PDB-4tu1: Structure of Toxoplasma gondii fructose 1,6 bisphosphate aldolase

ID or keywords:

Entry

Database: PDB / ID: 4tu1

Title

Structure of Toxoplasma gondii fructose 1,6 bisphosphate aldolase

Components

Fructose-1,6-bisphosphate aldolase

Keywords

LYASE / aldolase / F16BP / invasion / toxoplasma / glideosome / Structural Genomics / PSI-2 / Protein Structure Initiative / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

apical cytoplasm / biological process involved in symbiotic interaction / adhesion of symbiont to host cell / symbiont entry into host / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / positive regulation of ATP biosynthetic process / glycolytic process / actin filament binding ...
Similarity search - Function

Biological species

Toxoplasma gondii (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Boucher, L.E. / Bosch, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of Toxoplasma gondii fructose-1,6-bisphosphate aldolase.
Authors: Boucher, L.E. / Bosch, J.

History

Deposition	Jun 23, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 3, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 24, 2014	Group: Database references
Revision 1.2	Nov 22, 2017	Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4tu1.cif.gz	541.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4tu1.ent.gz	449.3 KB	Display	PDB format
PDBx/mmJSON format	4tu1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4tu1_validation.pdf.gz	471.7 KB	Display	wwPDB validaton report
Full document	4tu1_full_validation.pdf.gz	483.6 KB	Display
Data in XML	4tu1_validation.xml.gz	57.3 KB	Display
Data in CIF	4tu1_validation.cif.gz	84 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tu/4tu1 ftp://data.pdbj.org/pub/pdb/validation_reports/tu/4tu1	HTTPS FTP

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Related structure data

Related structure data	2pc4S S: Starting model for refinement
Similar structure data	1v8b-d 3r7t-1 4my2-1 5vy5-d 3onf-1 7ka2-d 7k9x-d 3dfn-d 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	TargetTrack: SSGCID-TogoA.01236.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (5)

Deposited unit

A: Fructose-1,6-bisphosphate aldolase

B: Fructose-1,6-bisphosphate aldolase

C: Fructose-1,6-bisphosphate aldolase

D: Fructose-1,6-bisphosphate aldolase

hetero molecules

154 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)	92.258, 134.458, 162.430
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	Fructose-1,6-bisphosphate aldolase Mass: 38554.117 Da / Num. of mol.: 4 / Fragment: UNP residues 78-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGVEG_236040 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: B9PW35, fructose-bisphosphate aldolase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 950 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.27 Å³/Da / Density % sol: 62.34 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 0.1 M MOP/HEPES pH 7.9, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, 0.02 M ammonium acetate, 12.5% ...Details: 0.1 M MOP/HEPES pH 7.9, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, 0.02 M ammonium acetate, 12.5% glycerol, 25% PEG-4000; seeded

Crystal

Density Matthews: 3.27 Å³/Da / Density % sol: 62.34 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 0.1 M MOP/HEPES pH 7.9, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, 0.02 M ammonium acetate, 12.5% ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127092 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.127092 Å / Relative weight: 1
Reflection	Resolution: 1.749→46.7 Å / Num. all: 184014 / Num. obs: 184014 / % possible obs: 90.49 % / Redundancy: 3.6 % / R_merge(I) obs: 0.0777 / Net I/σ(I): 11.44
Reflection shell	Resolution: 1.749→1.812 Å / Redundancy: 3.2 % / R_merge(I) obs: 1.858 / Mean I/σ(I) obs: 0.61 / % possible all: 58.27

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
Coot		model building
Blu-Ice		data collection
PHASER		phasing
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2PC4

2pc4

Resolution: 2→46.696 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.95 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2442	6505	4.93 %	Random selection
R_work	0.194	-	-	-
obs	0.1964	132055	96.63 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→46.696 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10277	0	6	950	11233

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10510
X-RAY DIFFRACTION	f_angle_d	1.015	14213
X-RAY DIFFRACTION	f_dihedral_angle_d	12.681	3977
X-RAY DIFFRACTION	f_chiral_restr	0.039	1601
X-RAY DIFFRACTION	f_plane_restr	0.005	1861

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 (%)
2-2.0227	0.3723	245	0.3185	4140	X-RAY DIFFRACTION	98
2.0227-2.0465	0.3084	213	0.2913	4207	X-RAY DIFFRACTION	98
2.0465-2.0715	0.4436	209	0.3839	3967	X-RAY DIFFRACTION	93
2.0715-2.0977	0.3142	193	0.2873	4049	X-RAY DIFFRACTION	94
2.0977-2.1253	0.3514	217	0.251	4146	X-RAY DIFFRACTION	97
2.1253-2.1544	0.3086	229	0.2453	4198	X-RAY DIFFRACTION	98
2.1544-2.1852	0.2831	225	0.232	4138	X-RAY DIFFRACTION	98
2.1852-2.2178	0.2849	213	0.2313	4206	X-RAY DIFFRACTION	98
2.2178-2.2525	0.4249	165	0.3503	3659	X-RAY DIFFRACTION	84
2.2525-2.2894	0.3283	194	0.2545	3827	X-RAY DIFFRACTION	89
2.2894-2.3289	0.3046	189	0.2233	4260	X-RAY DIFFRACTION	98
2.3289-2.3712	0.3016	195	0.2151	4232	X-RAY DIFFRACTION	98
2.3712-2.4168	0.255	223	0.2114	4206	X-RAY DIFFRACTION	98
2.4168-2.4662	0.2499	245	0.2043	4182	X-RAY DIFFRACTION	98
2.4662-2.5198	0.2669	227	0.2048	4218	X-RAY DIFFRACTION	98
2.5198-2.5784	0.2653	224	0.2026	4232	X-RAY DIFFRACTION	98
2.5784-2.6429	0.2678	233	0.2104	4215	X-RAY DIFFRACTION	98
2.6429-2.7143	0.2695	217	0.22	4139	X-RAY DIFFRACTION	96
2.7143-2.7942	0.2571	219	0.2092	4229	X-RAY DIFFRACTION	98
2.7942-2.8844	0.2849	206	0.209	4265	X-RAY DIFFRACTION	98
2.8844-2.9874	0.2548	203	0.2053	4264	X-RAY DIFFRACTION	98
2.9874-3.107	0.2685	231	0.2005	4224	X-RAY DIFFRACTION	98
3.107-3.2484	0.2397	222	0.1928	4237	X-RAY DIFFRACTION	98
3.2484-3.4196	0.2362	223	0.1839	4262	X-RAY DIFFRACTION	98
3.4196-3.6338	0.2394	196	0.1846	4223	X-RAY DIFFRACTION	97
3.6338-3.9142	0.2197	242	0.1631	4127	X-RAY DIFFRACTION	95
3.9142-4.3079	0.1986	193	0.1463	4327	X-RAY DIFFRACTION	97
4.3079-4.9306	0.1503	227	0.1343	4283	X-RAY DIFFRACTION	97
4.9306-6.2098	0.198	250	0.1564	4402	X-RAY DIFFRACTION	99
6.2098-46.7086	0.1856	237	0.1462	4486	X-RAY DIFFRACTION	97

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	2.9716	-2.6268	-2.0187	6.8931	4.2976	7.2649	0.1203	0.2592	0.4418	-0.3303	-0.2371	0.0537	-0.9167	-0.3047	0.0442	0.2693	-0.0769	-0.0284	0.2815	0.0859	0.3197	36.5866	54.9247	20.1132
2	1.331	0.1155	-0.5376	0.3225	0.2424	1.4624	-0.0441	0.1927	0.0061	-0.0973	-0.0073	-0.0353	-0.0555	0.2535	0.0737	0.2626	0.0165	-0.0268	0.358	0.0297	0.2352	48.6606	41.3444	19.6302
3	2.0089	0.196	0.1561	0.92	0.2063	1.6314	-0.058	0.3463	-0.1781	-0.1224	0.0087	0.0167	0.0735	-0.018	0.0314	0.1981	0.0166	0.0073	0.2137	-0.0205	0.178	28.5141	38.1728	22.3706
4	5.0393	-0.304	-2.0692	1.3108	0.1537	3.1553	-0.1126	0.634	0.0586	-0.1088	0.0223	-0.0555	-0.0759	-0.0128	0.1054	0.2728	-0.0012	-0.0253	0.5197	-0.0171	0.1991	41.1888	38.2732	3.4757
5	6.5275	-1.931	2.0773	6.3683	-3.0686	4.1275	0.3064	0.9992	-0.0944	-0.5758	-0.3021	0.5184	0.3989	0.0465	0.0319	0.3156	-0.0503	-0.0139	0.6484	-0.0903	0.3418	2.0563	41.688	18.2696
6	5.1325	-1.0222	1.9609	5.5409	-0.4778	4.7115	0.156	-0.0345	1.4507	0.375	-0.2365	0.4725	-0.6981	0.0245	0.1009	0.3726	0.0161	0.0127	0.5053	0.035	0.779	-17.0546	55.9819	23.5336
7	2.5551	0.2397	2.5324	0.6313	-0.1934	2.7049	-0.0529	0.1604	0.1255	-0.0348	0.0656	0.0059	-0.1036	-0.5674	-0.0332	0.2157	0.035	0.0133	0.3362	-0.036	0.2964	-6.6584	45.7623	29.9657
8	1.4428	0.2837	-0.4272	1.4711	0.237	1.752	0.0072	0.1342	0.2314	0.052	0.0028	0.1064	-0.2415	-0.1322	0.021	0.244	0.0669	-0.0413	0.184	-0.0102	0.2649	10.1142	52.3621	32.3511
9	3.0805	-1.0976	0.328	3.313	-1.1584	2.5952	-0.1535	0.3069	0.5979	-0.2745	0.0619	0.5112	-0.6192	-0.2765	0.096	0.4606	0.1111	-0.0723	0.329	0.0681	0.3807	12.3911	60.905	19.9231
10	6.0318	0.2891	0.1641	0.5991	0.2466	2.6572	0.0279	1.2188	1.9398	-0.4175	0.096	0.4306	-0.4402	0.0478	-0.1393	0.5826	0.0445	-0.0181	0.7923	0.3329	1.0654	-10.5728	63.6345	16.3768
11	7.7188	4.5204	0.8246	6.6808	0.1758	3.9935	0.003	-0.7309	-0.0765	0.1754	-0.1188	-0.3549	-0.3781	0.1049	0.1169	0.2623	0.0528	0.0019	0.4696	-0.0413	0.2341	6.1694	39.1603	65.0096
12	2.2192	0.4855	-1.5825	0.2485	-0.6425	3.3639	-0.09	-0.1982	-0.2005	0.0516	0.0734	0.042	0.4079	-0.5578	-0.001	0.2761	-0.0611	-0.011	0.4283	0.0198	0.3313	-7.9655	29.1229	58.4983
13	2.1112	-0.9688	-0.5183	1.2867	0.6266	1.868	-0.0598	-0.0548	-0.3162	0.0453	-0.0529	0.0647	0.1789	-0.0043	0.1197	0.2125	-0.0134	0.0066	0.157	0.0107	0.2534	11.5801	30.516	48.7603
14	1.8479	-0.255	0.0429	2.6334	0.0659	2.3109	-0.1864	-0.4221	-0.6733	0.1318	0.1287	0.276	0.477	-0.0066	0.0543	0.2825	0.0014	0.0692	0.2791	0.0823	0.441	15.8001	21.5185	58.5739
15	4.1382	3.5569	-1.0032	3.8042	-1.1562	4.1614	0.0197	-0.1296	-0.6914	0.4744	-0.017	0.0983	0.6284	0.4464	0.0473	0.5126	-0.0313	0.0949	0.465	0.0375	0.4937	2.0545	19.5962	65.17
16	5.5357	1.767	-2.2797	5.0975	-0.3077	4.874	-0.0424	-1.399	-1.5709	0.616	-0.2608	-0.5086	0.8197	0.4131	0.2197	0.6266	-0.0613	0.0444	0.7964	0.3275	0.6685	-4.2544	15.3436	73.0311
17	4.2478	3.9107	6.03	4.097	4.6473	2.0836	-0.2246	-0.9582	-0.7285	-0.0248	-0.3432	0.2568	0.4443	-0.3226	0.2086	0.3737	-0.0124	0.0167	0.5722	0.1048	0.49	37.9933	22.4189	54.8375
18	4.0008	2.8515	-2.4749	6.7277	-1.613	4.2403	-0.0265	0.8573	1.3626	0.1154	-0.3116	-0.5967	-1.2116	0.4593	0.3697	0.6972	-0.2429	-0.1875	1.119	0.4763	0.8879	54.3354	47.7221	64.1589
19	2.1726	2.5125	-1.1632	5.011	-0.9274	3.3947	-0.2866	0.3342	0.2677	-0.8099	-0.0994	-1.1413	-0.009	1.0548	0.5328	0.4356	-0.0283	0.0598	1.0072	0.2506	0.6534	60.0606	40.7434	68.6139
20	6.2362	-2.0362	2.5195	1.3155	-0.083	1.8311	0.0992	0.47	-0.1364	0.0674	-0.2834	-0.3753	-0.4206	0.8404	0.2163	0.2853	-0.0806	-0.0202	0.6868	0.1326	0.386	59.2847	35.2457	58.9717
21	1.9006	-0.7534	1.4969	2.0361	-1.1657	3.4049	0.0077	-0.1634	-0.0896	0.0421	-0.076	-0.0943	0.0115	0.4495	0.1292	0.163	-0.0285	0.019	0.3396	0.0368	0.188	47.4426	39.4284	49.7233
22	1.625	-0.1432	-0.3627	1.5704	-0.1609	1.4686	-0.0265	-0.2582	0.1172	0.093	-0.0155	0.0761	-0.1674	0.2234	0.023	0.2167	-0.0244	-0.0309	0.2516	-0.0259	0.1733	33.1658	45.2226	53.4607
23	2.745	-1.1272	1.7274	3.7703	0.7987	3.9861	-0.1805	-1.2555	0.1125	0.5256	0.2855	-0.3012	-0.0897	0.501	-0.0568	0.3354	-0.0289	-0.0086	0.6898	-0.0565	0.2855	31.2886	44.374	68.196
24	0.4335	-0.261	-0.8455	1.4216	-1.1105	3.6745	-0.4421	0.7107	1.389	0.3114	-0.1664	-0.5369	-0.4619	0.7809	0.4952	0.4415	-0.0533	-0.1584	0.7753	0.3652	0.7402	55.0738	45.0632	75.0656

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 16 through 52 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 53 through 177 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 178 through 289 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 290 through 355 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 17 through 52 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 53 through 100 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 101 through 156 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 157 through 262 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 263 through 312 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 313 through 355 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 17 through 52 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 53 through 156 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 157 through 236 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 237 through 306 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 307 through 333 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 334 through 355 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 18 through 39 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 40 through 63 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 64 through 88 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 89 through 108 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 109 through 156 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 157 through 262 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 263 through 318 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 319 through 355 )

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+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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi