PDB-3gg8: Crystal structure of the Toxoplasma gondii Pyruvate Kinase N term...

ID or keywords:

Entry

Database: PDB / ID: 3gg8

Title

Crystal structure of the Toxoplasma gondii Pyruvate Kinase N terminal truncated

Components

Pyruvate kinase

Keywords

TRANSFERASE / malaria / pyruvate kinase / genomics / proteomics / Glycolysis / Kinase / Magnesium / Pyruvate / Structural Genomics / 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 /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.21 Å

Authors

Wernimont, A.K. / Lew, J. / Allali-Hassani, A. / Vedadi, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hills, T. ...

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	Feb 27, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 26, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Non-polymer description / Version format compliance
Revision 1.2	Jun 8, 2016	Group: Other
Revision 1.3	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.4	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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	3gg8.cif.gz	366.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3gg8.ent.gz	298.5 KB	Display	PDB format
PDBx/mmJSON format	3gg8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3gg8_validation.pdf.gz	493.8 KB	Display	wwPDB validaton report
Full document	3gg8_full_validation.pdf.gz	526 KB	Display
Data in XML	3gg8_validation.xml.gz	69 KB	Display
Data in CIF	3gg8_validation.cif.gz	97.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gg/3gg8 ftp://data.pdbj.org/pub/pdb/validation_reports/gg/3gg8	HTTPS FTP

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Related structure data

Related structure data	3eoeSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1pky-d 3eoe-d 4yng-1 5ws9-d 1e0u-d 4yng-2 3e0v-1 6gg3-1 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)	109.023, 92.311, 112.443
Angle α, β, γ (deg.)	90.00, 105.57, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Pyruvate kinase Mass: 55929.391 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: 55m00007, pk / Production host: Escherichia coli (E. coli) / References: UniProt: Q969A2, pyruvate kinase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.44 Å³/Da / Density % sol: 49.51 %
Crystal grow	Method: vapor diffusion, hanging drop / pH: 7 Details: 5 % PEG 3350, 0.1 M Succinic Acid, pH 7.0, 3 mM Chembridge #5175181, 20% glycerol, Vapor diffusion, hanging drop

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 17, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. all: 108075 / Num. obs: 105806 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / R_merge(I) obs: 0.088 / R_sym value: 0.053
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.913 / Mean I/σ(I) obs: 2 / R_sym value: 0.913 / % possible all: 96.3

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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
Starting model: PDB entry 3EOE

3eoe

Resolution: 2.21→42.45 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.924 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 15.237 / SU ML: 0.188 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26516	5263	5 %	RANDOM
R_work	0.20634	-	-	-
obs	0.20923	100484	97.61 %	-
all	-	108075	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 35.302 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.94 Å²	0 Å²	2.35 Å²
2-	-	0.11 Å²	0 Å²
3-	-	-	-0.79 Å²

Refinement step

Cycle: LAST / Resolution: 2.21→42.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14240	0	16	484	14740

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	14510
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.282	1.968	19716
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.462	5	1915
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.129	24.911	560
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.413	15	2484
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.235	15	86
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	2404
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	10647
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	6808
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.296	0.2	9956
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	0.2	731
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	0.188	0.2	89
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.213	0.2	13
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	0.435	1.5	9848
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.701	2	15423
X-RAY DIFFRACTION	r_scbond_it	1.312	3	5144
X-RAY DIFFRACTION	r_scangle_it	2.111	4.5	4283
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.21→2.262 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.354	370	-
R_work	0.281	7000	-
obs	-	-	92.96 %

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	4.0079	0.8959	0.486	4.1459	-0.2149	2.3195	0.1098	0.1083	0.8957	0.2575	-0.0939	0.2737	-0.4957	0.0111	-0.0159	0.1622	0.0713	0.1151	-0.0761	0.0407	0.2061	4.1108	58.7882	175.4078
2	3.8745	-0.1864	-1.0096	1.7241	-2.6471	5.445	-0.3151	-0.7262	-0.3668	0.6019	0.4027	0.2401	-0.2197	-0.7021	-0.0876	0.203	0.0545	0.0259	0.2152	0.0389	0.1868	-11.009	32.9075	189.03
3	2.4109	1.3103	-0.3465	2.6833	-0.1363	2.0283	0.1074	-0.0241	0.1364	0.3652	-0.1169	0.1104	-0.0185	-0.0909	0.0094	-0.0339	0.0302	-0.0195	-0.0714	0.0149	-0.0145	6.483	42.7682	177.2782
4	2.3462	0.5226	1.1009	2.3825	3.3132	11.3137	-0.158	0.0184	-1.0591	0.1687	0.5175	-0.7781	1.0087	0.9891	-0.3595	0.267	0.0131	0.0977	0.2271	0.0137	0.5049	22.9785	39.7375	163.2388
5	5.285	0.9511	-2.9178	3.7719	-1.1286	4.4191	-0.172	0.2032	-0.0315	-0.2119	0.123	0.018	0.0494	0.0903	0.0489	-0.019	0.0311	0.0001	-0.0401	0.0389	-0.0349	14.9408	50.7843	158.1401
6	1.8754	-2.413	-1.22	14.4523	3.4576	4.9685	-0.0908	0.2804	0.066	-0.3993	-0.0874	0.4464	-0.3509	-0.4019	0.1782	0.1199	-0.0182	0.0864	0.1085	0.0807	0.0264	19.141	59.8052	151.4361
7	3.5246	-2.2572	1.0883	4.9107	-2.218	3.3646	-0.1652	-0.1706	0.8429	0.2958	0.0312	-1.1483	-1.1034	0.4142	0.1339	0.131	-0.1086	-0.0448	0.2311	-0.0078	0.1952	66.8742	21.3227	148.9395
8	3.0447	1.42	0.6765	10.2582	3.2987	4.7404	-0.0021	-0.1319	-0.3477	0.2336	0.1349	-1.6751	0.3588	1.0532	-0.1328	-0.0447	0.1277	-0.0357	0.2918	0.0281	0.2717	73.1723	3.2372	147.4515
9	2.3706	-0.8764	-3.0523	0.5572	1.9632	6.9181	0.2528	0.9262	0.3917	-0.2992	-0.0114	-0.1821	-0.9046	-0.6404	-0.2413	0.2561	0.0851	0.0409	0.2955	0.0505	0.2399	64.8371	1.4985	125.2964
10	11.2041	-6.1532	2.348	5.0948	1.035	6.7495	0.4808	1.4959	-0.9136	-0.7867	-0.4123	0.7987	-0.577	-1.257	-0.0685	0.4462	0.0621	-0.078	0.6909	-0.0234	0.4305	55.8794	-1.4458	118.0187
11	4.0175	-2.2704	0.8119	6.6076	-0.2987	2.4629	0.075	0.2057	-0.27	-0.4274	-0.0023	0.3933	0.3202	0.045	-0.0727	0.0031	-0.0123	0.0144	0.0048	-0.0382	-0.0277	51.2998	0.6657	144.0437
12	2.5143	-0.1398	0.4402	5.0385	-2.0437	4.3101	-0.0897	0.2029	0.0593	-0.5883	-0.035	-0.5445	-0.1427	0.6552	0.1246	0.0527	-0.0436	0.0812	0.0918	-0.016	0.0249	64.8939	17.6414	138.7383
13	21.3307	-10.0945	2.2215	22.1131	-5.5722	19.3861	-0.6172	-0.8156	0.7171	0.5796	0.2437	0.4557	-1.425	0.0107	0.3735	0.0695	-0.1101	-0.0845	0.0535	0.0222	0.0356	61.6516	24.8858	148.3928
14	120.303	-4.113	9.0844	55.6851	-1.9813	40.125	1.2245	2.9884	4.7019	1.0346	-3.2315	5.0079	-1.3609	1.0816	2.0069	0.6615	-0.001	-0.0023	0.6629	-0.0074	0.6647	45.6596	23.2426	157.4472
15	3.8035	-1.1008	-2.1177	4.3024	5.6516	9.0835	0.0592	0.2002	-0.149	0.498	-0.2532	0.3453	0.1925	-0.0995	0.194	0.0514	0.0528	-0.0247	-0.0259	0.0231	-0.0544	54.4065	13.3177	164.5299
16	9.4783	1.1556	4.7595	2.9096	4.4049	7.6733	-0.0246	-0.6804	-0.4371	0.9677	0.4247	-0.8606	0.8952	1.0069	-0.4002	0.3969	0.1155	-0.135	0.1917	-0.0485	0.2802	65.1212	12.5662	169.6981
17	19.5067	12.6372	-1.5906	16.8109	-0.2886	5.2111	0.1851	-0.3008	-0.5687	0.6689	-0.2573	-0.5665	0.2186	0.303	0.0722	0.1042	0.053	-0.051	0.0153	-0.0052	-0.0857	58.6225	18.2615	174.5076
18	15.095	-0.1445	9.6074	0.0014	-0.092	6.1148	1.1949	-0.3132	-0.521	-1.0044	-0.5754	0.1858	1.175	0.3543	-0.6195	0.3487	0.072	-0.0939	0.317	-0.0239	0.3435	15.6351	22.662	182.6652
19	2.388	0.9734	1.1402	2.4416	3.1903	4.7727	0.0431	-0.213	-0.3546	0.3167	0.0511	0.0042	0.792	0.1911	-0.0942	0.0302	0.0218	-0.0337	0.0113	0.0381	-0.0577	30.2487	28.3678	207.9089
20	0.4092	0.2104	0.2369	1.9454	0.1198	1.0111	0.0022	0.0505	0.2759	-0.045	0.0159	0.0995	-0.1537	0.0269	-0.0181	-0.0264	-0.0318	0.004	0.0253	0.0294	0.0047	30.8256	51.0429	200.3726
21	5.2985	-1.3766	-3.7691	4.3845	2.0351	9.1646	0.3985	0.5584	-0.0223	-0.774	-0.2628	-0.1998	-0.437	0.0611	-0.1357	0.157	-0.0039	-0.0598	0.049	0.0098	0.0406	25.1012	29.2277	186.4787
22	3.2625	-0.5845	-0.7183	4.7764	1.6774	7.2171	0.1363	0.1266	-0.0636	-0.1161	0.0019	-0.1978	-0.0992	-0.0101	-0.1382	-0.0051	0.0322	0.0102	-0.0521	-0.0091	-0.0471	41.854	22.403	186.6708
23	5.9251	2.3777	-3.0136	8.5268	-2.7646	8.8743	-0.0617	-0.4353	-0.6822	-0.0977	0.0091	-0.6602	0.114	0.0172	0.0527	0.058	0.1176	-0.0592	0.0092	0.0091	0.0578	43.6158	11.4672	185.8383
24	6.379	-14.1863	6.9113	61.9213	-28.1847	12.8948	0.2167	-0.1332	-1.2891	-2.5961	1.2974	1.8798	1.5142	-1.2263	-1.5141	0.3265	0.0107	-0.0224	0.4233	-0.0396	0.3316	34.3364	19.4182	130.8646
25	3.2251	1.4057	-1.1505	3.2049	-0.5462	2.8643	0.0961	0.5625	0.1977	-0.1927	0.0947	0.2542	-0.0359	-0.5572	-0.1908	-0.0132	0.049	-0.0022	0.0814	0.0379	-0.0845	46.1591	39.6047	116.0446
26	2.6589	0.1426	-0.3866	0.4561	-0.1758	0.9904	0.1094	-0.0906	0.017	0.1832	-0.0512	-0.1071	0.0239	0.0767	-0.0582	0.0613	-0.0066	-0.0259	-0.0353	-0.0303	-0.039	62.2714	38.5403	128.4222
27	2.3935	-4.6251	-9.1249	21.808	29.3967	45.5402	-0.5186	-1.4928	-0.5462	2.1427	-0.2979	0.9405	0.8942	0.3395	0.8164	0.4239	0.0485	0.0304	0.5095	0.1166	0.4801	38.1732	32.6759	145.7732
28	5.8462	-0.4839	-3.4355	3.8413	0.6194	5.3139	0.0237	-0.1555	0.2119	0.038	-0.0925	0.4608	0.2293	-0.0088	0.0688	0.0223	0.0055	0.0782	0.0587	-0.063	0.0523	31.3595	44.3759	136.3427
29	10.8029	4.009	-1.0922	12.5584	-1.1301	8.1058	-0.3444	1.4498	0.2003	-0.9598	0.3932	1.4867	0.1888	-1.0058	-0.0488	0.177	0.0085	0.0714	0.4449	-0.0726	0.3079	19.7152	44.2931	135.1262

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	21 - 103
2	X-RAY DIFFRACTION	2	A	104 - 225
3	X-RAY DIFFRACTION	3	A	226 - 369
4	X-RAY DIFFRACTION	4	A	370 - 393
5	X-RAY DIFFRACTION	5	A	394 - 461
6	X-RAY DIFFRACTION	6	A	462 - 511
7	X-RAY DIFFRACTION	7	B	22 - 47
8	X-RAY DIFFRACTION	8	B	48 - 96
9	X-RAY DIFFRACTION	9	B	97 - 143
10	X-RAY DIFFRACTION	10	B	144 - 198
11	X-RAY DIFFRACTION	11	B	201 - 315
12	X-RAY DIFFRACTION	12	B	316 - 362
13	X-RAY DIFFRACTION	13	B	363 - 374
14	X-RAY DIFFRACTION	14	B	376 - 385
15	X-RAY DIFFRACTION	15	B	391 - 450
16	X-RAY DIFFRACTION	16	B	451 - 480
17	X-RAY DIFFRACTION	17	B	481 - 511
18	X-RAY DIFFRACTION	18	C	16 - 36
19	X-RAY DIFFRACTION	19	C	37 - 100
20	X-RAY DIFFRACTION	20	C	101 - 353
21	X-RAY DIFFRACTION	21	C	354 - 387
22	X-RAY DIFFRACTION	22	C	391 - 462
23	X-RAY DIFFRACTION	23	C	463 - 511
24	X-RAY DIFFRACTION	24	D	40 - 56
25	X-RAY DIFFRACTION	25	D	57 - 128
26	X-RAY DIFFRACTION	26	D	129 - 389
27	X-RAY DIFFRACTION	27	D	390 - 407
28	X-RAY DIFFRACTION	28	D	410 - 482
29	X-RAY DIFFRACTION	29	D	484 - 531

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