PDB-3sth: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase fro...

ID or keywords:

Entry

Database: PDB / ID: 3sth

Title

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Toxoplasma gondii

Components

Glyceraldehyde-3-phosphate dehydrogenase

Glyceraldehyde 3-phosphate dehydrogenase

Keywords

OXIDOREDUCTASE /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID /

GAPDH / G3PD /

Glycolysis / NAD / Nucleotide Binding Domain

Function / homology

Function and homology information

glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding /

NADP binding
Similarity search - Function

Biological species

Toxoplasma gondii (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Staker, B.L. / Edwards, T.E. / Sankaran, B.

Citation

Journal: Mol.Microbiol. / Year: 2017
Title: Membrane skeletal association and post-translational allosteric regulation of Toxoplasma gondii GAPDH1.
Authors: Dubey, R. / Staker, B.L. / Foe, I.T. / Bogyo, M. / Myler, P.J. / Ngo, H.M. / Gubbels, M.J.

History

Deposition	Jul 10, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 3, 2011	Provider: repository / Type: Initial release
Revision 1.1	Feb 8, 2017	Group: Database references
Revision 1.2	Mar 8, 2017	Group: Database references
Revision 1.3	Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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	3sth.cif.gz	528.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3sth.ent.gz	437.2 KB	Display	PDB format
PDBx/mmJSON format	3sth.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/st/3sth ftp://data.pdbj.org/pub/pdb/validation_reports/st/3sth	HTTPS FTP

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Related structure data

Related structure data	3cpsS S: Starting model for refinement
Similar structure data	3doc-3 5c7o-d 1dc4-d 4bga-2 3h9e-d 3gnq-9 1gae-d 3cif-2 5xzu-d 7jwk-2 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	TargetDB: TogoA.00914.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (10)

Deposited unit

A: Glyceraldehyde-3-phosphate dehydrogenase

B: Glyceraldehyde-3-phosphate dehydrogenase

C: Glyceraldehyde-3-phosphate dehydrogenase

D: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

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

1

A: Glyceraldehyde-3-phosphate dehydrogenase

D: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

defined by software
79.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glyceraldehyde-3-phosphate dehydrogenase

C: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

defined by software
79.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	103.367, 104.322, 146.625
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase Mass: 38960.645 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGGT1_033520, TGME49_089690 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9BKE2, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

#1: Protein

Glyceraldehyde-3-phosphate dehydrogenase /

Glyceraldehyde 3-phosphate dehydrogenase

Mass: 38960.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Toxoplasma gondii (eukaryote) / Gene: TGGT1_033520, TGME49_089690 / Plasmid: AVA0421 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9BKE2,

glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

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Non-polymers , 5 types, 775 molecules

#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-UNX / UNKNOWN ATOM OR ION Num. of mol.: 4 / Source method: obtained synthetically
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 751 / 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: 2.54 Å³/Da / Density % sol: 51.51 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: TOGOA.00914.A.A1.PW28008 23.8 MG/ ML, PH 5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, PACT F11, 0.2 M Sodium citrate, 0.1M Bis Tris propand pH 6.5, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9774 Å / Relative weight: 1
Reflection	Resolution: 2.25→50 Å / Num. obs: 75704 / % possible obs: 99.7 % / Redundancy: 5.6 % / R_merge(I) obs: 0.12 / Net I/σ(I): 5.7
Reflection shell	Resolution: 2.25→2.29 Å / Redundancy: 5.7 % / R_merge(I) obs: 0.481 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3CPS

3cps

Resolution: 2.25→50 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.948 / SU B: 10.461 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.216	3830	5.1 %	RANDOM
R_work	0.172	-	-	-
obs	0.175	75385	-	-

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: 23.444 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.01 Å²	0 Å²	0 Å²
2-	-	-0.24 Å²	0 Å²
3-	-	-	1.25 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10169	0	232	751	11152

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	10679
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	6995
X-RAY DIFFRACTION	r_angle_refined_deg	1.277	1.975	14515
X-RAY DIFFRACTION	r_angle_other_deg	0.866	3	17160
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.212	5	1365
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.585	24.478	402
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.665	15	1703
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.602	15	39
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1655
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	11850
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2073
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.459	1.5	6753
X-RAY DIFFRACTION	r_mcbond_other	0.106	1.5	2786
X-RAY DIFFRACTION	r_mcangle_it	0.88	2	10874
X-RAY DIFFRACTION	r_scbond_it	1.541	3	3926
X-RAY DIFFRACTION	r_scangle_it	2.431	4.5	3641
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.25→2.31 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.299	264	-
R_work	0.221	5199	-
obs	-	-	98.81 %

