PDB-5ong: X-Ray crystal structure of a nucleosome core particle with its DN...

ID or keywords:

Entry

Database: PDB / ID: 5ong

Title

X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer

Components

(DNA (147-MER)) x 2
Histone H2A
Histone H2B 1.1
Histone H3.2
Histone H4

Keywords

DNA BINDING PROTEIN /

Nucleosome Core Particle /

Histones /

Disulfide / Convertible Nucleotide /

DNA

Function / homology

Function and homology information

structural constituent of chromatin /

nucleosome / protein heterodimerization activity /

DNA binding /

nucleoplasm /

nucleus
Similarity search - Function

Biological species

Homo sapiens (human)

Xenopus laevis (African clawed frog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.797 Å

Authors

Frouws, T.D. / Barth, P.D. / Richmond, T.J.

Funding support

Switzerland, 1items

Citation

Journal: J. Mol. Biol. / Year: 2018
Title: Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability.
Authors: Frouws, T.D. / Barth, P.D. / Richmond, T.J.

History

Deposition	Aug 3, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 27, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2	Jan 17, 2024	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 / struct_conn_type 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ong.cif.gz	644.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5ong.ent.gz	522.4 KB	Display	PDB format
PDBx/mmJSON format	5ong.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/on/5ong ftp://data.pdbj.org/pub/pdb/validation_reports/on/5ong	HTTPS FTP

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Related structure data

Related structure data	5omxC 5onwC 1kx5S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3lel-2 3x1u-d 1p3g-d 4wu9-d 1p34-d 3mgr-d 4xzq-d 1p3p-d 4ys3-d 3azj-d 1kx3-d 1p3f-d 1p3a-d 3av2-d 4j8v-d 4j8x-d 4j8u-d 2nqb-d 1p3k-d 6iq4-d 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
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

I: DNA (147-MER)

J: DNA (147-MER)

A: Histone H3.2

B: Histone H4

C: Histone H2A

D: Histone H2B 1.1

E: Histone H3.2

F: Histone H4

G: Histone H2A

H: Histone H2B 1.1

hetero molecules

200 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	106.240, 183.130, 109.490
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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DNA chain , 2 types, 2 molecules IJ

#1: DNA chain	DNA (147-MER) Mass: 45430.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Variant (production host): DH10B
#2: DNA chain	DNA (147-MER) Mass: 45421.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Variant (production host): DH10B

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Protein , 4 types, 8 molecules AEBFCGDH

#3: Protein	Histone H3.2 Mass: 15217.812 Da / Num. of mol.: 2 / Mutation: C110A, R40C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P84233
#4: Protein	Histone H4 / Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P62799
#5: Protein	Histone H2A / Mass: 13978.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#6: Protein	Histone H2B 1.1 / H2B1.1 Mass: 13524.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P02281

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Non-polymers , 3 types, 111 molecules

#7: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mn
#8: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#9: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	constructs were all sequenced and the expressed protein MW was confirmed by mass spec: 30268543:42- ...constructs were all sequenced and the expressed protein MW was confirmed by mass spec: 30268543:42-452 Expression vector pET3-H3 H3 gene for Xenopus laevis-like histone H3 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 30268542\|emb\|CAD89678.1\| Xenopus laevis-like histone H2B [Expression vector pET3-H2B] MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFER IAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Sequence details

constructs were all sequenced and the expressed protein MW was confirmed by mass spec: 30268543:42- ...

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.01 Å³/Da / Density % sol: 59.09 % / Description: hollow hexagonal rods
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 130-180 mM MnCl2, 100-160 mM KCl and equilibrated against a 1:4 dilution of the same solution

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Data collection

Diffraction	Mean temperature: 90 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 11, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.797→29.54 Å / Num. obs: 47952 / % possible obs: 90.3 % / Redundancy: 3.3 % / R_merge(I) obs: 0.084 / Net I/σ(I): 12.7
Reflection shell	Resolution: 2.797→2.95 Å / R_merge(I) obs: 0.231 / Mean I/σ(I) obs: 2.5 / % possible all: 68

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2447: ???)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1KX5

1kx5

Resolution: 2.797→29.499 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.76

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2468	4812	10.07 %	random
R_work	0.2057	-	-	-
obs	0.2098	47779	89.43 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.797→29.499 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5973	6027	24	87	12111

