145.6569
6	8.489	0.2619	-1.9212	0.8904	0.0683	7.6787	-0.0526	0.284	-0.5536	-0.1263	-0.0119	-0.0276	0.8776	-0.4072	0.0645	-0.0689	-0.2763	0.2224	-0.1103	-0.3487	-0.0275	74.3511	217.0285	99.3735
7	3.8909	0.5592	0.1214	2.4379	-0.0737	2.6571	0.2667	0.0642	0.1173	0.111	-0.1244	-0.1079	0.2413	-0.0226	-0.1423	-0.1261	-0.1073	0.2229	-0.2728	-0.2364	-0.1346	129.0689	220.3312	74.5247
8	6.5561	2.1404	-1.0836	11.3918	0.6955	9.5204	0.1241	-0.1105	0.3754	0.1367	-0.1166	-0.2756	0.219	0.1228	-0.0075	0.0697	-0.0596	0.0231	-0.3341	-0.1582	-0.0594	138.4665	192.4708	74.9002
9	5.5393	-1.2041	-3.2773	5.7907	-1.445	4.5441	-0.0283	-0.3691	0.8024	0.3323	0.1635	-0.5059	-0.3314	0.0849	-0.1352	-0.1156	-0.1616	0.3018	-0.2392	-0.3516	0.1631	121.9555	241.4035	82.642
10	2.9929	0.9418	0.4462	3.3851	0.8103	2.1553	0.0653	0.1622	0.1888	0.0014	-0.0679	0.1013	0.1715	0.01	0.0026	-0.1902	-0.1131	0.275	-0.1412	-0.2092	-0.1496	99.0315	206.6326	63.1041
11	7.9563	2.3894	-2.2296	9.5181	-0.2507	6.1517	0.2178	-0.0166	0.2969	-0.1291	-0.3035	0.0101	0.3054	-0.4575	0.0857	-0.1622	-0.0649	0.2001	-0.0177	-0.0126	-0.1267	107.9299	216.1434	36.7269
12	1.3164	1.0528	0.7	9.3374	2.1099	7.1963	0.028	-0.0809	-0.0927	0.4703	-0.0878	0.481	0.3302	-0.6463	0.0598	-0.1238	-0.2641	0.3533	-0.0072	-0.2402	-0.0916	86.4145	205.2416	83.0148
13	2.192	-0.0189	-0.1716	2.2399	0.481	3.6088	0.1252	-0.0729	-0.0651	-0.0846	-0.1757	0.0108	-0.134	0.1644	0.0505	0.2018	-0.0119	-0.0215	-0.4149	0.0679	-0.2336	138.9942	99.4127	29.3831
14	8.9112	2.2324	1.0866	9.0637	-0.6499	10.8153	0.3102	0.0127	-0.1525	-0.3499	-0.183	-0.292	-0.2212	0.0257	-0.1272	0.061	0.0011	-0.0941	-0.2592	0.2429	-0.222	157.9471	80.9892	42.4181
15	4.431	-1.1828	1.5952	7.0219	2.8059	4.4946	0.1293	0.4383	0.2162	-0.5611	-0.2159	-0.0482	-0.2886	-0.051	0.0866	0.4304	0.0725	-0.0284	-0.3649	0.067	-0.3084	130.6504	119.0492	19.4883
16	2.3999	-0.1135	-0.3858	2.3329	-0.9525	3.4726	0.1842	0.0686	-0.1	0.1416	-0.2633	-0.0075	-0.1003	-0.1015	0.079	0.2844	-0.0303	-0.0064	-0.415	-0.0393	-0.2829	122.9549	99.4164	60.2289
17	6.2467	-0.0126	0.9482	6.6743	2.2791	11.2017	0.3091	-0.1886	-0.1416	0.2176	-0.1739	0.1068	-0.039	-0.008	-0.1352	0.0897	0.0131	-0.0587	-0.2403	-0.1793	-0.174	103.9757	80.9902	47.1851
18	4.6598	1.1827	2.1706	6.6686	-2.6191	5.2889	0.2448	-0.54	0.3331	0.6261	-0.3401	0.118	-0.2231	-0.1544	0.0953	0.4954	-0.1761	-0.0284	-0.3226	-0.0566	-0.2792	131.1582	119.0559	70.088

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	-1 - 88	40 - 129
2	X-RAY DIFFRACTION	1	A	A	187 - 357	228 - 398
3	X-RAY DIFFRACTION	1	A	G - I	501 - 503
4	X-RAY DIFFRACTION	2	A	A	89 - 186	130 - 227
5	X-RAY DIFFRACTION	2	A	J	506
6	X-RAY DIFFRACTION	3	A	A	358 - 498	399 - 539
7	X-RAY DIFFRACTION	3	A	K - L	507 - 508
8	X-RAY DIFFRACTION	4	B	B	-2 - 88	39 - 129
9	X-RAY DIFFRACTION	4	B	B	187 - 357	228 - 398
10	X-RAY DIFFRACTION	4	B	N - Q	501 - 505
11	X-RAY DIFFRACTION	5	B	B	89 - 186	130 - 227
12	X-RAY DIFFRACTION	5	B	R	506
13	X-RAY DIFFRACTION	6	B	B	358 - 498	399 - 539
14	X-RAY DIFFRACTION	6	B	S - T	507 - 508
15	X-RAY DIFFRACTION	7	C	C	-1 - 88	40 - 129
16	X-RAY DIFFRACTION	7	C	C	187 - 357	228 - 398
17	X-RAY DIFFRACTION	7	C	U - X	501 - 505
18	X-RAY DIFFRACTION	8	C	C	89 - 186	130 - 227
19	X-RAY DIFFRACTION	8	C	Y	506
20	X-RAY DIFFRACTION	9	C	C	358 - 498	399 - 539
21	X-RAY DIFFRACTION	9	C	Z - AA	507 - 508
22	X-RAY DIFFRACTION	10	D	D	-2 - 88	39 - 129
23	X-RAY DIFFRACTION	10	D	D	187 - 357	228 - 398
24	X-RAY DIFFRACTION	10	D	CA - FA	501 - 505
25	X-RAY DIFFRACTION	11	D	D	89 - 186	130 - 227
26	X-RAY DIFFRACTION	11	D	GA	506
27	X-RAY DIFFRACTION	12	D	D	358 - 498	399 - 539
28	X-RAY DIFFRACTION	12	D	HA	507
29	X-RAY DIFFRACTION	13	E	E	-2 - 88	39 - 129
30	X-RAY DIFFRACTION	13	E	E	187 - 357	228 - 398
31	X-RAY DIFFRACTION	13	E	IA - LA	501 - 504
32	X-RAY DIFFRACTION	14	E	E	89 - 186	130 - 227
33	X-RAY DIFFRACTION	14	E	MA	506
34	X-RAY DIFFRACTION	15	E	E	358 - 498	399 - 539
35	X-RAY DIFFRACTION	15	E	NA - WA	507 - 508
36	X-RAY DIFFRACTION	16	F	F	-3 - 88	38 - 129
37	X-RAY DIFFRACTION	16	F	F	187 - 357	228 - 398
38	X-RAY DIFFRACTION	16	F	OA - QA	501 - 503
39	X-RAY DIFFRACTION	17	F	F	89 - 186	130 - 227
40	X-RAY DIFFRACTION	17	F	RA	506
41	X-RAY DIFFRACTION	18	F	F	358 - 498	399 - 539
42	X-RAY DIFFRACTION	18	F	SA - TA	507 - 508

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