PDB-7b2i: Heterodimeric tRNA-Guanine Transglycosylase from mouse

ID or keywords:

Entry

Database: PDB / ID: 7b2i

Title

Heterodimeric tRNA-Guanine Transglycosylase from mouse

Components

(Queuine tRNA-ribosyltransferase ...) x 2

Keywords

TRANSFERASE / TRANSGLYCOSYLASE / TIM BARREL / DIMER / TGT

Function / homology

Function and homology information

tRNA-guanosine34 queuine transglycosylase / transferase complex / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / mitochondrial outer membrane / tRNA binding / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / mitochondrion ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Sebastiani, M. / Heine, A. / Reuter, K.

Citation

Journal: Acs Chem.Biol. / Year: 2022
Title: Structural and Biochemical Investigation of the Heterodimeric Murine tRNA-Guanine Transglycosylase.
Authors: Sebastiani, M. / Behrens, C. / Dorr, S. / Gerber, H.D. / Benazza, R. / Hernandez-Alba, O. / Cianferani, S. / Klebe, G. / Heine, A. / Reuter, K.

History

Deposition	Nov 27, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 8, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jun 28, 2023	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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7b2i.cif.gz	380.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7b2i.ent.gz	255.2 KB	Display	PDB format
PDBx/mmJSON format	7b2i.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7b2i_validation.pdf.gz	489.4 KB	Display	wwPDB validaton report
Full document	7b2i_full_validation.pdf.gz	491.1 KB	Display
Data in XML	7b2i_validation.xml.gz	31.7 KB	Display
Data in CIF	7b2i_validation.cif.gz	47.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b2/7b2i ftp://data.pdbj.org/pub/pdb/validation_reports/b2/7b2i	HTTPS FTP

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Related structure data

Related structure data	6h62SC 7ov9C 7ovoC 7ovsC 7owzC 6fv5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1got-d 5cie-d 7aak-d 5tdh-1 5ipw-d 4f70-d 4q9z-d 2y4l-d 4g1v-3 3g7k-2 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: Queuine tRNA-ribosyltransferase accessory subunit 2

C: Queuine tRNA-ribosyltransferase catalytic subunit 1

hetero molecules

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

1

A: Queuine tRNA-ribosyltransferase accessory subunit 2

hetero molecules

C: Queuine tRNA-ribosyltransferase catalytic subunit 1

hetero molecules

defined by author&software
Evidence: mass spectrometry
dimer
91.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	100.587, 100.587, 202.235
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	95
Space group name H-M	P4₃22
Space group name Hall	P4cw2c
Symmetry operation	#1: x,y,z #2: -y,x,z+3/4 #3: y,-x,z+1/4 #4: x,-y,-z+1/2 #5: -x,y,-z #6: -x,-y,z+1/2 #7: y,x,-z+1/4 #8: -y,-x,-z+3/4

Components on special symmetry positions

ID	Model	Components
1	1	C-507- P6G

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Queuine tRNA-ribosyltransferase ... , 2 types, 2 molecules AC

#1: Protein	Queuine tRNA-ribosyltransferase accessory subunit 2 / Queuine tRNA-ribosyltransferase domain-containing protein 1 Mass: 46710.465 Da / Num. of mol.: 1 / Mutation: M1del Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qtrt2, Qtrtd1 / Plasmid: pETDuet-1 / Production host: Vibrio natriegens (bacteria) / Variant (production host): Vmax References: UniProt: B8ZXI1, tRNA-guanosine34 preQ1 transglycosylase
#2: Protein	Queuine tRNA-ribosyltransferase catalytic subunit 1 / Guanine insertion enzyme / tRNA-guanine transglycosylase Mass: 43428.980 Da / Num. of mol.: 1 / Mutation: M1_L10del Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qtrt1, Tgt, Tgut / Plasmid: pETDuet-1 / Production host: Vibrio natriegens (bacteria) / Variant (production host): Vmax References: UniProt: Q9JMA2, tRNA-guanosine34 preQ1 transglycosylase

#1: Protein

Queuine tRNA-ribosyltransferase accessory subunit 2 / Queuine tRNA-ribosyltransferase domain-containing protein 1

Mass: 46710.465 Da / Num. of mol.: 1 / Mutation: M1del
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Qtrt2, Qtrtd1 / Plasmid: pETDuet-1 / Production host:

Vibrio natriegens (bacteria) / Variant (production host): Vmax
References: UniProt: B8ZXI1, tRNA-guanosine34 preQ1 transglycosylase

#2: Protein

Queuine tRNA-ribosyltransferase catalytic subunit 1 / Guanine insertion enzyme / tRNA-guanine transglycosylase

Mass: 43428.980 Da / Num. of mol.: 1 / Mutation: M1_L10del
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Qtrt1, Tgt, Tgut / Plasmid: pETDuet-1 / Production host:

Vibrio natriegens (bacteria) / Variant (production host): Vmax
References: UniProt: Q9JMA2, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 8 types, 497 molecules