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	12813
X-RAY DIFFRACTION	f_angle_d	0.597	18563
X-RAY DIFFRACTION	f_dihedral_angle_d	26.102	6679
X-RAY DIFFRACTION	f_chiral_restr	0.036	2109
X-RAY DIFFRACTION	f_plane_restr	0.024	1473

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 (%)
2.7973-2.8291	0.4036	97	0.3838	822	X-RAY DIFFRACTION	52
2.8291-2.8623	0.4231	118	0.3508	1076	X-RAY DIFFRACTION	69
2.8623-2.8972	0.3384	135	0.3028	1145	X-RAY DIFFRACTION	72
2.8972-2.9339	0.3339	130	0.2771	1096	X-RAY DIFFRACTION	70
2.9339-2.9724	0.3258	149	0.2772	1289	X-RAY DIFFRACTION	82
2.9724-3.0131	0.3088	164	0.2629	1450	X-RAY DIFFRACTION	92
3.0131-3.0561	0.3014	141	0.243	1483	X-RAY DIFFRACTION	92
3.0561-3.1017	0.291	163	0.2528	1446	X-RAY DIFFRACTION	92
3.1017-3.1501	0.2869	170	0.2406	1431	X-RAY DIFFRACTION	91
3.1501-3.2017	0.2714	143	0.2427	1518	X-RAY DIFFRACTION	94
3.2017-3.2568	0.292	166	0.2703	1521	X-RAY DIFFRACTION	96
3.2568-3.316	0.2828	164	0.2519	1528	X-RAY DIFFRACTION	95
3.316-3.3797	0.3054	151	0.2726	1496	X-RAY DIFFRACTION	95
3.3797-3.4485	0.2998	186	0.2746	1464	X-RAY DIFFRACTION	93
3.4485-3.5234	0.2672	169	0.2464	1488	X-RAY DIFFRACTION	94
3.5234-3.6052	0.2854	156	0.2124	1478	X-RAY DIFFRACTION	94
3.6052-3.6952	0.2571	173	0.2231	1510	X-RAY DIFFRACTION	95
3.6952-3.7949	0.2452	194	0.2127	1525	X-RAY DIFFRACTION	95
3.7949-3.9064	0.2453	170	0.196	1528	X-RAY DIFFRACTION	96
3.9064-4.0321	0.2204	184	0.1911	1492	X-RAY DIFFRACTION	95
4.0321-4.1759	0.2336	174	0.182	1500	X-RAY DIFFRACTION	94
4.1759-4.3426	0.2223	150	0.1744	1529	X-RAY DIFFRACTION	93
4.3426-4.5395	0.219	164	0.1756	1480	X-RAY DIFFRACTION	92
4.5395-4.7779	0.2018	166	0.1688	1522	X-RAY DIFFRACTION	94
4.7779-5.0759	0.2076	176	0.1722	1512	X-RAY DIFFRACTION	94
5.0759-5.4655	0.2157	188	0.1803	1508	X-RAY DIFFRACTION	94
5.4655-6.0113	0.2386	165	0.1943	1515	X-RAY DIFFRACTION	93
6.0113-6.8716	0.25	171	0.204	1497	X-RAY DIFFRACTION	91
6.8716-8.6215	0.227	170	0.17	1533	X-RAY DIFFRACTION	92
8.6215-29.5008	0.2045	165	0.1725	1585	X-RAY DIFFRACTION	90

