PDB-5huo: Crystal Structure of NadC Deletion Mutant in C2221 Space Group

ID or keywords:

Entry

Database: PDB / ID: 5huo

Title

Crystal Structure of NadC Deletion Mutant in C2221 Space Group

Components

Nicotinate-nucleotide diphosphorylase (Carboxylating)

Keywords

TRANSFERASE / Quinolinate phosphoribosyltransferase

Function / homology

Function and homology information

quinolinate catabolic process / nicotinate-nucleotide diphosphorylase (carboxylating) / nicotinate-nucleotide diphosphorylase (carboxylating) activity / NAD+ biosynthetic process / cytoplasm
Similarity search - Function

Biological species

Streptococcus pyogenes GA06023 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Booth, W.T. / Chruszcz, M.

Citation

Journal: FEBS J. / Year: 2017
Title: Streptococcus pyogenes quinolinate-salvage pathway-structural and functional studies of quinolinate phosphoribosyl transferase and NH3 -dependent NAD(+) synthetase.
Authors: Booth, W.T. / Morris, T.L. / Mysona, D.P. / Shah, M.J. / Taylor, L.K. / Karlin, T.W. / Clary, K. / Majorek, K.A. / Offermann, L.R. / Chruszcz, M.

History

Deposition	Jan 27, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 25, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jul 12, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Aug 23, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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 / 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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Validation report

Summary document	5huo_validation.pdf.gz	511.7 KB	Display	wwPDB validaton report
Full document	5huo_full_validation.pdf.gz	552.9 KB	Display
Data in XML	5huo_validation.xml.gz	60.8 KB	Display
Data in CIF	5huo_validation.cif.gz	82.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hu/5huo ftp://data.pdbj.org/pub/pdb/validation_reports/hu/5huo	HTTPS FTP

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Related structure data

Related structure data	5huhC 5hujC 5hulSC 5hupC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5hul-2 5hup-2 5hup-1 4i9a-1 5ayz-2 4kwv-d 5hul-1 5ayx-d 5ayz-1 2jbm-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Nicotinate-nucleotide diphosphorylase (Carboxylating)

B: Nicotinate-nucleotide diphosphorylase (Carboxylating)

C: Nicotinate-nucleotide diphosphorylase (Carboxylating)

E: Nicotinate-nucleotide diphosphorylase (Carboxylating)

F: Nicotinate-nucleotide diphosphorylase (Carboxylating)

H: Nicotinate-nucleotide diphosphorylase (Carboxylating)

hetero molecules

208 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Nicotinate-nucleotide diphosphorylase (Carboxylating)

C: Nicotinate-nucleotide diphosphorylase (Carboxylating)

E: Nicotinate-nucleotide diphosphorylase (Carboxylating)

hetero molecules

A: Nicotinate-nucleotide diphosphorylase (Carboxylating)

C: Nicotinate-nucleotide diphosphorylase (Carboxylating)

E: Nicotinate-nucleotide diphosphorylase (Carboxylating)

hetero molecules

defined by author&software
208 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Nicotinate-nucleotide diphosphorylase (Carboxylating)

F: Nicotinate-nucleotide diphosphorylase (Carboxylating)

H: Nicotinate-nucleotide diphosphorylase (Carboxylating)

hetero molecules

B: Nicotinate-nucleotide diphosphorylase (Carboxylating)

F: Nicotinate-nucleotide diphosphorylase (Carboxylating)

H: Nicotinate-nucleotide diphosphorylase (Carboxylating)

