PDB-6ora: An Unexpected Intermediate in the Reaction Catalyzed by Quinolina...

ID or keywords:

Entry

Database: PDB / ID: 6ora

Title

An Unexpected Intermediate in the Reaction Catalyzed by Quinolinate Synthase

Components

Quinolinate synthase A

Keywords

TRANSFERASE / BIOSYNTHESIS

Function / homology

Function and homology information

quinolinate synthase / quinolinate synthetase A activity / 'de novo' NAD+ biosynthetic process from L-aspartate / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Pyrococcus horikoshii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Esakova, O.A. / Grove, T.L. / Silakov, A. / Yennawar, N.H. / Booker, S.J.

Funding support

United States, 4items

Organization	Grant number	Country
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	GM - 122595	United States
National Science Foundation (NSF, United States)	MCB - 1716686	United States
National Science Foundation (NSF, United States)	CHE - 1659679	United States
Howard Hughes Medical Institute (HHMI)		United States

Citation

Journal: J.Am.Chem.Soc. / Year: 2019
Title: An Unexpected Species Determined by X-ray Crystallography that May Represent an Intermediate in the Reaction Catalyzed by Quinolinate Synthase.
Authors: Esakova, O.A. / Silakov, A. / Grove, T.L. / Warui, D.M. / Yennawar, N.H. / Booker, S.J.

History

Deposition	Apr 29, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 21, 2019	Provider: repository / Type: Initial release
Revision 1.1	Sep 25, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 20, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ora.cif.gz	263.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6ora.ent.gz	212.8 KB	Display	PDB format
PDBx/mmJSON format	6ora.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ora_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	6ora_full_validation.pdf.gz	1 MB	Display
Data in XML	6ora_validation.xml.gz	25.9 KB	Display
Data in CIF	6ora_validation.cif.gz	36.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/or/6ora ftp://data.pdbj.org/pub/pdb/validation_reports/or/6ora	HTTPS FTP

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Related structure data

Related structure data	6nsoC 6nsuC 6or8C 1wzuS 4zk6 4zkz PDB Unreleased entry 5fev PDB Unreleased entry 5ffk PDB Unreleased entry C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ktp-d 6nsu-d 6or8-d 5kto-d 5ktt-d 5f35-d 4zk6-1 5ktm-d 2qgq-6 6nso-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

Deposited unit

A: Quinolinate synthase A

B: Quinolinate synthase A

hetero molecules

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

1

A: Quinolinate synthase A

hetero molecules

defined by author&software
Evidence: gel filtration
34.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Quinolinate synthase A

hetero molecules

defined by author&software
34.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.052, 52.134, 97.803
Angle α, β, γ (deg.)	90.00, 96.27, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Quinolinate synthase A Mass: 34189.043 Da / Num. of mol.: 2 / Mutation: E198Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: nadA, PH0013 / Production host: Escherichia coli (E. coli) / Variant (production host): ROSETTA 2 (DE3) / References: UniProt: O57767, quinolinate synthase

#1: Protein

Quinolinate synthase A

Mass: 34189.043 Da / Num. of mol.: 2 / Mutation: E198Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: nadA, PH0013 / Production host:

Escherichia coli (E. coli) / Variant (production host): ROSETTA 2 (DE3) / References: UniProt: O57767, quinolinate synthase

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Non-polymers , 6 types, 269 molecules

#2: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-5XW / (2~{Z})-2-(1-oxidanyl-3-oxidanylidene-propyl)iminobutanedioic acid Mass: 203.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₉NO₆ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-5XR / 2-hydroxy-N-[(1S)-1-hydroxy-3-oxopropyl]-L-aspartic acid Mass: 221.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₁₁NO₇ / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 1.97 Å³/Da / Density % sol: 37.53 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE, PH 4.6, 30% PEG 4000, 10 MM OAA, 10 MM DHAP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K PH range: 4.6

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 25676 / % possible obs: 94.4 % / Redundancy: 2.3 % / R_merge(I) obs: 0.115 / Net I/σ(I): 5.7
Reflection shell	Resolution: 2.2→2.25 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.557 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1766 / % possible all: 94.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.11_2561)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1WZU

1wzu

Resolution: 2.2→45.945 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.26

	R_factor	Num. reflection	% reflection
R_free	0.2427	1999	7.79 %
R_work	0.1958	-	-
obs	0.1996	25676	94.18 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.2→45.945 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4758	0	55	261	5074

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5033
X-RAY DIFFRACTION	f_angle_d	0.465	6809
X-RAY DIFFRACTION	f_dihedral_angle_d	11.44	3146
X-RAY DIFFRACTION	f_chiral_restr	0.044	763
X-RAY DIFFRACTION	f_plane_restr	0.003	870