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	2.0744	0.1589	0.2685	2.1049	0.7135	0.2138	1.1736	-0.8087	0.8527	2.5658	-1.3786	2.2344	-0.1767	-0.7504	-0.0987	1.7174	0.0718	0.4319	1.6236	-0.046	1.6799	9.6346	111.8531	19.4256
2	4.0147	-3.9246	-0.0241	4.0769	-0.6589	1.8688	0.3548	0.5799	-1.5657	0.8115	0.442	1.5324	0.2	-1.1332	0.3414	1.0233	-0.5449	0.148	1.0603	0.1066	1.7645	14.3378	65.7429	19.4159
3	1.3558	-1.0474	0.0449	0.9251	-0.5801	1.7551	-0.2891	-0.4906	-0.5862	0.1569	-0.3297	-0.9212	0.9059	1.1955	-2.126	0.7614	0.3555	-0.1825	1.1192	0.3074	1.124	67.2307	71.4162	20.9835
4	2.2379	0.2645	1.4192	1.175	0.6977	1.9165	0.1186	-0.1171	1.2973	-0.4303	-0.1837	-0.1339	-0.9526	-0.1328	-0.0453	0.9237	-0.0887	0.1875	0.4749	0.0475	0.9163	44.881	124.8368	1.7113
5	2.0526	0.1051	0.1446	0.9116	0.3826	0.1501	0.1458	0.4312	-0.942	-0.0947	-0.5667	1.658	0.4609	-0.6133	0.1862	1.0445	-0.283	-0.0035	1.0283	-0.1348	0.9463	14.4384	74.639	-5.5661
6	2.1309	-0.0068	0.4932	0.0282	-0.0925	0.5091	-0.2547	-0.186	-1.5428	-1.3592	0.2786	-0.2679	0.8323	0.1049	0.1119	1.5401	0.1462	0.2683	0.9031	-0.1639	1.5313	52.4968	50.0233	-2.4507
7	1.9973	0.0553	-0.1191	0.6057	-1.0141	1.5365	0.5659	0.1519	-0.3137	-0.3167	-1.0556	-2.2272	-0.0104	0.9782	-0.2702	1.0514	0.2495	0.4443	1.2001	0.0349	1.737	82.555	92.2212	-8.8689
8	1.3906	-0.859	-0.2763	0.7935	-0.252	1.5614	0.8389	0.1657	0.2923	-1.0209	-1.4779	-1.5467	0.0095	0.6523	-0.0656	0.844	-0.0371	0.4086	1.4744	0.1775	1.5302	85.1536	102.8163	-11.9129
9	0.1965	0.1867	-0.3998	2.0941	0.1204	0.8239	-0.5337	0.031	-1.5423	-0.4362	0.0165	-0.0494	0.8755	0.3189	0.1772	1.3489	0.1639	0.1445	0.7045	-0.1214	1.6208	58.0826	54.3866	-3.2055
10	1.3359	0.2715	0.1892	0.086	-0.1956	1.4198	0.2823	0.2528	-0.7325	-0.0859	-0.9664	1.9412	0.3839	-0.9915	-0.6209	0.6192	-0.0845	-0.099	1.2293	-0.3091	1.0295	11.0782	83.2297	-6.552
11	1.2004	-0.0006	1.0017	1.7757	-0.3553	2.1627	-0.1463	0.076	0.8047	0.0273	-0.1103	-0.6187	-1.0569	0.383	-0.2502	0.9983	-0.2561	0.0688	0.546	0.0652	0.8878	52.5542	124.2774	2.7742
12	0.0388	-0.0439	0.1575	1.5208	0.8594	1.3696	0.4998	-0.8288	-0.4236	0.3496	0.0909	-1.4465	0.6293	0.3281	4.5429	0.4731	0.4392	-0.2196	2.1883	0.4227	1.5688	85.0413	84.6061	18.2396
13	3.8091	-1.0505	-0.7814	1.3979	-0.3511	1.448	-0.6848	0.0425	-1.5578	0.2888	0.5355	0.1457	1.1088	0.0189	-0.0922	1.2142	0.1757	0.0637	0.6356	0.1599	1.1222	49.4277	57.3249	22.1767
14	0.9071	-0.5147	0.2434	0.5368	-0.0921	1.8951	0.2234	-0.3015	0.1741	0.8259	1.0462	3.9804	-0.6157	-1.8657	-0.1292	1.6491	-0.2126	0.1353	1.1902	0.4091	2.659	9.1927	74.1298	18.0998
15	0.4902	0.3419	0.0498	0.212	0.0388	-0.008	0.0861	-1.1855	0.6149	0.363	-0.8421	1.1553	-0.0528	-0.1033	0.343	1.5229	0.3154	0.3431	1.4448	0.0451	1.5245	11.5047	116.1599	19.1574