hetero molecules

defined by author&software
208 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	106.203, 186.261, 221.906
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-423- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASP	ASP	A	A	6 - 288	31 - 313
2	1	ASP	ASP	B	B	6 - 288	31 - 313
1	2	ASP	ASP	A	A	6 - 288	31 - 313
2	2	ASP	ASP	C	C	6 - 288	31 - 313
1	3	ASP	ASP	A	A	6 - 288	31 - 313
2	3	ASP	ASP	E	D	6 - 288	31 - 313
1	4	LEU	LEU	A	A	6 - 287	31 - 312
2	4	LEU	LEU	F	E	6 - 287	31 - 312
1	5	ASP	ASP	A	A	6 - 288	31 - 313
2	5	ASP	ASP	H	F	6 - 288	31 - 313
1	6	ASP	ASP	B	B	6 - 288	31 - 313
2	6	ASP	ASP	C	C	6 - 288	31 - 313
1	7	ASP	ASP	B	B	6 - 288	31 - 313
2	7	ASP	ASP	E	D	6 - 288	31 - 313
1	8	LEU	LEU	B	B	6 - 287	31 - 312
2	8	LEU	LEU	F	E	6 - 287	31 - 312
1	9	ASP	ASP	B	B	6 - 288	31 - 313
2	9	ASP	ASP	H	F	6 - 288	31 - 313
1	10	ASP	ASP	C	C	6 - 288	31 - 313
2	10	ASP	ASP	E	D	6 - 288	31 - 313
1	11	ASP	ASP	C	C	6 - 288	31 - 313
2	11	ASP	ASP	F	E	6 - 288	31 - 313
1	12	ASP	ASP	C	C	6 - 288	31 - 313
2	12	ASP	ASP	H	F	6 - 288	31 - 313
1	13	ASP	ASP	E	D	6 - 288	31 - 313
2	13	ASP	ASP	F	E	6 - 288	31 - 313
1	14	ASP	ASP	E	D	6 - 288	31 - 313
2	14	ASP	ASP	H	F	6 - 288	31 - 313
1	15	ASP	ASP	F	E	6 - 288	31 - 313
2	15	ASP	ASP	H	F	6 - 288	31 - 313

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	Nicotinate-nucleotide diphosphorylase (Carboxylating) Mass: 34425.902 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes GA06023 (bacteria) Gene: nadC, HMPREF1231_0804 / Plasmid: pjExpress411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A0H3BVM1, UniProt: U2UIT5*PLUS, nicotinate-nucleotide diphosphorylase (carboxylating)
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.66 Å³/Da / Density % sol: 53.7 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.4 Details: 20% PEG 6000, 0.1 M BIS-TRIS, 0.48 M Ammonium sulfate, 1.25 mM Sodium Bromide

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 17, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.8→40 Å / Num. obs: 54566 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / R_merge(I) obs: 0.108 / R_sym value: 0.108 / Net I/σ(I): 14.6
Reflection shell	Resolution: 2.8→2.85 Å / Redundancy: 8.5 % / R_merge(I) obs: 0.785 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5HUL

5hul

Resolution: 2.8→40 Å / Cor.coef. F_o:F_c: 0.925 / Cor.coef. F_o:F_c free: 0.892 / SU B: 33.335 / SU ML: 0.302 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.366 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25539	2766	5.1 %	RANDOM
R_work	0.21599	-	-	-
obs	0.21799	51653	99.92 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 124.789 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.92 Å²	0 Å²	0 Å²
2-	-	-2.04 Å²	0 Å²
3-	-	-	-1.87 Å²

Refinement step

Cycle: 1 / Resolution: 2.8→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12807	0	100	149	13056

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	13094
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	12388
X-RAY DIFFRACTION	r_angle_refined_deg	1.543	1.96	17742
X-RAY DIFFRACTION	r_angle_other_deg	2.206	3	28329
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.736	5	1689
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.062	23.982	570
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.971	15	2153
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.212	15	83
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	2111
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	14925
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	2994
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	2.635	2.351	6771
X-RAY DIFFRACTION	r_mcbond_other	2.633	2.351	6770
X-RAY DIFFRACTION	r_mcangle_it	4.396	3.51	8449
X-RAY DIFFRACTION	r_mcangle_other	4.396	3.51	8450
X-RAY DIFFRACTION	r_scbond_it	2.797	2.414	6322
X-RAY DIFFRACTION	r_scbond_other	2.633	2.324	6240
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.357	3.457	9171
X-RAY DIFFRACTION	r_long_range_B_refined	8.026	17.986	14308
X-RAY DIFFRACTION	r_long_range_B_other	8.017	17.969	14300
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	33476	0.1
1	2	B	33476	0.1
2	1	A	28658	0.14
2	2	C	28658	0.14
3	1	A	31914	0.11
3	2	E	31914	0.11
4	1	A	33680	0.08
4	2	F	33680	0.08
5	1	A	32476	0.1
5	2	H	32476	0.1
6	1	B	28944	0.13
6	2	C	28944	0.13
7	1	B	32546	0.1
7	2	E	32546	0.1
8	1	B	33448	0.09
8	2	F	33448	0.09
9	1	B	32746	0.09
9	2	H	32746	0.09
10	1	C	27366	0.15
10	2	E	27366	0.15
11	1	C	28406	0.14
11	2	F	28406	0.14
12	1	C	28866	0.14
12	2	H	28866	0.14
13	1	E	32262	0.1
13	2	F	32262	0.1
14	1	E	31204	0.11
14	2	H	31204	0.11
15	1	F	32450	0.1
15	2	H	32450	0.1

LS refinement shell

Resolution: 2.8→2.872 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.324	222	-
R_work	0.317	3736	-
obs	-	-	100 %