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 (%)
2.2002-2.2552	0.3461	137	0.287	1629	X-RAY DIFFRACTION	92
2.2552-2.3162	0.3078	144	0.2769	1714	X-RAY DIFFRACTION	96
2.3162-2.3843	0.3175	144	0.2523	1698	X-RAY DIFFRACTION	96
2.3843-2.4613	0.3233	145	0.2436	1717	X-RAY DIFFRACTION	96
2.4613-2.5492	0.2865	143	0.2351	1696	X-RAY DIFFRACTION	95
2.5492-2.6513	0.2878	145	0.2361	1725	X-RAY DIFFRACTION	95
2.6513-2.772	0.2959	143	0.2352	1686	X-RAY DIFFRACTION	96
2.772-2.9181	0.2711	144	0.218	1701	X-RAY DIFFRACTION	95
2.9181-3.1009	0.2918	146	0.222	1721	X-RAY DIFFRACTION	95
3.1009-3.3402	0.2415	141	0.1962	1676	X-RAY DIFFRACTION	94
3.3402-3.6762	0.2223	141	0.1757	1683	X-RAY DIFFRACTION	94
3.6762-4.2079	0.1941	142	0.1468	1680	X-RAY DIFFRACTION	93
4.2079-5.3002	0.1704	144	0.1416	1695	X-RAY DIFFRACTION	92
5.3002-45.9546	0.1723	140	0.1416	1656	X-RAY DIFFRACTION	89

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	3.4877	3.7436	5.9645	7.0478	6.2701	2.0086	-0.1357	-0.2832	0.0877	0.7204	-0.5913	0.5855	0.3873	-0.9433	0.6896	0.1941	-0.0489	0.0939	0.2679	0.0476	0.4445	-40.9069	17.9908	0.3293
2	1.0586	0.7751	2.4177	3.2107	1.8138	5.5072	-0.1621	-0.1016	-0.0095	0.1849	0.0146	0.1386	-0.1036	-0.0096	0.1674	0.071	-0.0161	0.0158	0.1303	0.0087	0.1728	-24.3099	18.3218	0.9405
3	3.339	-1.2723	-0.3726	3.8012	0.8304	4.1496	-0.1549	-0.1404	-0.1463	-0.1226	0.1798	-0.1083	0.0715	0.0222	0.0164	0.0574	0.0076	-0.0188	0.1263	0.0236	0.171	-24.4752	18.2564	-10.1252
4	3.3361	-1.7458	-0.7036	2.877	1.0373	2.4935	-0.0588	0.1154	0.3248	-0.3735	-0.0311	0.3113	-0.0977	-0.1609	0.0812	0.1181	-0.015	-0.0307	0.1219	0.0676	0.172	-26.3151	26.8423	-9.3502
5	4.6528	-3.1502	-1.8246	5.1799	0.7967	9.6525	0.0655	0.4375	0.9271	-0.4932	0.1595	0.0647	-1.0862	0.1458	-0.2455	0.2426	-0.1008	-0.0226	0.175	0.0461	0.224	-10.2821	35.9567	-13.6223
6	5.4846	-1.3845	-1.487	3.9305	0.1662	3.8003	-0.0143	0.5293	0.4157	-0.3094	0.0047	-0.2482	-0.1116	0.2359	0.0005	0.2127	-0.0952	0.0282	0.3168	0.0368	0.1486	-4.3581	29.3417	-18.1797
7	9.367	-3.6008	2.2323	5.788	2.8251	3.612	0.041	0.8612	0.5139	-0.55	-0.2391	-0.1533	-0.6702	-0.2315	0.2015	0.259	-0.0469	0.021	0.3069	0.0236	0.1142	-13.5864	28.7634	-19.555
8	4.1534	-3.0811	5.0616	3.6402	-2.3285	7.6828	0.3899	0.1005	-0.3301	-0.0674	-0.1586	0.3228	0.2946	0.2423	-0.24	0.1055	-0.031	-0.0297	0.209	-0.0228	0.2157	-8.2684	19.0875	-11.1279
9	3.8421	-1.2123	-0.7657	5.5597	-0.4127	3.5166	0.111	0.1104	0.0421	-0.1492	0.0742	-0.3142	0.196	0.4086	-0.2075	0.0892	-0.0223	-0.0327	0.2202	-0.045	0.1931	0.0074	24.2947	-9.6496
10	2.5649	1.2882	-0.3336	3.69	-0.4133	2.2562	-0.0251	-0.154	0.0289	0.4281	0.076	-0.0335	-0.0333	0.1813	-0.0489	0.1181	0.0372	-0.0398	0.1658	-0.0213	0.1533	-8.0566	20.3852	11.1581
11	4.048	-0.0889	0.1998	1.5258	0.7389	2.1477	-0.1309	0.1779	0.0016	-0.1596	0.0054	0.199	-0.0867	-0.0772	0.133	0.0948	-0.0233	-0.0143	0.0455	0.0478	0.1677	-23.8321	25.098	-8.3875
12	2.1008	0.3121	0.3134	0.7639	-0.2611	5.2234	0.033	0.1982	0.0821	-0.3909	0.0865	-0.202	-0.3367	0.6199	-0.1334	0.5288	-0.0599	0.0519	0.2212	-0.0466	0.2344	-16.2464	3.199	-52.7075
13	1.437	-0.9428	-0.1652	0.9489	0.0746	5.1686	0.1204	0.1453	0.0517	-0.5381	-0.1852	0.0788	-0.3484	-0.7529	0.0288	0.5486	0.0144	-0.0761	0.3117	0.0106	0.2105	-30.2711	3.5673	-53.7573
14	1.7505	-1.0587	-2.0284	1.2236	0.9196	4.2498	-0.4608	0.0877	0.1607	0.2352	0.115	0.0336	0.7869	-0.1823	0.3415	0.5406	-0.0568	-0.083	0.2064	0.0221	0.2122	-27.2864	-9.9264	-48.9223
15	1.9805	-1.4286	-1.0536	2.5803	1.0065	2.8082	-0.0472	0.2247	-0.4423	-0.1101	-0.0424	0.2554	0.9091	-1.4028	0.0656	0.8129	-0.3606	-0.0986	0.7637	-0.0762	0.4058	-46.7593	-8.2847	-41.3009
16	1.6549	0.2354	0.2339	4.7999	3.6147	6.0401	-0.0857	0.6368	0.0811	-0.7123	-0.2325	0.5964	-0.1179	-0.8807	0.34	0.4715	-0.0283	-0.132	0.5196	0.0359	0.236	-42.8545	1.707	-41.8117
17	5.1965	0.1067	0.0725	4.0805	0.9863	3.7817	0.1479	0.0737	-0.2204	-0.1764	-0.1655	0.5759	0.5041	-0.8733	0.0012	0.3078	-0.1098	-0.0068	0.3157	0.0085	0.1827	-39.192	-3.8619	-30.3841
18	6.0007	2.4983	4.2092	2.0019	0.0183	9.9053	0.1805	-0.1886	-0.2387	0.0849	-0.1253	-0.145	0.5946	0.468	-0.0521	0.217	0.0236	0.0134	0.2311	0.0216	0.2668	-17.0712	0.5727	-17.4794
19	4.8499	-0.3966	-0.5697	3.4805	-1.9406	6.3379	-0.0791	-0.0077	0.044	-0.2693	-0.0477	0.1571	-0.0153	-0.168	0.123	0.1931	-0.0317	-0.0024	0.1286	-0.0439	0.1237	-28.5478	3.4805	-27.2396
20	3.5694	3.1053	1.4296	8.5166	-0.0822	3.6778	-0.0373	0.2004	-0.1896	-0.4195	0.2042	-0.5572	0.1442	0.3656	-0.1537	0.2253	0.0101	-0.0106	0.2066	-0.0412	0.1229	-17.178	2.9394	-30.8739
21	3.6147	0.0097	0.4935	1.9691	0.8111	3.4684	0.0137	0.2957	-0.1702	-0.099	0.1509	-0.1997	0.3976	0.324	-0.1434	0.5472	0.0107	0.0377	0.1761	-0.0051	0.2091	-19.0814	-6.4209	-54.825
22	4.3526	-1.7017	-0.6156	2.8938	1.7309	7.3357	0.2139	0.6769	-0.1258	-0.9676	-0.3827	0.7624	-0.7527	-2.0322	0.1501	0.5487	0.1064	-0.1126	0.7788	0.061	0.3514	-43.083	2.68	-52.4402

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:15)
2	X-RAY DIFFRACTION	2	(chain A and resid 16:41)
3	X-RAY DIFFRACTION	3	(chain A and resid 42:68)
4	X-RAY DIFFRACTION	4	(chain A and resid 69:85)
5	X-RAY DIFFRACTION	5	(chain A and resid 86:93)
6	X-RAY DIFFRACTION	6	(chain A and resid 94:113)
7	X-RAY DIFFRACTION	7	(chain A and resid 114:120)
8	X-RAY DIFFRACTION	8	(chain A and resid 121:129)
9	X-RAY DIFFRACTION	9	(chain A and resid 130:169)
10	X-RAY DIFFRACTION	10	(chain A and resid 170:250)
11	X-RAY DIFFRACTION	11	(chain A and resid 251:299)
12	X-RAY DIFFRACTION	12	(chain B and resid 2:37)
13	X-RAY DIFFRACTION	13	(chain B and resid 38:75)
14	X-RAY DIFFRACTION	14	(chain B and resid 76:85)
15	X-RAY DIFFRACTION	15	(chain B and resid 86:113)
16	X-RAY DIFFRACTION	16	(chain B and resid 114:134)
17	X-RAY DIFFRACTION	17	(chain B and resid 135:182)
18	X-RAY DIFFRACTION	18	(chain B and resid 183:191)
19	X-RAY DIFFRACTION	19	(chain B and resid 192:222)
20	X-RAY DIFFRACTION	20	(chain B and resid 223:255)
21	X-RAY DIFFRACTION	21	(chain B and resid 256:278)
22	X-RAY DIFFRACTION	22	(chain B and resid 279:299)

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 269 molecules

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 269 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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Yorodumi