16	0.7788	-0.706	-0.0492	0.6497	-0.0031	0.6201	0.0696	-0.1256	-0.0862	-0.0708	-0.3364	-0.4092	-0.1665	0.4229	-1.2476	0.3838	-0.3424	0.4167	0.8281	-0.0248	0.8929	72.6655	113.6031	-3.458
17	2.5143	0.1244	-0.1685	3.0498	0.587	1.7374	0.0061	-1.0664	-0.0926	0.5993	-0.2386	-0.9009	-0.0068	0.4769	0.0019	0.2024	-0.1408	-0.0249	0.7875	0.0187	0.6664	70.3955	95.2141	15.7005
18	0.4588	-0.604	0.098	2.2821	-0.5325	1.8093	-0.3216	-0.078	0.5184	0.4989	-0.1586	-1.1876	-0.4061	0.7872	-0.0072	0.1993	-0.1139	-0.0269	0.375	0.0229	0.5165	61.4884	99.5426	9.5716
19	4.808	0.7423	1.2722	5.1982	0.4976	4.1485	0.4506	-1.1945	-0.0935	0.8805	-0.7618	1.0566	-0.5565	-0.4063	-0.0203	0.4495	-0.0919	0.1386	0.5133	-0.1168	0.5507	50.035	106.5553	10.284
20	0.4955	0.2956	0.7685	1.0717	0.2049	2.488	-0.0304	-0.2475	0.061	0.6098	-0.5493	-1.1474	-0.5368	0.8307	-0.1388	0.6107	-0.2036	-0.0066	0.487	-0.0226	0.7978	67.3193	108.7102	9.0032
21	0.7205	1.7109	-0.0566	6.1909	-0.7391	0.9874	0.018	-0.452	0.0071	1.2143	-0.065	-0.2736	-0.0054	0.0307	0.0643	0.3074	0.0678	-0.0659	0.5245	-0.0024	0.3832	59.2601	94.5953	17.8604
22	0.2835	0.0076	0.3224	3.4235	-0.8198	0.5764	-0.159	-0.1817	0.0548	-0.5915	0.2293	-0.4864	0.43	0.3161	0.1261	0.2638	0.0874	-0.023	0.5897	0.1089	0.4096	60.1506	82.6925	11.8279
23	2.8968	-1.0599	0.506	1.6075	0.7281	2.5324	-0.1666	0.0808	-0.683	-0.3573	0.2407	0.3488	0.4428	0.0151	-0.1605	0.5358	-0.0251	0.0412	0.3194	0.0269	0.4058	35.6843	68.4409	21.3428
24	3.1947	-3.3952	0.482	5.5645	0.6094	0.7939	-0.434	-0.827	-0.1648	0.0259	0.7027	0.2206	-0.2078	0.1686	0.0433	0.3717	0.0054	0.1016	0.3766	0.0735	0.2495	32.9355	85.208	26.3936
25	4.6532	-1.0052	-2.5038	4.9455	-1.5201	2.2447	-0.5635	-0.9157	-0.1688	0.294	0.7282	-0.2767	-0.1703	-1.3193	-0.0052	0.2703	0.0626	-0.0606	0.8002	0.0207	0.3186	18.358	96.843	23.7279
26	1.6068	-0.7601	0.9423	1.2179	-0.3944	0.5622	-0.2845	0.2418	-0.0097	0.1492	0.1991	0.1188	-0.3184	-0.5476	-0.048	0.2541	-0.0002	0.0487	0.4772	0.0465	0.1984	29.3231	97.5309	18.9306
27	0.9922	0.6083	-0.8689	3.4427	-0.9444	4.3148	-0.1513	-0.1437	0.1501	0.0008	-0.2614	-0.5238	-0.0936	0.9181	-1.4756	0.0172	0.0012	0.0248	0.3182	-0.0676	0.4609	40.4434	94.7753	20.7828
28	1.4505	-0.7409	3.5847	6.5423	-2.484	8.9277	-0.6904	0.5189	0.4384	-0.5658	-0.0602	-1.0125	0.6017	0.4569	-0.0325	0.5009	0.0246	-0.0024	0.3353	-0.0019	0.304	37.398	92.8994	11.0128
29	1.4092	-0.4084	0.1462	4.5557	0.223	0.5417	-0.0288	0.2258	-0.2106	-0.3165	0.5739	-0.0451	-0.291	-0.0188	0.0341	0.2908	0.0288	0.0619	0.3195	0.0657	0.1843	29.4864	102.8808	13.6992
