PDB-4zk6: Crystallographic Capture of Quinolinate Synthase (NadA) from Pyro...

ID or keywords:

Entry

Database: PDB / ID: 4zk6

Title

Crystallographic Capture of Quinolinate Synthase (NadA) from Pyrococcus horikoshii in its Substrates and Product-Bound States

Components

Quinolinate synthase A

Keywords

TRANSFERASE / quinolicnic acid / biosynthesis of nicotinamide adenine dinucleotide.

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: 1.895 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2016
Title: Structure of Quinolinate Synthase from Pyrococcus horikoshii in the Presence of Its Product, Quinolinic Acid.
Authors: Esakova, O.A. / Silakov, A. / Grove, T.L. / Saunders, A.H. / McLaughlin, M.I. / Yennawar, N.H. / Booker, S.J.

History

Deposition	Apr 29, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 29, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Sep 27, 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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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PDBx/mmCIF format	4zk6.cif.gz	263.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4zk6.ent.gz	213.5 KB	Display	PDB format
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Validation report

Summary document	4zk6_validation.pdf.gz	482.1 KB	Display	wwPDB validaton report
Full document	4zk6_full_validation.pdf.gz	485.9 KB	Display
Data in XML	4zk6_validation.xml.gz	26 KB	Display
Data in CIF	4zk6_validation.cif.gz	36.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zk/4zk6 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/4zk6	HTTPS FTP

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Related structure data

Related structure data	1wzuS 4zkz PDB Unreleased entry 5fev PDB Unreleased entry 5ffk PDB Unreleased entry S: Starting model for refinement
Similar structure data	6ora-2 6f4d-d 5kto-d 6nso-d 6nsu-d 6i0r-d 5ktp-d 6i0p-d 6f4l-d 5f33-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
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
34.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	52.562, 51.588, 97.541
Angle α, β, γ (deg.)	90.00, 94.95, 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: 34190.027 Da / Num. of mol.: 2 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) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: O57767, quinolinate synthase

#1: Protein

Quinolinate synthase A

Mass: 34190.027 Da / Num. of mol.: 2
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) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: O57767, quinolinate synthase

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Non-polymers , 6 types, 299 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-NTM / QUINOLINIC ACID Mass: 167.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₅NO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 287 / 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: 1.93 Å³/Da / Density % sol: 36.16 %
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 QA

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Data collection

Diffraction	Mean temperature: 77 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.85 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2014
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.85 Å / Relative weight: 1
Reflection	Resolution: 1.895→50 Å / Num. obs: 41502 / % possible obs: 100 % / Redundancy: 3.7 % / R_merge(I) obs: 0.085 / Net I/σ(I): 10.14
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.891 / Mean I/σ(I) obs: 1.3 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1WZU

1wzu

Resolution: 1.895→48.589 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2305	2017	4.86 %
R_work	0.1836	-	-
obs	0.1859	41481	99.46 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.895→48.589 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4758	0	54	287	5099

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	5031
X-RAY DIFFRACTION	f_angle_d	0.879	6823
X-RAY DIFFRACTION	f_dihedral_angle_d	12.892	3160
X-RAY DIFFRACTION	f_chiral_restr	0.05	766
X-RAY DIFFRACTION	f_plane_restr	0.005	871

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 (%)
1.8946-1.942	0.3395	130	0.2859	2632	X-RAY DIFFRACTION	93
1.942-1.9945	0.3044	139	0.2442	2810	X-RAY DIFFRACTION	100
1.9945-2.0532	0.2775	154	0.2393	2790	X-RAY DIFFRACTION	100
2.0532-2.1195	0.2795	132	0.2274	2822	X-RAY DIFFRACTION	100
2.1195-2.1952	0.3018	145	0.2209	2808	X-RAY DIFFRACTION	100
2.1952-2.2831	0.2725	158	0.2068	2813	X-RAY DIFFRACTION	100
2.2831-2.387	0.2714	140	0.2013	2815	X-RAY DIFFRACTION	100
2.387-2.5129	0.255	138	0.1922	2840	X-RAY DIFFRACTION	100
2.5129-2.6703	0.2402	150	0.1916	2802	X-RAY DIFFRACTION	100
2.6703-2.8764	0.2438	138	0.2004	2856	X-RAY DIFFRACTION	100
2.8764-3.1659	0.2451	152	0.1879	2818	X-RAY DIFFRACTION	100
3.1659-3.6238	0.1966	151	0.1641	2845	X-RAY DIFFRACTION	100
3.6238-4.5651	0.1716	141	0.1362	2873	X-RAY DIFFRACTION	100
4.5651-48.6046	0.1819	149	0.1501	2940	X-RAY DIFFRACTION	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	9.3919	2.0612	-3.1358	4.8868	-5.255	8.035	-0.7018	0.7961	-0.6801	-0.4088	-0.1989	-0.8459	0.5435	0.4498	0.867	0.2374	-0.0067	0.0444	0.315	-0.1186	0.6651	18.7939	-7.0696	-49.8426
2	0.7498	-1.7547	2.4437	5.7915	-4.2884	9.1222	-0.1694	0.1301	-0.0041	-0.0629	-0.0123	-0.2769	0.0075	0.0102	0.1841	0.0536	-0.0079	-0.0152	0.1141	-0.0255	0.1453	2.0813	-6.4163	-49.4744
3	4.2743	2.1038	-1.2344	3.1281	-0.7034	6.0772	-0.131	0.1608	0.0054	0.1928	0.1818	-0.1787	0.0366	-0.1962	-0.0486	0.0575	0.0165	-0.0335	0.1439	-0.0065	0.1366	2.6885	-6.366	-38.3795
4	2.2598	1.7451	-1.5688	4.2927	-0.6363	1.2151	-0.1755	0.0248	0.1053	0.5505	0.1163	-0.1039	-0.1463	-0.1308	0.0463	0.0882	0.0083	-0.0438	0.1794	-0.0297	0.1555	4.4532	1.9539	-39.2961
5	7.3066	5.2741	-0.6476	5.8433	-4.3976	7.6709	0.3203	-0.4324	0.8597	0.4154	-0.0162	-0.3006	-0.7474	0.8123	-0.3215	0.188	0.0497	-0.022	0.3541	-0.0683	0.2777	-11.7655	11.034	-34.5676
6	6.9679	3.0226	1.4606	6.0687	-0.6686	2.0938	-0.1683	-0.2448	-0.0649	0.2917	0.0904	0.1912	-0.3204	0.0019	0.0755	0.2397	0.1136	-0.0257	0.3016	-0.0211	0.0883	-16.9536	4.0253	-30.2688
7	2.0023	3.7122	-9.4691	8.0951	-2.2022	7.2896	0.4449	-0.768	0.2942	0.5408	0.1427	-0.531	-0.07	0.786	-0.5645	0.1953	0.0534	-0.084	0.3112	-0.0757	0.2631	-7.5983	4.252	-29.0109
8	0.3149	0.7693	0.2319	3.7258	2.5958	7.4698	0.1201	0.2718	-0.0366	0.0844	0.1639	0.2017	0.0776	0.1443	-0.248	0.0947	0.0793	-0.0552	0.2585	0.0081	0.1516	-13.6654	-5.7999	-37.1733
9	6.223	2.6508	-0.6772	7.5129	0.3553	4.0029	-0.0105	0.0231	-0.1453	0.1073	0.1133	0.5847	0.0085	-0.3034	-0.0901	0.0582	0.0463	-0.0289	0.192	0.0062	0.1768	-22.1178	-1.0718	-38.104
10	4.5151	-2.3812	-0.1754	4.6338	1.6576	2.04	-0.1097	0.0428	0.0016	-0.1417	0.0313	0.2268	-0.0221	-0.159	0.0694	0.0921	-0.0337	-0.0237	0.1659	0.0284	0.1075	-14.3298	-4.6089	-59.2958
11	3.3108	0.6674	-0.0702	2.9318	-0.7282	2.0462	-0.1976	-0.1757	0.0552	0.1599	0.0633	-0.3488	-0.0689	0.0805	0.114	0.0698	0.0691	-0.0471	0.103	-0.0476	0.1925	1.5151	-0.0342	-39.7308
12	4.0184	-1.2031	-0.318	2.8719	-0.7719	4.1548	-0.0431	0.0237	0.1081	-0.1994	0.1082	-0.3335	-0.1357	0.4383	-0.0918	0.3504	-0.0377	0.0318	0.1695	-0.0396	0.1402	13.4624	4.1789	-101.6938
13	8.5181	-0.0432	-0.3334	3.6514	3.1082	3.3415	0.0205	-0.1223	-0.1126	0.0274	-0.1184	0.225	-0.1156	-0.3119	0.0945	0.3774	0.0534	0.0312	0.1835	0.0253	0.1	-0.8477	4.4323	-102.4914
14	6.1193	-0.2373	-1.7194	5.0062	-2.1917	1.5022	-0.3763	-0.5579	-0.0143	0.0845	0.2891	0.0275	1.0329	0.0464	0.1107	0.3886	-0.0034	-0.0118	0.1861	0.002	0.1187	2.1097	-8.8551	-97.5264
15	5.0683	-1.7246	1.4264	6.6946	-0.7592	9.6163	0.3733	1.014	-0.9419	-0.3709	-0.4641	0.0996	1.1675	-0.4268	0.0926	0.4022	-0.0163	-0.0517	0.3894	-0.1189	0.3772	-17.5929	-7.4568	-89.9546
16	5.9219	0.6112	1.0129	4.2247	-1.1924	4.3225	0.1332	0.5944	-0.0979	-0.4365	-0.0476	0.084	0.2247	-0.3882	-0.0651	0.3129	-0.0059	0.001	0.3916	0.028	0.126	-13.3186	2.8671	-90.3323
17	5.7887	-1.1093	1.6604	1.8177	0.0263	1.0036	0.013	-0.1377	-0.352	0.0603	0.0001	0.3413	0.1744	-0.201	-0.0098	0.3638	-0.0747	0.0666	0.1982	0.0185	0.1257	-9.2457	-2.6072	-78.8016
18	6.8357	0.4891	0.2701	2.0021	-3.9567	6.8248	-0.0164	-0.3442	-0.2809	0.9636	-0.3171	-0.3224	0.4945	0.2542	0.3337	0.3572	-0.0018	-0.0193	0.2101	0.0259	0.1174	12.6223	1.4857	-66.1679
19	5.0255	5.0317	-2.0367	5.8526	-1.6226	1.0743	-0.1976	0.1955	0.1674	-0.2463	0.2666	0.2693	0.1492	-0.1618	-0.066	0.2292	-0.0214	-0.0371	0.1667	0.0114	0.0924	1.5431	5.3177	-76.0114
20	3.135	2.2769	0.2359	3.9877	-0.8191	4.7951	-0.2124	0.1296	-0.2934	-0.4945	0.0793	-0.4505	0.3804	0.314	0.1327	0.2775	0.0103	0.0339	0.1724	-0.0109	0.098	12.52	4.0162	-79.8797
21	3.41	1.7748	0.3525	2.5958	0.2159	0.5302	-0.2529	0.2678	-0.2642	-0.1407	0.0383	-0.1934	0.0113	0.1414	0.2019	0.394	0.0381	0.0486	0.1639	-0.0332	0.1338	10.5675	-5.2635	-103.7459
22	6.6683	-2.3028	-0.5733	5.3357	4.1344	6.6823	0.4083	0.215	-0.3885	-0.879	-0.4174	0.517	-1.1595	-1.9671	0.0389	0.4193	0.1242	-0.0385	0.6066	0.1363	0.3242	-13.8055	3.5609	-101.2339

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, 299 molecules

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Experiment

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-Protein , 1 types, 2 molecules AB

-Non-polymers , 6 types, 299 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

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Viewer log

-
This page

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This web site

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Options

+
Open data

-
Basic information

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Structure visualization

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Downloads & links

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Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

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Components

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Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 299 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
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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Yorodumi