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	2.896	-0.4766	1.4119	2.1025	-0.3962	3.5337	-0.003	0.01	-0.114	-0.0181	0.0105	-0.0169	0.16	0.1115	-0.0075	0.081	-0.0084	-0.0043	0.0355	0.0095	0.0686	44.9634	19.6116	54.7495
2	9.1352	2.0591	9.4739	5.3254	4.3254	6.8192	0.2894	0.201	-0.4057	-0.0667	-0.0167	0.1799	0.1579	-0.1401	-0.2726	0.0543	0.0751	-0.0158	0.2063	-0.001	0.1941	52.9295	14.603	51.848
3	0.9907	0.0865	0.0912	1.153	-0.4438	1.3617	0.0129	-0.1826	-0.0385	0.1973	-0.0486	0.0117	-0.0071	0.0286	0.0358	0.0748	0.0189	-0.0128	0.0764	-0.0106	0.0769	45.0025	23.4442	59.117
4	2.7274	0.4574	-0.603	0.4472	-0.2516	0.7775	0.0313	-0.1888	0.0519	0.0603	-0.0482	-0.0344	-0.0682	0.0427	0.0169	0.0858	0.0001	-0.0202	0.0648	0.0014	0.0869	38.8413	41.5412	45.4083
5	1.2078	0.3136	0.1378	1.2029	0.1715	0.7228	-0.0187	0.0537	0.0251	-0.0678	-0.0079	-0.2059	-0.0009	0.1463	0.0265	0.0495	0.0013	0.002	0.1046	0.0307	0.1138	51.2687	37.4645	36.728
6	0.5779	0.1649	0.1522	0.7386	-0.1185	0.9055	0.0344	0.0077	0.0339	0.013	-0.0151	-0.1137	0.0483	0.1122	-0.0193	0.0571	0.0084	0.0021	0.099	0.0121	0.104	52.0088	32.7628	44.1801
7	2.0151	0.2569	-0.7065	1.2369	-0.5313	1.9377	0.0419	-0.1916	0.1763	0.1434	-0.0247	-0.0669	-0.1478	-0.0027	-0.0172	0.078	0.0118	0.001	0.0571	-0.021	0.0899	9.7726	43.8392	57.6755
8	1.6937	-0.083	0.092	1.612	0.6364	2.9127	-0.0508	-0.2112	-0.1802	0.1977	-0.0298	0.1319	0.2923	-0.1691	0.0806	0.1236	-0.0175	0.0563	0.0997	0.0302	0.1201	-0.9292	28.5337	60.9452
9	1.7328	0.497	0.1284	1.8252	0.4917	0.6288	-0.0144	-0.0126	-0.0494	0.0104	-0.0509	0.1361	0.0407	-0.0838	0.0653	0.0667	-0.0175	0.0245	0.0828	-0.0026	0.0784	-0.0945	18.8762	41.1293
10	1.8797	0.2113	0.4145	0.5389	0.1666	0.2424	0.03	-0.1929	-0.1137	0.0994	-0.0378	0.0456	0.0692	-0.0452	0.0078	0.0787	-0.0003	0.0149	0.0675	-0.005	0.0788	13.1584	19.6184	46.0847
11	2.5767	1.2507	0.182	1.9401	-0.1326	1.1267	-0.065	0.1675	0.0731	-0.202	0.015	0.2447	-0.0749	-0.2148	0.05	0.0717	0.0169	-0.0301	0.1037	-0.0075	0.1209	-2.2518	27.5363	32.612
12	0.3804	0.086	-0.0128	0.722	0.2116	1.2246	0.0601	0.0379	-0.0528	0.0024	-0.0636	0.0956	-0.0684	-0.2293	0.0035	0.056	0.0065	-0.0036	0.1152	-0.0016	0.1252	-0.2741	27.9791	43.6166
13	4.2043	-0.3047	0.0181	4.4316	2.3991	4.2101	-0.1403	0.1568	-0.0882	-0.0134	0.1961	-0.1955	0.1383	0.3163	-0.0558	0.0404	-0.0354	0.0287	0.1016	-0.004	0.0814	37.7756	10.0781	18.3294
14	2.4079	1.8631	0.3849	4.0061	1.9549	1.6796	-0.3527	0.602	0.0677	-0.6531	0.4982	-0.2175	-0.2719	0.2374	-0.1455	0.1125	-0.0542	0.029	0.2205	0.0015	0.0676	42.3075	15.1904	14.8229
15	2.242	0.305	-0.8234	0.8469	0.109	1.6652	-0.1384	0.4075	0.037	-0.2275	0.0584	0.1239	0.0519	-0.0332	0.08	0.0831	-0.0205	-0.052	0.1069	-0.0317	0.092	21.7125	3.7588	16.3745
16	0.8639	-0.0996	-0.6009	1.9627	-0.7295	0.8017	-0.0166	0.2661	0.0382	-0.293	0.0439	-0.0011	-0.0463	-0.0602	-0.0274	0.1092	-0.0447	-0.0125	0.1185	-0.014	0.0605	16.8418	26.2464	25.2056
17	1.4805	0.4814	-0.0169	1.2161	0.2003	0.9096	0.0079	-0.0041	-0.2366	0.0432	-0.044	0.0158	0.1692	-0.0428	0.0361	0.0728	-0.0025	0.008	0.0468	-0.0201	0.1089	18.4525	5.4799	35.2549
18	2.2047	-0.2861	-0.9338	0.5137	0.1973	1.3757	-0.036	0.1353	-0.2355	-0.0088	-0.018	0.0168	0.1656	0.0428	0.054	0.0835	0.0027	-0.0154	0.0599	-0.0328	0.1049	24.0649	4.2736	27.899
19	3.4254	2.0734	-0.7112	3.7204	-1.8421	1.2499	-0.3155	0.4996	-0.0847	-0.5369	0.3755	0.019	0.167	-0.2378	-0.06	0.0959	-0.0358	-0.0083	0.1373	-0.0155	0.0529	11.937	47.1087	15.1455
20	4.3231	1.1849	0.9077	3.8314	0.6522	5.5662	-0.2408	0.6927	-0.1508	-0.496	0.1536	-0.4364	-0.034	0.0857	0.0872	0.0786	-0.0519	0.0917	0.1408	0.008	0.0862	27.4978	56.9432	10.9527
21	1.2627	-0.0648	0.506	0.6508	0.2706	0.7145	0.0039	0.1898	0.1767	-0.0243	-0.0084	-0.0247	-0.1042	0.0463	0.0046	0.0972	-0.019	0.0266	0.1	0.0498	0.1561	34.5339	57.6668	25.7343
22	3.2761	0.0299	0.2481	1.0252	0.7207	0.067	0.0745	0.4141	0.2105	-0.3376	-0.0402	-0.0056	-0.1534	0.0143	-0.0343	0.1012	0.0019	-0.0087	0.0942	0.0071	0.07	34.5264	31.7636	23.5668
23	1.3319	0.369	0.0534	1.3506	-0.2414	0.596	0.0042	0.0179	0.25	-0.0175	-0.0042	-0.0554	-0.1542	0.0247	0	0.0713	-0.0083	-0.0075	0.0578	0.0086	0.1294	33.0849	55.6009	34.6682
24	1.7435	-0.1155	0.3135	0.726	-0.1595	0.7434	-0.0037	0.0643	0.1521	-0.0169	-0.006	-0.049	-0.0931	-0.0478	0.0097	0.0993	0.0007	0.0242	0.0633	0.0093	0.1318	28.7233	56.5457	29.8482

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 20
2	X-RAY DIFFRACTION	2	A	21 - 28
3	X-RAY DIFFRACTION	3	A	29 - 159
4	X-RAY DIFFRACTION	4	A	160 - 217
5	X-RAY DIFFRACTION	5	A	218 - 304
6	X-RAY DIFFRACTION	6	A	305 - 339
7	X-RAY DIFFRACTION	7	B	1 - 104
8	X-RAY DIFFRACTION	8	B	105 - 152
9	X-RAY DIFFRACTION	9	B	153 - 181
10	X-RAY DIFFRACTION	10	B	182 - 251
11	X-RAY DIFFRACTION	11	B	252 - 303
12	X-RAY DIFFRACTION	12	B	304 - 339
13	X-RAY DIFFRACTION	13	C	0 - 23
14	X-RAY DIFFRACTION	14	C	24 - 93
15	X-RAY DIFFRACTION	15	C	94 - 173
16	X-RAY DIFFRACTION	16	C	174 - 211
17	X-RAY DIFFRACTION	17	C	212 - 305
18	X-RAY DIFFRACTION	18	C	306 - 339
19	X-RAY DIFFRACTION	19	D	1 - 103
20	X-RAY DIFFRACTION	20	D	104 - 139
21	X-RAY DIFFRACTION	21	D	140 - 181
22	X-RAY DIFFRACTION	22	D	182 - 210
23	X-RAY DIFFRACTION	23	D	211 - 300
24	X-RAY DIFFRACTION	24	D	301 - 339

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