30	1.9324	0.8505	-0.2498	0.4752	-0.4514	1.6598	-0.0272	-0.3764	1.9649	0.8797	0.1767	-0.1678	-1.1065	-0.3065	-0.1638	0.9312	0.1109	-0.0555	0.8985	-0.2366	0.9549	35.2114	123.7005	14.6502
31	2.1519	0.1407	0.2722	0.4277	-0.6906	1.6744	-0.1299	-0.0455	-0.2432	0.3825	-0.1658	0.5013	0.7047	-0.707	0.0876	0.6137	-0.1682	0.0251	0.4085	0.0695	0.2967	22.6424	80.6206	22.7109
32	6.2435	-2.1733	-0.097	1.9767	0.2368	2.2534	0.0371	0.6828	-0.0967	-0.126	-0.1759	-0.0858	0.7491	-0.1372	-0.064	0.3998	-0.0383	0.0227	0.2552	-0.0107	0.2417	38.4818	80.2396	14.6818
33	1.4887	-0.0184	0.8711	0.857	-0.8686	1.4152	-0.5377	0.0305	-0.0842	0.4238	0.4211	-0.0727	0.6129	0.3164	0.4663	0.6176	0.23	0.0794	0.411	0.1024	0.3783	45.5591	76.7593	26.4415
34	2.5227	1.2291	-0.7986	5.7478	-0.4734	3.5905	-0.1094	-0.1105	0.7131	-0.0346	0.4047	0.9499	-0.6243	-0.8444	0.1715	0.6343	0.1673	0.0534	0.438	-0.1281	0.4322	23.8723	118.744	9.7664
35	0.6128	-0.1381	1.1448	3.6614	1.2318	2.67	0.1526	0.0593	-0.1451	-1.013	-0.1041	0.5094	-0.4714	-0.0355	-0.0429	0.3791	-0.0038	-0.0705	0.5365	-0.04	0.2981	23.1304	96.4902	-5.8569
36	0.7089	0.2599	-0.3197	2.8843	-0.9932	0.4189	-0.3863	1.0623	-0.6338	-0.7662	-0.798	1.1109	0.6323	-0.7022	-0.3702	0.5774	-0.0811	-0.1314	0.7442	-0.1461	0.4529	23.1323	83.4224	-11.3389
37	0.3608	0.3165	0.4409	1.7015	0.4521	1.5154	0.3189	0.1339	0.2354	0.0887	-0.1001	0.014	-0.0633	-0.406	0.0857	0.2705	0.1356	0.0648	0.1507	-0.0331	0.344	34.5082	105.5658	2.8024
38	3.3925	-1.4871	1.2006	1.905	-1.7073	1.5448	-0.0447	0.1901	-0.0379	-0.2884	-0.5725	0.0996	0.0903	-0.1446	-1.232	0.3844	0.1977	0.1607	0.196	-0.0274	0.4055	44.4056	108.0556	-2.3793
39	8.417	-0.3713	5.3455	3.5193	1.4898	4.64	-0.0941	1.6713	0.2386	-1.7656	0.0061	-1.8701	-0.021	0.7368	-0.0942	0.8899	-0.0271	0.2428	0.4045	0.0224	0.6848	45.8173	100.6839	-2.483
40	5.2534	3.0474	-0.8701	8.2671	-2.971	3.9294	-0.5575	0.0634	-0.318	-0.6619	-0.43	-0.6717	-0.0415	-0.3308	-0.0674	0.718	0.0478	0.0351	0.9284	-0.0684	0.3297	19.8753	95.7554	-19.6522
41	0.1581	0.0124	0.4822	0.187	-0.262	2.6944	0.0492	0.2937	0.3982	-0.596	-0.3104	0.1734	-0.151	-0.4767	-0.1753	0.5058	0.1949	0.0398	0.2683	0.0397	0.4099	27.9587	110.7331	-1.4715
42	1.8315	0.2929	0.0292	3.8489	0.9043	1.0015	-0.4867	0.3802	-0.1609	-0.209	0.788	-0.5165	0.0608	-0.2748	0.0795	0.3102	-0.0192	0.0055	0.3891	-0.0836	0.2206	31.9735	90.8442	-7.4967
43	3.7	-0.3228	0.9639	1.2985	1.1617	3.5934	0.3701	-0.063	-0.3029	0.2822	0.0438	0.3122	0.9118	-0.0093	-0.0048	0.2943	0.0142	0.0093	0.2873	-0.0529	0.2934	32.7693	86.1628	3.6712
44	2.6838	-0.0151	2.5712	2.5007	1.3182	3.3317	0.3149	0.5831	-0.8711	0.0572	-0.0064	0.2224	0.9912	0.5204	1.3979	0.9481	0.1605	0.407	0.4517	-0.2974	0.892	57.6242	63.0571	-13.7248