#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#7: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#8: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#9: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.84 Å³/Da / Density % sol: 56.63 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Citrate pH 6.5, 700 mM Ammonium sulfate, 1 M Lithium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.65→50 Å / Num. obs: 125031 / % possible obs: 99.9 % / Redundancy: 13.2 % / B_iso Wilson estimate: 22.6 Å² / R_sym value: 0.072 / Net I/σ(I): 23.17
Reflection shell	Resolution: 1.65→1.75 Å / Num. unique obs: 19850 / CC_1/2: 0.822

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
Coot	0.8.9	model building
XDS	1.02	data reduction
XDS	1.02	data scaling
PHASER	7.0.047	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6H62, 6FV5

6h62

6fv5

Resolution: 1.65→45.17 Å / SU ML: 0.1469 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.1182
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2009	6251	5 %	Random selections
R_work	0.1772	118761	-	-
obs	0.1784	125012	99.93 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 30.98 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→45.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5705	0	104	484	6293

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0056	6134
X-RAY DIFFRACTION	f_angle_d	0.7735	8331
X-RAY DIFFRACTION	f_chiral_restr	0.0517	938
X-RAY DIFFRACTION	f_plane_restr	0.0053	1084
X-RAY DIFFRACTION	f_dihedral_angle_d	18.0699	3679

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 (%)
1.65-1.67	0.2605	201	0.2432	3824	X-RAY DIFFRACTION	99.04
1.67-1.69	0.2356	206	0.2299	3913	X-RAY DIFFRACTION	99.71
1.69-1.71	0.2495	206	0.2262	3911	X-RAY DIFFRACTION	99.88
1.71-1.73	0.2618	206	0.2208	3900	X-RAY DIFFRACTION	99.9
1.73-1.75	0.2381	204	0.2134	3893	X-RAY DIFFRACTION	99.93
1.75-1.78	0.2031	205	0.198	3889	X-RAY DIFFRACTION	99.93
1.78-1.8	0.2264	207	0.1994	3931	X-RAY DIFFRACTION	99.98
1.8-1.83	0.2068	208	0.1823	3943	X-RAY DIFFRACTION	99.98
1.83-1.86	0.2179	203	0.1806	3874	X-RAY DIFFRACTION	100
1.86-1.89	0.1933	207	0.1739	3928	X-RAY DIFFRACTION	99.93
1.89-1.92	0.1934	207	0.1743	3932	X-RAY DIFFRACTION	100
1.92-1.96	0.2253	206	0.1769	3900	X-RAY DIFFRACTION	100
1.96-1.99	0.1999	207	0.1636	3940	X-RAY DIFFRACTION	100
1.99-2.03	0.2027	206	0.1696	3923	X-RAY DIFFRACTION	100
2.03-2.08	0.1963	207	0.1665	3929	X-RAY DIFFRACTION	100
2.08-2.13	0.1891	208	0.1637	3941	X-RAY DIFFRACTION	100
2.13-2.18	0.1998	207	0.1672	3932	X-RAY DIFFRACTION	100
2.18-2.24	0.1992	208	0.1683	3970	X-RAY DIFFRACTION	100
2.24-2.3	0.2165	208	0.1616	3934	X-RAY DIFFRACTION	100
2.3-2.38	0.1944	208	0.1672	3961	X-RAY DIFFRACTION	100
2.38-2.46	0.2107	208	0.1722	3953	X-RAY DIFFRACTION	99.98
2.46-2.56	0.2025	208	0.18	3956	X-RAY DIFFRACTION	100
2.56-2.68	0.2042	210	0.1782	3978	X-RAY DIFFRACTION	100
2.68-2.82	0.1922	209	0.1803	3979	X-RAY DIFFRACTION	100
2.82-3	0.1895	210	0.1876	3996	X-RAY DIFFRACTION	100
3-3.23	0.2224	211	0.1953	4010	X-RAY DIFFRACTION	100
3.23-3.55	0.1962	213	0.1734	4029	X-RAY DIFFRACTION	100
3.55-4.07	0.1942	213	0.1592	4058	X-RAY DIFFRACTION	100
4.07-5.12	0.1608	217	0.1525	4118	X-RAY DIFFRACTION	99.98