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	0.8432	-0.1738	-0.0119	3.6459	2.1812	1.7539	0.121	-0.0627	-0.1989	-0.3993	-0.2482	0.0407	-0.2872	-0.6887	0.1272	0.5402	0.172	-0.024	0.6966	-0.014	0.3536	35.0732	12.587	104.3724
2	0.2805	0.3439	0.1759	0.6836	-0.0768	0.5097	-0.061	0.0278	-0.1243	0.0011	0.1039	-0.0527	-0.1233	-0.1128	-0.0429	0.563	0.0193	0.0051	0.5157	0.0352	0.424	47.0848	3.0981	98.0728
3	0.96	0.5821	0.3938	1.8183	-0.0472	0.5886	0.3133	-0.177	-0.4223	0.3827	-0.2447	-0.6369	0.0487	-0.0007	-0.0686	0.5231	-0.0446	-0.1266	0.4021	0.1046	0.5223	52.7039	-20.3562	104.3663
4	1.5602	3.1486	0.7466	8.1973	0.4317	1.0091	0.1003	-0.2547	0.074	0.3698	-0.4064	-0.0889	-0.0531	-0.1771	0.306	0.4814	0.0525	0.0092	0.5057	-0.0011	0.6307	42.456	41.4507	62.1519
5	0.2117	0.1806	-0.5188	0.894	0.9048	3.7749	0.0096	-0.0627	-0.1183	0.1192	-0.3843	-0.0449	-0.0141	-0.4838	0.3747	0.3696	0.1004	0.0167	0.5838	-0.129	0.5152	28.5659	43.446	65.8864
6	0.0603	0.0749	0.251	0.8997	0.2997	1.2095	-0.0083	-0.1052	0.023	-0.1953	0.0103	0.1378	-0.0804	-0.2256	-0.0019	0.404	0.0368	-0.0535	0.53	-0.0594	0.5618	26.1475	30.3117	42.1388
7	1.1578	0.9435	-0.4257	1.0529	0.2138	1.4634	0.0488	-0.0855	0.4395	-0.0564	-0.2364	0.4133	-0.0045	-0.2671	0.1877	0.3682	-0.0239	-0.0065	0.5519	-0.1059	0.6737	13.1199	-8.9445	92.3171
8	13.9971	-14.2996	0.8993	20.5952	1.2954	0.8794	-0.3072	-0.0375	-0.2517	-0.0145	0.436	0.2989	-0.0812	0.1856	-0.1288	0.5041	-0.0966	-0.11	0.6537	-0.2193	0.6554	-8.2925	-14.8552	120.3125
9	0.681	0.4701	-0.7034	0.7724	0.1986	2.3123	-0.2407	-0.1239	0.1703	-0.065	-0.5448	0.4221	0.5359	-0.6217	0.7856	0.2397	-0.2779	0.1365	1.049	-0.5972	0.7501	-8.5188	-14.6097	105.2117
10	7.0214	-2.1174	-2.2578	1.575	1.5485	1.584	0.5576	0.2421	0.6413	0.433	-0.6407	0.0082	0.4072	-0.5309	0.0831	0.4431	-0.3222	0.2467	0.7021	-0.1841	0.4909	11.7321	-10.5736	118.1808
11	0.4196	0.4367	0.3763	0.652	0.4717	0.3706	0.3488	-0.2021	0.1253	0.2664	-0.429	0.0334	0.2626	-0.2621	0.0802	0.6191	-0.3251	0.1189	0.6706	-0.0777	0.3823	17.1304	-24.6171	108.9221
12	1.5935	1.1415	-1.1865	1.0511	-0.3098	2.384	0.0834	0.2018	0.0689	0.1631	0.034	-0.0551	0.433	-0.2817	-0.1174	0.5768	-0.0847	-0.0473	0.4635	0.0178	0.5058	28.0327	-30.1145	91.1135
13	1.3255	-0.834	1.2201	1.215	-0.1955	1.663	-0.0785	0.0097	0.19	-0.0698	-0.0353	0.0005	-0.2119	0.0516	0.1138	0.4879	-0.0212	0.0149	0.5324	0.0369	0.4747	65.4716	18.2483	48.6569
14	0.7304	-0.1962	0.0069	0.2713	-0.0026	0.0233	0.0285	-0.0036	0.0836	-0.0498	0.0184	0.0709	0.095	0.0152	-0.0469	0.5601	-0.0313	-0.0069	0.5105	0.0307	0.4318	45.5692	5.6723	45.5479
15	3.377	0.2739	-0.2175	0.639	-0.024	0.5146	0.0142	-0.2317	-0.1134	-0.0151	0.0095	0.1292	0.2553	0.0098	-0.0237	0.5411	-0.0369	-0.0297	0.4349	0.0572	0.3924	43.1252	-2.9793	45.5229
16	0.3802	0.4059	0.2459	2.3546	1.2346	0.6751	0.0435	0.022	0.0457	-0.1199	0.1636	-0.287	0.0051	0.0298	-0.207	0.4803	0.033	0.0302	0.5077	-0.0256	0.5464	47.1348	28.8669	41.2481
17	0.0874	-0.2277	0.0574	1.8037	0.8324	0.8476	0.0452	-0.0277	0.0328	-0.1174	-0.1001	-0.0868	-0.0216	-0.1122	0.0549	0.5169	0.065	0.0273	0.426	-0.0251	0.5758	43.7482	42.8363	35.6445
18	0.8208	-0.4252	0.2857	0.8022	0.4663	0.805	-0.027	-0.3361	0.067	-0.056	-0.1539	-0.0151	-0.129	-0.4157	0.181	0.485	0.052	-0.0208	0.4803	-0.0235	0.4591	38.9524	62.1047	51.4997

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 39
2	X-RAY DIFFRACTION	2	A	40 - 168
3	X-RAY DIFFRACTION	3	A	169 - 288
4	X-RAY DIFFRACTION	4	B	6 - 36
5	X-RAY DIFFRACTION	5	B	37 - 84
6	X-RAY DIFFRACTION	6	B	85 - 288
7	X-RAY DIFFRACTION	7	C	6 - 169
8	X-RAY DIFFRACTION	8	C	170 - 177
9	X-RAY DIFFRACTION	9	C	181 - 288
10	X-RAY DIFFRACTION	10	E	6 - 39
11	X-RAY DIFFRACTION	11	E	40 - 182
12	X-RAY DIFFRACTION	12	E	183 - 288
13	X-RAY DIFFRACTION	13	F	5 - 39
14	X-RAY DIFFRACTION	14	F	40 - 232
15	X-RAY DIFFRACTION	15	F	233 - 288
16	X-RAY DIFFRACTION	16	H	6 - 36
17	X-RAY DIFFRACTION	17	H	37 - 168
18	X-RAY DIFFRACTION	18	H	169 - 288

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