PDB-3eoe: Crystal Structure of Pyruvate Kinase from toxoplasma gondii, 55.m00007

ID or keywords:

Entry

Database: PDB / ID: 3eoe

Title

Crystal Structure of Pyruvate Kinase from toxoplasma gondii, 55.m00007

Components

Pyruvate kinase

Keywords

TRANSFERASE / malaria kinase pyruvate structural genomics / Glycolysis / Magnesium / Metal-binding / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

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

Biological species

Toxoplasma gondii (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.31 Å

Authors

Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Wasney, G. / Hassani, A. / Vedadi, M. / Cossar, D. / Schapiro, M. / Bochkarev, A. / Arrowsmith, C.H. ...

Citation

Journal: Plos One / Year: 2010
Title: The crystal structure of Toxoplasma gondii pyruvate kinase 1.
Authors: Bakszt, R. / Wernimont, A. / Allali-Hassani, A. / Mok, M.W. / Hills, T. / Hui, R. / Pizarro, J.C.

History

Deposition	Sep 26, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 14, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3	Feb 21, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3eoe.cif.gz	349.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3eoe.ent.gz	281.4 KB	Display	PDB format
PDBx/mmJSON format	3eoe.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3eoe_validation.pdf.gz	480.8 KB	Display	wwPDB validaton report
Full document	3eoe_full_validation.pdf.gz	498.5 KB	Display
Data in XML	3eoe_validation.xml.gz	66.9 KB	Display
Data in CIF	3eoe_validation.cif.gz	94.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eo/3eoe ftp://data.pdbj.org/pub/pdb/validation_reports/eo/3eoe	HTTPS FTP

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Related structure data

Related structure data	3gg8C C: citing same article (ref.)
Similar structure data	3gg8-d 1pky-d 4yng-1 6gg3-1 4l27-d 22773 4fxj-d 6gg3-2 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 (13)

Deposited unit

A: Pyruvate kinase

B: Pyruvate kinase

C: Pyruvate kinase

D: Pyruvate kinase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	98.039, 130.684, 113.848
Angle α, β, γ (deg.)	90.000, 117.400, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Pyruvate kinase Mass: 55929.391 Da / Num. of mol.: 4 / Fragment: sequence database residues 39-531 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: pk / Production host: Escherichia coli (E. coli) / References: UniProt: Q969A2, pyruvate kinase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.89 Å³/Da / Density % sol: 57.5 %

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 2.31→50 Å / Num. all: 110952 / Num. obs: 103408 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / B_iso Wilson estimate: 49.7 Å² / R_merge(I) obs: 0.069 / R_sym value: 0.053 / Χ²: 1.368
Reflection shell	Resolution: 2.31→2.4 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.588 / Mean I/σ(I) obs: 1.2 / Num. unique all: 5921 / R_sym value: 0.484 / Χ²: 0.917 / % possible all: 53.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.31→42.68 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.922 / WR_factor R_free: 0.259 / WR_factor R_work: 0.214 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.818 / SU B: 14.108 / SU ML: 0.177 / SU R Cruickshank DPI: 0.319 / SU R_free: 0.248 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.253	5074	5 %	RANDOM
R_work	0.206	-	-	-
obs	0.208	100883	90.94 %	-

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 max: 81.95 Å² / B_iso mean: 36.264 Å² / B_iso min: 24.26 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.16 Å²	0 Å²	-0.47 Å²
2-	-	0.72 Å²	0 Å²
3-	-	-	-2.31 Å²

Refinement step

Cycle: LAST / Resolution: 2.31→42.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13350	0	18	639	14007

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	13580
X-RAY DIFFRACTION	r_angle_refined_deg	1.118	1.969	18452
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.059	5	1798
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.766	24.676	494
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.361	15	2272
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.33	15	78
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	2268
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	9916
X-RAY DIFFRACTION	r_nbd_refined	0.187	0.2	6485
X-RAY DIFFRACTION	r_nbtor_refined	0.292	0.2	9354
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	779
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.165	0.2	64
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.14	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	0.289	1.5	9278
X-RAY DIFFRACTION	r_mcangle_it	0.497	2	14539
X-RAY DIFFRACTION	r_scbond_it	0.91	3	4723
X-RAY DIFFRACTION	r_scangle_it	1.49	4.5	3911

LS refinement shell

Resolution: 2.31→2.374 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.33	182	-
R_work	0.295	3094	-
all	-	3276	-
obs	-	4480	40.06 %

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	3.0151	-0.0219	-0.206	2.4195	-0.9626	1.726	0.0506	-0.1071	-0.6006	-0.1128	-0.063	-0.133	1.0051	-0.1079	0.0124	0.4121	-0.165	0.0505	0.045	0.0071	0.1199	2.8583	-11.5902	-5.921
2	1.1491	0.0259	0.561	1.1569	-0.3972	4.0599	0.0433	0.0896	0.0324	-0.127	-0.0166	-0.0353	0.2042	-0.18	-0.0267	-0.045	-0.05	0.0043	-0.0123	-0.0084	-0.0084	-1.4699	8.5813	-18.9476
3	4.4881	-0.3905	-0.375	2.0919	0.1925	4.0023	-0.1575	0.0325	-0.3659	-0.171	-0.0726	-0.2283	0.7629	0.2298	0.2301	0.2373	-0.0467	0.0548	-0.0403	0.0399	0.0871	14.1902	-5.2617	-6.0163
4	3.5045	0.4265	-5.2506	0.3584	-0.1513	8.6427	0.0392	-1.0392	1.5339	0.1993	0.6616	-0.3086	-0.3706	0.7818	-0.7009	0.3923	-0.035	-0.0444	0.5701	-0.0183	0.3402	5.5281	7.9472	14.6293
5	4.1842	0.4533	2.0614	3.0951	0.386	6.3825	0.0653	-0.5897	-0.2131	0.2362	0.0215	-0.0388	0.52	-0.2864	-0.0868	0.1818	-0.1277	0.0194	0.229	0.0686	-0.0343	-2.193	-3.2832	14.3983
6	16.675	-7.3406	0.3982	9.7213	-16.3217	40.1809	-0.002	-1.7254	-4.9626	-0.8163	0.4437	0.5421	1.621	1.0733	-0.4417	0.6064	-0.1092	-0.051	0.6043	0.045	0.6	-0.9025	-16.0564	21.2911
7	33.1173	-15.4523	5.9999	13.8491	-4.1747	9.8996	0.7416	0.0801	-0.9061	0.0697	-0.4733	0.2007	1.4803	0.33	-0.2683	0.472	-0.0917	-0.0276	0.406	0.0365	-0.019	-1.1446	-6.8353	26.0846
8	25.9476	2.1335	7.3703	2.5597	2.2004	3.1596	-0.3847	-0.7225	1.4921	-0.3642	0.0691	0.5527	-0.2552	-0.45	0.3156	0.2674	-0.0049	0.0714	0.244	0.0306	0.3313	13.8878	26.7244	-8.6606
9	3.8902	-1.2078	-1.0158	1.2888	0.3041	2.4543	0.2366	0.0013	0.6615	-0.1584	-0.0274	-0.1298	-0.4453	0.2331	-0.2092	0.017	-0.0419	0.0575	-0.0317	-0.0113	0.0375	39.0376	23.4757	-14.7278
10	1.2149	0.3742	-0.445	3.3471	0.6091	0.9263	-0.0938	-0.0522	-0.2479	-0.2712	0.027	-0.0587	0.2678	0.043	0.0668	0.0724	0.0415	0.0004	0.0078	0.0526	0.0457	43.5405	-6.0311	-11.0037
11	1.7415	-0.027	0.3946	1.7116	-0.0947	1.7925	0.0527	-0.2325	0.0031	0.0408	0.0241	0.063	0.1137	0.0383	-0.0768	-0.054	0.002	0.0341	-0.011	0.0071	-0.0493	31.6502	10.8753	-3.6642
