PDB-5upr: X-ray structure of a putative triosephosphate isomerase from Toxo...

ID or keywords:

Entry

Database: PDB / ID: 5upr

Title

X-ray structure of a putative triosephosphate isomerase from Toxoplasma gondii ME49

Components

Triosephosphate isomerase

Keywords

ISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function

Biological species

Toxoplasma gondii (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Cardona-Correa, A. / Bishop, B. / Anderson, W.F. / Ngo, H. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: X-ray structure of a putative triosephosphate isomerase from Toxoplasma gondii ME49
Authors: Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Cardona-Correa, A. / Bishop, B. / Anderson, W.F. / Ngo, H. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Feb 3, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jul 19, 2017	Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.3	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5upr.cif.gz	418.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5upr.ent.gz	345.3 KB	Display	PDB format
PDBx/mmJSON format	5upr.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/up/5upr ftp://data.pdbj.org/pub/pdb/validation_reports/up/5upr	HTTPS FTP

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Related structure data

Similar structure data	1r2r-1 6mnj-2 2jk2-d 4poc-d 1ssd-d 6oog-1 1tpv-d 6cg9-d 4jeq-4 7tim-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
Other databases	TargetTrack: idp92134

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (8)

Deposited unit

A: Triosephosphate isomerase

B: Triosephosphate isomerase

C: Triosephosphate isomerase

D: Triosephosphate isomerase

hetero molecules

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

1

A: Triosephosphate isomerase

hetero molecules

D: Triosephosphate isomerase

hetero molecules

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

2

B: Triosephosphate isomerase

C: Triosephosphate isomerase

hetero molecules

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

Unit cell

Length a, b, c (Å)	56.368, 115.533, 78.719
Angle α, β, γ (deg.)	90.00, 90.02, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	ALA	ALA	ALA	A	A	113 - 370	3 - 260
2	1	ALA	ALA	ALA	ALA	B	B	113 - 370	3 - 260
1	2	ARG	ARG	LYS	LYS	A	A	118 - 372	8 - 262
2	2	ARG	ARG	LYS	LYS	C	C	118 - 372	8 - 262
1	3	ALA	ALA	ALA	ALA	A	A	117 - 371	7 - 261
2	3	ALA	ALA	ALA	ALA	D	D	117 - 371	7 - 261
1	4	ARG	ARG	ALA	ALA	B	B	118 - 370	8 - 260
2	4	ARG	ARG	ALA	ALA	C	C	118 - 370	8 - 260
1	5	ALA	ALA	ALA	ALA	B	B	117 - 370	7 - 260
2	5	ALA	ALA	ALA	ALA	D	D	117 - 370	7 - 260
1	6	ARG	ARG	ALA	ALA	C	C	118 - 371	8 - 261
2	6	ARG	ARG	ALA	ALA	D	D	118 - 371	8 - 261

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Triosephosphate isomerase Mass: 28399.596 Da / Num. of mol.: 4 / Fragment: UNP residues 111-375 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (strain ATCC 50611 / Me49) (eukaryote) Strain: ATCC 50611 / Me49 / Gene: TPI-II, TGME49_233500 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A0A125YP67, triose-phosphate isomerase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1023 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Ammonium Sulphate, 0.1 M Bis-Tris, 25 % PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97875 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2016 / Details: beryllium lenses
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97875 Å / Relative weight: 1
Reflection	Resolution: 2→30 Å / Num. obs: 67710 / % possible obs: 99.9 % / Redundancy: 3.9 % / R_merge(I) obs: 0.1 / Net I/σ(I): 15.04
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.65 / Mean I/σ(I) obs: 2.86 / Num. unique all: 3393 / Num. unique obs: 3393 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-2000		data scaling
PHENIX		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2→30 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.939 / SU B: 7.721 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.16 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20794	3412	5.1 %	RANDOM
R_work	0.16575	-	-	-
obs	0.16784	63148	97.87 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 30.016 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.18 Å²	-0 Å²	-0.08 Å²
2-	-	-0.54 Å²	0 Å²
3-	-	-	0.36 Å²

Refinement step

Cycle: 1 / Resolution: 2→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7778	0	29	1023	8830

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	7973
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	7434
X-RAY DIFFRACTION	r_angle_refined_deg	1.812	1.952	10823
X-RAY DIFFRACTION	r_angle_other_deg	1.011	3	17255
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.242	5	1038
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.005	25.087	346
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.72	15	1304
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.017	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	1229
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	9033
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1547
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	1.144	1.676	4152
X-RAY DIFFRACTION	r_mcbond_other	1.143	1.675	4151
X-RAY DIFFRACTION	r_mcangle_it	1.754	2.506	5190
X-RAY DIFFRACTION	r_mcangle_other	1.754	2.506	5191
X-RAY DIFFRACTION	r_scbond_it	1.682	1.892	3821
X-RAY DIFFRACTION	r_scbond_other	1.643	1.88	3802
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.583	2.743	5604
X-RAY DIFFRACTION	r_long_range_B_refined	5.718	22.061	9271
X-RAY DIFFRACTION	r_long_range_B_other	5.463	20.938	8941
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	15976	0.07
1	2	B	15976	0.07
2	1	A	16074	0.07
2	2	C	16074	0.07
3	1	A	15942	0.07
3	2	D	15942	0.07
4	1	B	15718	0.07
4	2	C	15718	0.07
5	1	B	15690	0.07
5	2	D	15690	0.07
6	1	C	15944	0.08
6	2	D	15944	0.08

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.235	215	-
R_work	0.211	3974	-
obs	-	-	83.36 %

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	0.6787	0.6644	-0.0017	1.2457	-0.1943	0.0672	0.0178	0.0416	0.008	-0.2465	0.0267	0.1352	0.1002	0.0086	-0.0445	0.2276	-0.0195	0.0172	0.1433	0.0004	0.1376	59.5749	82.4731	32.3227
2	2.3636	-0.13	-1.0578	2.0636	0.2043	2.0539	-0.0532	0.2202	-0.1792	-0.4952	0.0893	-0.0247	0.2588	-0.2117	-0.0361	0.1954	-0.0455	-0.021	0.1205	-0.0158	0.0296	60.7025	84.3378	26.245
3	5.6877	0.3968	6.2132	1.9787	-1.2524	13.0608	0.4834	-0.154	0.0882	-0.7305	-0.4217	1.3708	1.4976	-1.4584	-0.0617	0.6316	-0.092	-0.4156	0.849	-0.5907	1.218	54.2303	83.74	24.5472
4	0.6761	0.2852	-0.2089	1.8972	-0.4886	0.7293	0.0214	0.0503	-0.017	0.0933	0.0038	0.2183	0.0868	-0.033	-0.0253	0.0781	-0.0105	0.0531	0.0586	-0.0245	0.0652	61.2112	87.2883	45.4038
5	11.1419	6.2491	-0.1727	3.5201	-0.093	0.0054	-0.2693	0.3911	-0.0284	-0.1584	0.2578	-0.0158	0.0084	0.0028	0.0115	0.1339	-0.0139	-0.0085	0.1119	-0.0118	0.0837	52.9565	68.2281	35.9745
6	4.7921	-6.1086	-0.1782	7.9253	0.2153	0.0085	-0.7475	-0.4334	0.2031	0.9739	0.7344	-0.4247	0.0188	-0.0084	0.0131	0.3037	0.1085	0.0107	0.4466	-0.0108	0.4076	58.6475	72.0921	15.1323
7	2.9522	-0.6732	-0.0542	1.11	0.6075	1.6086	-0.084	-0.5421	-0.423	0.2837	0.2146	0.2361	0.0145	-0.0246	-0.1306	0.1642	0.0087	0.0714	0.3265	0.1145	0.1222	38.6302	84.6166	11.1911
8	4.1274	4.7472	-5.511	5.4842	-6.3469	7.3647	0.206	-0.4173	-0.247	0.3325	-0.52	-0.2832	-0.3273	0.5515	0.314	0.5165	0.0237	-0.0114	0.3442	-0.0102	0.1415	43.4325	85.0831	19.8276
9	1.2577	-0.56	0.2074	1.2327	-0.0993	0.5046	0.0584	-0.1127	-0.0607	-0.0137	-0.0614	-0.0994	-0.0245	-0.016	0.003	0.0874	-0.0174	-0.0079	0.1085	0.0242	0.0198	53.1787	85.0459	-2.8148
10	3.8445	0.2448	-0.1543	1.8247	-0.2609	1.0073	0.0241	-0.3224	-0.4505	0.2102	-0.0136	-0.0399	0.0893	-0.0663	-0.0106	0.0858	-0.039	-0.0389	0.1057	0.0942	0.097	52.6516	72.3055	4.8034
11	0.4538	-0.5812	-0.0642	1.2149	-0.4661	1.1165	-0.0813	-0.1769	0.1225	0.1186	0.1025	-0.0311	0.026	-0.0039	-0.0212	0.1626	0.0284	-0.0192	0.2236	-0.1052	0.126	37.1776	112.5319	3.3589
12	1.7515	0.3496	-0.0124	0.1517	0.2812	1.3806	-0.1199	-0.2129	0.1844	0.0167	-0.0564	0.0839	-0.0769	-0.2995	0.1763	0.1737	0.09	0.0295	0.2801	-0.0982	0.0817	32.821	110.751	4.4749
13	4.9682	-3.204	-1.6538	7.7747	0.754	0.5682	0.281	-0.1216	0.4432	0.1796	-0.1203	0.0752	-0.1117	0.0446	-0.1607	0.1001	0.0296	0.0889	0.2102	-0.0373	0.169	26.1328	113.4392	7.3388
14	0.8852	-0.6537	0.369	1.1209	-0.3764	0.5346	0.0289	-0.1348	-0.0129	-0.1167	0.0087	0.0878	0.0454	-0.1022	-0.0375	0.1224	-0.0032	-0.0124	0.1228	-0.0239	0.0293	35.64	98.8027	-9.5227
15	1.5455	-0.2087	0.8937	1.566	0.0132	1.5095	-0.1145	-0.0703	0.3032	-0.0948	-0.0113	0.0532	-0.1139	-0.0329	0.1257	0.0822	0.0053	-0.0323	0.0255	-0.0206	0.0729	34.6358	115.5438	-15.8743
16	3.3713	-1.9705	0.8572	3.1087	0.2252	0.5829	-0.1794	-0.3534	0.1481	0.3398	0.0798	-0.1157	0.0934	-0.1009	0.0996	0.0925	0.0059	0.0277	0.13	-0.0272	0.0885	43.2267	55.7965	-23.9655
17	3.0302	-0.1402	-0.4155	2.4661	0.6718	1.6107	-0.0595	-0.1617	0.2319	0.4723	0.0634	-0.0474	0.2242	-0.0907	-0.0039	0.1422	0.0051	-0.0011	0.1226	-0.0398	0.026	43.7772	53.5881	-18.5079
18	9.0722	-8.1586	-1.2078	9.0389	3.7012	6.4732	-0.5008	-0.1776	-0.6749	1.242	0.2829	0.5695	0.723	-0.9297	0.2179	0.501	0.2347	0.0492	0.5196	-0.0909	0.128	40.5654	52.7854	-11.65
19	0.7711	-0.0866	0.1509	1.5546	0.6214	0.6951	-0.0345	-0.071	-0.0185	0.0759	-0.1138	0.2155	0.0606	-0.0655	0.1483	0.0596	-0.015	0.0519	0.1052	-0.0437	0.0786	34.1992	46.2077	-33.9178
20	1.8749	0.3402	0.5001	1.9418	0.7785	0.9928	-0.0995	-0.0526	0.2674	-0.0582	-0.1401	0.2704	-0.1364	-0.1154	0.2396	0.0424	0.0174	-0.0119	0.0831	-0.081	0.1404	30.5469	63.5135	-32.4348

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	113 - 137
2	X-RAY DIFFRACTION	2	A	138 - 169
3	X-RAY DIFFRACTION	3	A	170 - 176
4	X-RAY DIFFRACTION	4	A	177 - 369
5	X-RAY DIFFRACTION	5	A	370 - 375
6	X-RAY DIFFRACTION	6	B	113 - 122
7	X-RAY DIFFRACTION	7	B	123 - 168
8	X-RAY DIFFRACTION	8	B	169 - 174
9	X-RAY DIFFRACTION	9	B	175 - 306
10	X-RAY DIFFRACTION	10	B	307 - 371
11	X-RAY DIFFRACTION	11	C	118 - 144
12	X-RAY DIFFRACTION	12	C	145 - 170
13	X-RAY DIFFRACTION	13	C	171 - 175
14	X-RAY DIFFRACTION	14	C	176 - 252
15	X-RAY DIFFRACTION	15	C	253 - 373
16	X-RAY DIFFRACTION	16	D	117 - 137
17	X-RAY DIFFRACTION	17	D	138 - 169
18	X-RAY DIFFRACTION	18	D	170 - 174
19	X-RAY DIFFRACTION	19	D	175 - 252
20	X-RAY DIFFRACTION	20	D	253 - 372

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-Aug 12, 2020. Covid-19 info

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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

-
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