PDB-7qon: Monoclinic triose phosphate isomerase from Fasciola hepatica.

ID or keywords:

Entry

Database: PDB / ID: 7qon

Title

Monoclinic triose phosphate isomerase from Fasciola hepatica.

Components

Triosephosphate isomerase

Keywords

ISOMERASE / Fasciolysis

Function / homology

Function and homology information

triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process
Similarity search - Function

Biological species

Fasciola hepatica (liver fluke)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.51 Å

Authors

Kontellas, G. / Isupov, M.N. / Littlechild, J.A.

Funding support

1items

Citation

Journal: To Be Published
Title: Monoclinic triose phosphate isomerase from Fasciola hepatica.
Authors: Kontellas, G. / Isupov, M.N. / Littlechild, J.A.

History

Deposition	Dec 24, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 18, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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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PDBx/mmCIF format	7qon.cif.gz	454 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7qon_validation.pdf.gz	479.4 KB	Display	wwPDB validaton report
Full document	7qon_full_validation.pdf.gz	493.9 KB	Display
Data in XML	7qon_validation.xml.gz	51.7 KB	Display
Data in CIF	7qon_validation.cif.gz	76.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qo/7qon ftp://data.pdbj.org/pub/pdb/validation_reports/qo/7qon	HTTPS FTP

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Related structure data

Related structure data	2jk2S S: Starting model for refinement
Similar structure data	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 (8)

Deposited unit

AAA: Triosephosphate isomerase

BBB: Triosephosphate isomerase

CCC: Triosephosphate isomerase

DDD: Triosephosphate isomerase

hetero molecules

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

1

AAA: Triosephosphate isomerase

BBB: Triosephosphate isomerase

hetero molecules

defined by author&software
Evidence: gel filtration
56.4 kDa, 2 polymers

2

CCC: Triosephosphate isomerase

DDD: Triosephosphate isomerase

hetero molecules

defined by author&software
Evidence: gel filtration
56.4 kDa, 2 polymers

Unit cell

Length a, b, c (Å)	42.393, 110.464, 118.143
Angle α, β, γ (deg.)	90.000, 97.367, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB
3	2	AAA
4	2	CCC
5	3	AAA
6	3	DDD
7	4	BBB
8	4	CCC
9	5	BBB
10	5	DDD
11	6	CCC
12	6	DDD

NCS domain segments:

Dom-ID	Component-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	1	SER	SER	ARG	ARG	AAA	A	3 - 252	3 - 252
2	2	1	SER	SER	ARG	ARG	BBB	B	3 - 252	3 - 252
3	3	2	SER	SER	ARG	ARG	AAA	A	3 - 252	3 - 252
4	4	2	SER	SER	ARG	ARG	CCC	C	3 - 252	3 - 252
5	5	3	SER	SER	GLY	GLY	AAA	A	3 - 253	3 - 253
6	6	3	SER	SER	GLY	GLY	DDD	D	3 - 253	3 - 253
7	7	4	ALA	ALA	GLY	GLY	BBB	B	2 - 253	2 - 253
8	8	4	ALA	ALA	GLY	GLY	CCC	C	2 - 253	2 - 253
9	9	5	SER	SER	ARG	ARG	BBB	B	3 - 252	3 - 252
10	10	5	SER	SER	ARG	ARG	DDD	D	3 - 252	3 - 252
11	11	6	SER	SER	ARG	ARG	CCC	C	3 - 252	3 - 252
12	12	6	SER	SER	ARG	ARG	DDD	D	3 - 252	3 - 252

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein	Triosephosphate isomerase Mass: 27823.805 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fasciola hepatica (liver fluke) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S4UI50, triose-phosphate isomerase

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Non-polymers , 5 types, 1128 molecules

#2: Chemical	... ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1090 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 50.1 %
Crystal grow	Temperature: 291 K / Method: microbatch / Details: 0.2 M Li2SO4, 0.1 M ADA pH 6.5, 30 % v/v PEG 400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.51→51.809 Å / Num. obs: 167030 / % possible obs: 99.1 % / Redundancy: 3.2 % / CC_1/2: 0.999 / R_merge(I) obs: 0.059 / Net I/σ(I): 10.9
Reflection shell	Resolution: 1.51→1.54 Å / R_merge(I) obs: 1.457 / Num. unique obs: 8244 / CC_1/2: 0.321

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XSCALE		data scaling
PARROT		phasing
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2JK2

2jk2

Resolution: 1.51→51.809 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.969 / SU B: 2.055 / SU ML: 0.069 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1932	8336	4.992 %
R_work	0.1651	158658	-
all	0.167	-	-
obs	-	166994	99.073 %

Solvent computation

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

Displacement parameters

B_iso mean: 27.833 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.797 Å²	0 Å²	0.712 Å²
2-	-	0.347 Å²	0 Å²
3-	-	-	0.257 Å²

Refinement step

Cycle: LAST / Resolution: 1.51→51.809 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7766	0	74	1090	8930

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	8805
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	8547
X-RAY DIFFRACTION	r_angle_refined_deg	1.41	1.64	11959
X-RAY DIFFRACTION	r_angle_other_deg	1.351	1.587	19882
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.269	5	1214
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.041	22.559	465
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.901	15	1641
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.23	15	61
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	1142
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	10174
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2000
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	1727
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.178	0.2	7437
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	3935
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	3816
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	728
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.149	0.2	7
X-RAY DIFFRACTION	r_metal_ion_refined	0.272	0.2	10
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.231	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.271	0.2	95
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.137	0.2	37
X-RAY DIFFRACTION	r_mcbond_it	4.499	6.737	4308
X-RAY DIFFRACTION	r_mcbond_other	4.491	6.732	4306
X-RAY DIFFRACTION	r_mcangle_it	6.02	11.317	5436
X-RAY DIFFRACTION	r_mcangle_other	6.014	11.316	5436
X-RAY DIFFRACTION	r_scbond_it	6.29	8.059	4497
X-RAY DIFFRACTION	r_scbond_other	6.272	8.058	4477
X-RAY DIFFRACTION	r_scangle_it	8.68	12.872	6421
X-RAY DIFFRACTION	r_scangle_other	8.68	12.874	6422
X-RAY DIFFRACTION	r_lrange_it	10.192	36.102	10046
X-RAY DIFFRACTION	r_lrange_other	10.133	35.393	9768
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.079	0.05	8437
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.095	0.05	8371
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.069	0.05	8491
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.085	0.05	8501
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.084	0.05	8473
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.091	0.05	8286

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.07929	0.05008
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.07929	0.05008
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.09517	0.05008
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.09517	0.05008
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.06897	0.05009
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.06897	0.05009
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.08529	0.05009
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.08529	0.05009
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.08414	0.05008
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.08414	0.05008
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.09058	0.05008
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.09058	0.05008

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 (%)
1.51-1.549	0.319	644	0.329	11690	X-RAY DIFFRACTION	99.709
1.549-1.592	0.312	616	0.305	11472	X-RAY DIFFRACTION	99.6702
1.592-1.638	0.284	611	0.284	11172	X-RAY DIFFRACTION	99.527
1.638-1.688	0.272	548	0.262	10830	X-RAY DIFFRACTION	99.3885
1.688-1.744	0.254	570	0.244	10474	X-RAY DIFFRACTION	99.7111
1.744-1.805	0.256	510	0.224	10165	X-RAY DIFFRACTION	99.6453
1.805-1.873	0.249	549	0.207	9785	X-RAY DIFFRACTION	99.4706
1.873-1.949	0.221	508	0.182	9411	X-RAY DIFFRACTION	99.2893
1.949-2.036	0.204	468	0.172	9056	X-RAY DIFFRACTION	99.2807
2.036-2.135	0.185	450	0.161	8655	X-RAY DIFFRACTION	99.4647
2.135-2.251	0.183	397	0.154	8243	X-RAY DIFFRACTION	99.2077
2.251-2.387	0.193	388	0.149	7716	X-RAY DIFFRACTION	98.8413
2.387-2.552	0.179	385	0.141	7236	X-RAY DIFFRACTION	98.1329
2.552-2.756	0.177	367	0.142	6767	X-RAY DIFFRACTION	98.6176
2.756-3.019	0.194	317	0.15	6253	X-RAY DIFFRACTION	98.427
3.019-3.375	0.193	282	0.153	5561	X-RAY DIFFRACTION	97.5785
3.375-3.897	0.15	298	0.126	4835	X-RAY DIFFRACTION	96.2859
3.897-4.771	0.138	211	0.116	4212	X-RAY DIFFRACTION	98.3763
4.771-6.742	0.183	137	0.153	3283	X-RAY DIFFRACTION	97.6027
6.742-51.809	0.172	80	0.182	1843	X-RAY DIFFRACTION	98.3632

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Protein , 1 types, 4 molecules AAABBBCCCDDD

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