12	2.9612	-0.5535	6.3087	0.797	0.0787	32.5595	0.1268	-1.3418	0.131	0.8334	-0.2122	0.5536	0.4618	-1.0391	0.0854	0.4259	-0.146	0.1501	0.4465	-0.0697	0.3081	20.2006	19.7539	11.3431
13	3.4371	-0.4058	-1.597	3.763	1.6267	3.4182	0.1846	-0.341	0.2895	0.2889	-0.0725	0.0591	-0.102	-0.0249	-0.1122	0.0245	-0.0462	0.062	0.0553	-0.0915	0.0955	32.5157	29.5904	8.8441
14	6.8509	1.2505	0.5297	7.1061	-0.5151	6.5235	0.0231	0.2245	0.8656	-0.0266	-0.2049	0.2064	-0.8503	0.1526	0.1817	0.3354	-0.0998	0.1603	0.1743	-0.1672	0.3449	30.1455	41.6672	9.2049
15	6.5255	3.3086	0.7252	9.7603	-2.3116	0.9687	0.1791	0.4972	1.0723	-0.9112	0.4392	2.0884	-0.7096	-0.3243	-0.6182	0.4861	0.0772	-0.0479	0.5346	0.1849	0.3277	-11.366	27.5249	46.4155
16	1.0395	-0.6857	0.2265	2.3727	-1.0529	4.7232	0.1151	0.1726	-0.1069	-0.0661	0.0509	0.5355	0.4535	-0.7703	-0.1659	0.0384	-0.0613	-0.0106	0.0933	0.0237	-0.0122	-11.8775	11.7754	65.2091
17	2.533	1.2371	0.9132	1.3073	0.639	1.4962	0.1004	-0.355	0.2157	0.0438	-0.1268	0.0542	0.1006	0.0639	0.0264	0.0216	0.0549	-0.0131	0.0892	-0.0013	-0.0262	15.6997	15.3227	77.8037
18	2.138	-0.4129	-0.0774	1.4021	0.1372	2.3082	0.0245	0.1432	-0.0143	-0.0421	0.0511	-0.0974	0.2853	0.0795	-0.0756	0.0248	0.0388	0.0019	0.0046	0.0269	-0.0955	6.3886	14.7312	58.312
19	4.6125	-2.07	-6.0334	5.0126	4.5713	10.2827	-0.076	0.5189	-0.1616	-0.8065	0.0979	-0.0976	-0.191	0.1085	-0.0219	0.135	0.0192	-0.0334	0.2774	0.0522	0.0787	-2.4856	22.3305	46.4531
20	2.0837	-0.1752	-0.9392	3.6915	0.3141	8.8392	0.0583	0.332	-0.0413	-0.357	0.0024	0.1003	0.3355	-0.4196	-0.0607	0.1579	-0.0586	-0.0647	0.2177	0.0041	-0.0294	-5.2992	6.3611	40.7938
21	9.0054	-0.9453	0.0369	2.2334	-1.4325	13.9983	-0.2139	-0.3659	-0.0053	-0.0402	0.1842	1.1166	0.1922	-1.9747	0.0297	0.3384	-0.1618	-0.1146	0.6936	-0.0504	0.3368	-15.4727	5.1113	34.0742
22	2.2417	0.8525	-0.4805	2.2729	-1.9139	1.6409	0.0046	-0.1897	-0.1935	0.4593	-0.1582	-0.8671	0.097	0.3397	0.1535	0.156	-0.0217	-0.1064	0.1979	0.012	0.1498	25.2077	40.5682	55.1016
23	6.6526	-1.2698	1.7509	4.4004	-0.6047	3.0763	-0.0032	-0.853	-0.2771	0.5796	0.0785	-0.4849	-0.6452	0.2143	-0.0753	0.361	-0.0827	-0.0976	0.1322	0.0147	0.1015	21.0285	56.3012	54.8727
24	6.6591	-2.1221	1.2105	7.7446	1.285	2.4146	-0.0585	-0.5565	0.1848	0.5956	0.1053	0.0234	-0.6116	-0.3345	-0.0469	0.3404	0.0374	-0.0042	0.0671	0.0525	0.0013	11.0725	63.2241	49.797
25	1.7122	-0.448	0.4895	3.5098	-1.3985	2.1949	0.0001	-0.1998	-0.0492	0.1444	0.1663	0.0734	-0.1922	-0.214	-0.1664	0.0721	0.0023	0.0045	0.0604	0.0218	-0.029	10.2837	44.638	48.8082
26	0.9469	-0.2902	5.3598	0.258	-2.1465	31.8397	0.5089	0.5891	-0.3004	-0.7351	-0.3135	0.4017	1.8436	0.0345	-0.1954	0.6283	-0.042	-0.0406	0.5231	-0.0505	0.4048	16.3636	29.1105	35.3412
27	2.2779	-2.0285	-1.6211	5.8958	2.9498	5.0266	0.0613	0.1813	0.0695	-0.4097	0.0086	-0.536	0.045	0.0148	-0.0699	0.1305	-0.041	0.0967	0.0711	-0.0047	0.1225	25.7923	41.0208	33.1877
28	73.9505	11.6747	-29.878	8.1267	0.5667	16.5144	0.3678	0.7601	0.8518	0.2303	0.437	-1.575	-2.9106	-0.8066	-0.8047	0.6483	-0.0015	0.0012	0.65	-0.0018	0.6512	41.2287	42.6036	32.6187
29	9.8154	-3.2675	7.0946	7.9819	-3.8259	16.1012	-0.2585	-0.4346	0.0053	0.4759	0.1951	-0.8263	-0.3884	1.213	0.0634	0.2764	-0.0602	0.1549	0.4079	-0.1537	0.3274	36.2705	35.2761	29.5453

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	21 - 108
2	X-RAY DIFFRACTION	2	A	109 - 314
3	X-RAY DIFFRACTION	3	A	315 - 369
4	X-RAY DIFFRACTION	4	A	370 - 394
5	X-RAY DIFFRACTION	5	A	395 - 461
6	X-RAY DIFFRACTION	6	A	467 - 482
7	X-RAY DIFFRACTION	7	A	484 - 511
8	X-RAY DIFFRACTION	8	B	21 - 36
9	X-RAY DIFFRACTION	9	B	37 - 97
10	X-RAY DIFFRACTION	10	B	98 - 237
11	X-RAY DIFFRACTION	11	B	238 - 369
12	X-RAY DIFFRACTION	12	B	370 - 388
13	X-RAY DIFFRACTION	13	B	390 - 462
14	X-RAY DIFFRACTION	14	B	464 - 511
15	X-RAY DIFFRACTION	15	C	23 - 38
16	X-RAY DIFFRACTION	16	C	39 - 100
17	X-RAY DIFFRACTION	17	C	101 - 232
18	X-RAY DIFFRACTION	18	C	233 - 354
19	X-RAY DIFFRACTION	19	C	355 - 387
20	X-RAY DIFFRACTION	20	C	391 - 460
21	X-RAY DIFFRACTION	21	C	463 - 511
22	X-RAY DIFFRACTION	22	D	19 - 68
23	X-RAY DIFFRACTION	23	D	69 - 160
24	X-RAY DIFFRACTION	24	D	193 - 223
25	X-RAY DIFFRACTION	25	D	224 - 369
26	X-RAY DIFFRACTION	26	D	370 - 390
27	X-RAY DIFFRACTION	27	D	391 - 460
28	X-RAY DIFFRACTION	28	D	466 - 476
29	X-RAY DIFFRACTION	29	D	480 - 511

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi