PDB-2xe5: Molecular insights into clinically isolated OmpC mutants and thei...

ID or keywords:

Entry

Database: PDB / ID: 2xe5

Title

Molecular insights into clinically isolated OmpC mutants and their role in multi-drug resistance (OmpC26)

Components

OUTER MEMBRANE PORIN C

Keywords

TRANSPORT PROTEIN /

CELL MEMBRANE /

ION TRANSPORT /

PORIN

Function / homology

Function and homology information

porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.28 Å

Authors

Bamford, V.A. / Naismith, J.H.

Citation

Journal: Plos One / Year: 2011
Title: Altered Antibiotic Transport in Ompc Mutants Isolated from a Series of Clinical Strains of Multi-Drug Resistant E. Coli.
Authors: Lou, H. / Chen, M. / Black, S.S. / Bushell, S.R. / Ceccarelli, M. / Mach, T. / Beis, K. / Low, A.S. / Bamford, V.A. / Booth, I.R. / Bayley, H. / Naismith, J.H.

History

Deposition	May 11, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 26, 2010	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2011	Group: Database references / Version format compliance
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2xe5.cif.gz	830 KB	Display	PDBx/mmCIF format
PDB format	pdb2xe5.ent.gz	697.3 KB	Display	PDB format
PDBx/mmJSON format	2xe5.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/xe/2xe5 ftp://data.pdbj.org/pub/pdb/validation_reports/xe/2xe5	HTTPS FTP

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Related structure data

Related structure data	2xe1SC 2xe2C 2xe3C 2xg6C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2xe3-1 6rck-d 6rcp-5 2xg6-1 2xg6-2 3o0e-2 2xe3-2 6rcp-3 6rcp-6 4lsi-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#152 - Aug 2012 cAMP-dependent Protein Kinase similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: OUTER MEMBRANE PORIN C

B: OUTER MEMBRANE PORIN C

C: OUTER MEMBRANE PORIN C

D: OUTER MEMBRANE PORIN C

E: OUTER MEMBRANE PORIN C

F: OUTER MEMBRANE PORIN C

hetero molecules

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

1

D: OUTER MEMBRANE PORIN C

E: OUTER MEMBRANE PORIN C

F: OUTER MEMBRANE PORIN C

hetero molecules

defined by author&software
117 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: OUTER MEMBRANE PORIN C

B: OUTER MEMBRANE PORIN C

C: OUTER MEMBRANE PORIN C

hetero molecules

defined by author&software
119 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.180, 93.680, 115.910
Angle α, β, γ (deg.)	98.74, 108.79, 109.71
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	OUTER MEMBRANE PORIN C / OUTER MEMBRANE PROTEIN C / OMPC Mass: 38296.230 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: O6 / Description: OMPC26 ISOLATED FROM CLINICAL MUTANTS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9K597

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Non-polymers , 10 types, 439 molecules

#2: Chemical	ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE Mass: 306.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₅ / Comment: C8E, detergent*YM
#3: Chemical	ChemComp-HEX / HEXANE / Hexane Mass: 86.175 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₆H₁₄
#4: Chemical	ChemComp-D12 / DODECANE / Dodecane Mass: 170.335 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₂H₂₆
#5: Chemical	ChemComp-OCT / N-OCTANE / Octane Mass: 114.229 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₈H₁₈
#6: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#7: Chemical	ChemComp-D10 / DECANE / Decane Mass: 142.282 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₂₂
#8: Chemical	ChemComp-ASZ / 2-(DIMETHYLAMINO)ETHANESULFONIC ACID Mass: 153.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₁NO₃S
#9: Chemical	ChemComp-OES / N-OCTYL-2-HYDROXYETHYL SULFOXIDE Mass: 206.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₂S
#10: Chemical	ChemComp-HP6 / HEPTANE / Heptane Mass: 100.202 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₇H₁₆
#11: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	THIS IS FROM A CLINICAL SEQUENCE DESCRIBED IN PUBMED ID: 11722730. A.S.LOW,F.M.MACKENZIE,I.M.GOULD, ...THIS IS FROM A CLINICAL SEQUENCE DESCRIBED IN PUBMED ID: 11722730. A.S.LOW,F.M.MACKENZIE,I.M.GOULD, I.R.BOOTH. PROTECTED ENVIRONMENTS ALLOW PARALLEL EVOLUTION OF A BACTERIAL PATHOGEN IN A PATIENT SUBJECTED TO LONG-TERM ANTIBIOTIC THERAPY. MOL.MICROBIOL. 42,619

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.8 % Description: DATA WERE TRUNCATED USING WEBSERVER STRONG ET AL., 2006, PROC NATL ACAD SCI U S A, 103, 8060-5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.934 Å / Relative weight: 1
Reflection	Resolution: 2.28→79 Å / Num. obs: 118130 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / R_merge(I) obs: 0.08 / Net I/σ(I): 9.9
Reflection shell	Resolution: 2.28→2.34 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.45 / Mean I/σ(I) obs: 1.8 / % possible all: 96

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0060	refinement
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XE1

2xe1

Resolution: 2.28→29.41 Å / Cor.coef. F_o:F_c: 0.904 / Cor.coef. F_o:F_c free: 0.875 / SU B: 15.665 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.491 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS USED REFMAC V5.6 WHICH HAS LOCAL NCS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26707	4815	5 %	RANDOM
R_work	0.22605	-	-	-
obs	0.22804	95882	79.09 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 23.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.05 Å²	-0.05 Å²	0 Å²
2-	-	-0.13 Å²	-0.21 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 2.28→29.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16260	0	420	392	17072

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.021	16999
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	11415
X-RAY DIFFRACTION	r_angle_refined_deg	1.361	1.939	22856
X-RAY DIFFRACTION	r_angle_other_deg	2.944	3	27564
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.203	5	2052
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.299	25	960
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.479	15	2520
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.446	15	78
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	2254
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	19542
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	3762
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.28→2.339 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.274	50	-
R_work	0.238	789	-
obs	-	-	9.41 %

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	2.6402	-1.287	-1.7983	4.1855	5.0375	6.1247	-0.1616	0.6144	0.3197	-0.1182	0.0046	0.202	-0.0518	-0.1645	0.157	0.3397	-0.1126	-0.0868	0.5736	0.2722	0.1456	-10.68	3.757	-9.487
2	2.7367	0.0006	-0.7974	0.7745	0.232	0.5749	-0.1028	0.6557	-0.0338	0.0541	-0.0341	0.0588	0.1305	-0.215	0.1369	0.2219	-0.104	-0.0309	0.4917	0.0912	0.0943	-19.082	-5.904	-6.592
3	2.6027	0.3711	0.0409	2.1327	-0.0005	1.7951	-0.0628	0.2699	0.0359	0.0556	0.0146	0.2232	0.231	-0.3269	0.0482	0.0777	-0.0437	0.0226	0.3557	0.0492	0.0724	-27.583	-4.463	1.798
4	1.9543	0.7984	-0.0057	2.2735	-0.5708	1.9486	0.0218	0.3176	0.5464	0.3206	-0.0069	0.3229	-0.4034	-0.1961	-0.0149	0.178	0.0553	-0.0459	0.3485	0.1381	0.2475	-25.681	10.326	6.481
5	6.8681	-1.3675	2.8285	1.933	-1.2991	2.6173	-0.1937	0.8445	0.4054	0.0148	0.1269	-0.0737	-0.264	0.0926	0.0668	0.2941	-0.0998	0.004	0.3664	0.1386	0.1024	6.977	9.84	-8.051
6	3.2791	-0.3144	0.2462	1.6008	0.4705	0.6757	-0.159	0.3519	0.9482	0.0355	0.1235	-0.0448	-0.2193	0.0456	0.0355	0.2913	-0.0504	-0.0381	0.2581	0.1459	0.3529	3.41	20.522	-1.298
7	5.8419	-0.5182	0.03	1.845	-0.6719	2.2645	-0.2092	-0.0809	1.4561	0.2036	0.1912	-0.1235	-0.1987	-0.0727	0.018	0.4079	-0.0823	-0.1138	0.0886	-0.1034	0.6304	9.97	24.719	7.961
8	3.6932	0.3877	-0.18	3.276	1.5278	6.3938	-0.1215	-0.2962	0.6762	0.2452	0.0101	-0.3134	-0.3448	0.5036	0.1114	0.1572	-0.0255	-0.0753	0.1201	0.0112	0.3589	22.186	15.171	8.348
9	3.8031	2.9282	-2.0649	3.8667	-1.69	2.0975	-0.2103	0.6845	-0.2707	-0.3071	-0.082	-0.1377	0.041	0.0734	0.2922	0.2861	-0.0651	-0.0163	0.538	-0.0004	0.1028	3.634	-8.233	-11.524
10	1.8609	0.3313	0.447	2.1247	0.0689	1.4074	-0.3003	0.5566	-0.2833	-0.1231	0.1384	-0.2593	0.1002	0.1955	0.1619	0.2052	-0.0774	0.0262	0.3358	-0.0413	0.1723	15.544	-11.942	-7.164
11	2.351	0.2264	-0.0026	1.7148	-0.251	1.9822	-0.1878	0.2508	-0.5556	0.0772	0.0022	-0.1542	0.2093	0.1377	0.1856	0.2219	-0.0225	0.0714	0.3048	-0.0536	0.2719	17.099	-21.966	-0.734
12	2.6699	-0.3908	0.6604	1.7591	-0.2577	2.4775	-0.0965	0.2379	-0.721	0.0461	0.0379	0.0654	0.4957	0.1845	0.0585	0.3276	-0.1238	0.1102	0.1955	-0.1626	0.3544	2.831	-28.239	-0.228
13	3.9971	-2.2898	1.9655	3.6393	-2.0028	1.814	-0.1027	-0.8589	0.1504	0.2976	0.0021	-0.0171	-0.0474	-0.145	0.1006	0.2753	0.0735	0.0138	0.493	-0.0682	0.0701	-33.589	-13.899	60.097
14	2.1769	-0.3011	-0.6289	1.9929	-0.0258	1.4667	-0.1627	-0.5566	0.2827	0.1459	0.0711	-0.3135	-0.0857	0.1749	0.0915	0.1897	0.0648	-0.0371	0.3075	-0.0199	0.1158	-21.685	-10.199	55.769
15	2.7161	-0.1415	-0.0516	1.6918	0.3939	2.0511	-0.1756	-0.2618	0.5806	-0.0182	0.0241	-0.1256	-0.1812	0.1957	0.1515	0.2441	-0.0027	-0.0821	0.2271	-0.0636	0.2459	-20.153	-0.208	49.3
16	3.6056	0.6642	-1.0672	2.1715	-1.1769	3.0718	-0.0769	-0.2674	0.8482	-0.1384	0.123	0.2156	-0.2786	0.0661	-0.046	0.3214	0.0759	-0.1093	0.1708	-0.192	0.3827	-34.402	6.029	48.728
17	2.3003	1.5101	1.8853	3.7776	4.4752	5.5908	-0.1735	-0.5698	-0.255	0.0135	-0.0293	0.2069	-0.128	-0.2485	0.2028	0.2991	0.0098	0.0139	0.5404	0.2062	0.1089	-47.917	-25.875	58.118
18	3.0538	-0.0915	0.836	0.9508	0.1681	0.3121	-0.183	-0.6435	0.0852	0.0186	0.0734	0.0835	-0.035	-0.1863	0.1095	0.2334	0.0725	0.0032	0.5048	0.0604	0.1264	-56.311	-16.299	55.154
19	2.5207	0.0343	-0.0099	1.6724	-0.0476	1.3418	-0.1512	-0.262	0.1079	-0.0411	0.1274	0.1889	-0.1	-0.1873	0.0238	0.1465	0.0797	-0.0157	0.3752	0.078	0.0551	-64.76	-17.783	46.738
20	1.8537	-0.382	0.4376	1.841	-0.7979	2.0701	-0.0662	-0.2206	-0.3697	-0.1654	0.0556	0.1868	0.05	-0.2445	0.0106	0.2006	-0.0597	0.0407	0.333	0.1303	0.2027	-62.806	-32.57	42.108
21	4.9816	1.2057	-1.9258	2.0008	-1.4353	2.3756	-0.147	-0.4559	-0.4015	0.0475	0.1861	-0.138	0.2538	-0.2726	-0.0391	0.276	0.0268	-0.0261	0.3965	0.1435	0.1098	-30.176	-31.986	56.728
22	2.3016	0.622	-0.4093	1.5391	0.4583	1.1026	-0.2743	-0.1895	-0.7111	-0.1003	0.13	-0.1342	0.307	0.0554	0.1443	0.2917	0.0121	0.0494	0.2209	0.1049	0.2994	-33.702	-42.711	50.056
23	4.2384	0.323	-0.1004	2.2317	-0.1321	1.7005	-0.1585	0.1475	-0.939	-0.2541	0.0208	-0.2057	0.3198	0.0408	0.1377	0.3681	0.0286	0.1717	0.0196	-0.0684	0.4774	-27.128	-46.998	40.824
24	3.9534	0.7513	-0.286	2.8182	1.1676	4.3902	-0.3858	0.1446	-0.7011	-0.358	0.1594	-0.3953	0.1852	0.6373	0.2264	0.3014	0.0517	0.0965	0.1102	0.0246	0.421	-14.931	-37.444	40.337

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 50
2	X-RAY DIFFRACTION	2	A	51 - 150
3	X-RAY DIFFRACTION	3	A	151 - 275
4	X-RAY DIFFRACTION	4	A	276 - 343
5	X-RAY DIFFRACTION	5	B	1 - 50
6	X-RAY DIFFRACTION	6	B	51 - 150
7	X-RAY DIFFRACTION	7	B	151 - 275
8	X-RAY DIFFRACTION	8	B	276 - 343
9	X-RAY DIFFRACTION	9	C	1 - 50
10	X-RAY DIFFRACTION	10	C	51 - 150
11	X-RAY DIFFRACTION	11	C	151 - 275
12	X-RAY DIFFRACTION	12	C	276 - 343
13	X-RAY DIFFRACTION	13	D	1 - 50
14	X-RAY DIFFRACTION	14	D	51 - 150
15	X-RAY DIFFRACTION	15	D	151 - 275
16	X-RAY DIFFRACTION	16	D	276 - 343
17	X-RAY DIFFRACTION	17	E	1 - 50
18	X-RAY DIFFRACTION	18	E	51 - 150
19	X-RAY DIFFRACTION	19	E	151 - 275
20	X-RAY DIFFRACTION	20	E	276 - 343
21	X-RAY DIFFRACTION	21	F	1 - 50
22	X-RAY DIFFRACTION	22	F	51 - 150
23	X-RAY DIFFRACTION	23	F	151 - 275
24	X-RAY DIFFRACTION	24	F	276 - 343

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Protein , 1 types, 6 molecules ABCDEF

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-Non-polymers , 10 types, 439 molecules

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Protein , 1 types, 6 molecules ABCDEF

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Non-polymers , 10 types, 439 molecules

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Details

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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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Yorodumi