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	0.520488969371	0.0586704905672	-0.338439303335	0.214009079008	-0.0651996116944	0.229319244664	0.0288813957522	-0.455440846816	0.237151447995	0.26220983708	-0.284481474632	-0.054521380299	-0.492113621958	0.753330677776	-0.0608965387773	0.440025213941	-0.132524684559	-0.108270653482	0.387123518727	0.037752137436	0.287434376941	53.2034210317	25.1282478678	71.9990119306
2	1.31722563258	-0.621646148597	0.950505357357	0.308290485954	-0.453598076927	0.686762042439	-0.0221306515125	0.161549055808	0.696153627529	0.0305157880822	-0.14125981491	0.0725161706295	-0.290926456468	0.0872832886508	-0.186660221525	0.28720480997	-0.0089834025063	-0.00106841535084	0.130380866525	-0.0195625950418	0.350090667317	42.6225026392	30.4559322345	54.7529999842
3	0.139476731409	-0.0373188666524	0.0563097306751	0.151742625051	-0.186966898604	0.209666678348	-0.107297651209	0.106084824688	0.115515777176	0.105643146821	0.093824218527	-0.181359506036	0.0834450320996	-0.0265532925683	2.16044596428E-5	0.270464340347	-0.0371480177407	-0.0184525051007	0.278984287566	0.0222349061262	0.298935719453	56.0955985713	36.74143272	48.9488374994
4	0.766968456995	0.329301865598	-0.783713388134	0.682258727466	-0.412275847848	0.903433350607	-0.117102629142	-0.0169767870466	-0.379397728459	-0.0617377557786	-0.286527637694	-0.475017025974	0.134290468684	0.513841839206	-0.104475886176	0.243628658696	0.0299939608155	-0.000561645854201	0.374575627212	0.133587149499	0.482571763166	66.6334887807	21.8799819874	53.6578693538
5	0.868456577426	0.306704461046	-0.062253850666	0.675663857913	-0.468646094993	0.688709630809	0.057084340113	-0.116928306801	-0.160865972081	0.015362198669	-0.0768252897407	-0.0945789328647	0.165308062337	0.0163068193341	-0.125819221028	0.251967283443	0.0136695748871	-0.010604018249	0.144046501781	0.0212649907646	0.192904053893	40.754669363	16.184307264	56.9372018086
6	0.413208697448	-0.0184651434444	0.124019957113	0.128873375219	-0.101453149335	0.107605565488	0.0811187152992	-0.0483695516855	-0.00996325878369	0.130828654298	-0.0445886605666	0.0561037876936	0.0559116588781	-0.00874593553807	-0.000183479777119	0.30335982959	-0.00472934874284	-0.0174876146612	0.155503286313	0.0247647961211	0.198106092148	39.6874936946	16.4080598361	64.6654259075
7	0.299889512494	-0.10060847911	0.0214369307031	0.157964977559	0.0226114581429	0.24689649649	0.0059416934874	-0.0186699181068	0.0445772065622	0.0304224172929	-0.0326004189784	-0.051816262307	0.0200532193444	-0.0767631474712	-1.24680352197E-5	0.17747835035	0.0107887918861	-0.00231775590325	0.203164970884	0.00545558983933	0.165361998647	17.6994391964	39.4971242878	42.3586360676
8	0.309675826598	-0.340488240688	-0.137470256644	0.736414636834	-0.0646957496754	0.298153470788	0.00957871090586	0.140924477716	-0.0960280204552	-0.0454530380935	-0.0730764879394	0.031416665644	0.0603104133328	-0.160368239376	6.15595977499E-5	0.144487046566	-0.0287366942831	-0.0109356119064	0.263954232824	-0.0340244765296	0.201447015679	9.62484246215	30.599851514	24.1171519731
9	0.596327127304	0.313324095811	0.430446753396	0.743166964689	0.38220317036	0.445383583777	-0.0516661908011	0.129313500314	-0.0139610435549	-0.0661119371232	0.0138922811794	0.00503864138136	-0.0364418279937	-0.141599880288	5.78054598633E-6	0.170145034771	0.0399179417576	-0.0154741549796	0.239244254248	0.00803562495938	0.165642657224	10.8876078603	47.994016472	27.285963818
10	0.668537218501	-0.254933691285	0.245800289062	0.317256069536	-0.228197566713	0.479003705981	0.0309529978471	0.0281393786388	-0.0301305809831	-0.0439641242626	-0.0548587982921	-0.0568052525006	0.00819150882516	0.0139811662936	-2.50079521502E-5	0.193246854231	0.0125244371747	0.00382026262666	0.174038359341	0.00993446741673	0.194159623316	37.5922943222	45.0173372854	38.538186327
11	0.333799301891	0.0977045595556	0.0938710947826	0.121035707026	0.0725638430411	0.0803901298272	-0.00969909580509	-0.00165325503392	0.200848808267	-0.0316780226399	0.0467065423153	-0.11457892636	-0.284477382395	0.145688054475	-5.96829103536E-5	0.279929084775	0.0151894990176	-0.00763969105862	0.208999697577	0.0262801569701	0.235240364914	28.3489552847	63.2660344732	29.5867378581

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 34 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 35 through 59 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 60 through 91 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 92 through 229 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 230 through 372 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 373 through 414 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 12 through 104 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 105 through 188 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 189 through 272 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 273 through 365 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 366 through 402 )

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Queuine tRNA-ribosyltransferase ... , 2 types, 2 molecules AC

-
Non-polymers , 8 types, 497 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
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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-Basic information

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-Related structure data

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-Assembly

-Components

-Queuine tRNA-ribosyltransferase ... , 2 types, 2 molecules AC

-Non-polymers , 8 types, 497 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

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Queuine tRNA-ribosyltransferase ... , 2 types, 2 molecules AC

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Non-polymers , 8 types, 497 molecules

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