45	5.5663	0.3944	-3.7075	0.5398	-0.4968	4.2442	0.0723	-0.4527	-1.0877	0.3627	-0.4772	-0.8961	0.0978	0.7302	-0.01	0.8415	0.1199	0.1075	0.3866	0.0137	0.7184	53.5158	64.8841	-1.2892
46	2.4293	1.5295	0.8524	3.7958	-0.1664	2.1084	-0.354	-0.1698	0.1349	0.2304	-0.6919	0.4896	0.3196	-0.3969	-0.0593	0.6964	0.2591	0.1187	0.7515	-0.1305	0.4723	44.5082	65.107	0.5924
47	3.0682	1.1102	1.2754	1.7004	0.9632	0.7277	-0.6236	1.4804	-0.3494	-1.1767	0.5617	-0.4066	-0.0341	0.1621	0.0674	0.7286	0.1318	0.1977	0.6901	-0.0588	0.4571	58.5252	79.9926	-13.7023
48	2.0056	0.2033	0.9123	0.9491	-0.1884	2.4772	-0.0175	0.3023	0.5773	-0.3284	-0.5894	-0.482	0.0676	0.0072	-1.0287	0.7449	0.3208	0.3367	0.7785	0.1646	0.8064	73.7419	88.6878	-12.0699
49	0.701	1.3269	0.6627	2.5085	1.2537	0.6284	-0.446	0.4596	-0.3888	-0.5671	0.0953	0.1608	0.4026	0.8624	-0.5278	0.4183	0.1343	0.1877	0.6297	-0.0101	0.5837	63.4262	92.4151	-8.8487
50	4.1632	0.1219	0.6444	3.9034	-0.309	5.9519	-0.092	0.8046	0.4662	-0.1242	-0.1962	0.9479	-0.0984	-0.3505	-0.0118	0.5298	0.0273	0.153	0.3338	0.0676	0.4475	53.3624	90.7091	-6.3182
51	0.169	0.7411	0.014	3.8293	-0.5898	0.7442	-0.2056	0.0837	0.2192	0.178	0.0646	-0.5961	-1.081	0.7053	0.0951	0.444	-0.1324	0.0519	0.4813	0.0158	0.5598	64.4944	98.2274	-4.529
52	1.2659	-0.3064	-0.8812	0.2288	0.4152	2.0434	-0.2496	0.8638	0.8072	0.0566	-0.5894	-0.69	-0.2212	-0.506	-0.0268	0.9118	-0.0643	0.1669	0.7331	0.2252	1.0727	61.1728	117.7313	-8.5479
53	3.4174	-3.0345	5.3244	2.861	-4.8996	8.4705	0.2744	-0.5404	0.8392	-0.3062	-0.3124	0.2085	0.7005	-0.2139	-0.0002	1.2247	0.0453	0.0021	0.5547	-0.0281	0.5649	65.1283	68.2014	1.8873
54	0.9763	0.4309	1.1308	1.1218	0.4432	1.3011	0.2344	0.5689	0.0267	-0.4986	0.1849	-0.5605	-0.1559	0.6618	1.9792	0.5616	0.3954	0.4591	0.8205	0.0411	0.7498	68.3065	76.3388	-13.9303
55	3.758	0.933	-0.0722	1.2539	-0.3542	1.4031	0.0835	-0.7253	0.0035	-0.3242	-0.2289	-0.3059	0.2024	0.2017	-0.0341	0.486	0.1198	0.09	0.401	-0.058	0.3911	51.8775	77.5863	-1.1694
56	6.3441	0.7996	-4.6624	0.1644	-0.5663	3.5558	0.3553	0.5399	-0.697	-0.4898	-0.1729	0.0433	-0.2132	0.1933	0.0616	0.6005	0.0931	0.0063	0.2998	-0.1686	0.5699	37.0605	66.6074	-1.5037
57	2.7472	-2.3492	-1.1366	2.6616	1.1696	0.5303	0.0307	-0.1226	0.4746	-0.9739	-0.1708	-0.0027	-0.1516	-0.5086	-0.1293	0.512	-0.0933	-0.0631	0.2559	-0.1096	0.2027	42.1947	77.0195	-8.8871
58	1.8167	-0.1976	1.0604	7.1874	1.8696	1.1581	-0.4196	1.0392	-0.0854	-1.1874	0.3928	-0.6884	-0.438	0.1858	0.0889	0.8271	0.0147	0.073	0.4956	-0.1478	0.3862	48.128	72.3466	-17.8824

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'I' and (resid -73 through -54 )
2	X-RAY DIFFRACTION	2	chain 'I' and (resid -53 through -44 )
3	X-RAY DIFFRACTION	3	chain 'I' and (resid -43 through -14 )
4	X-RAY DIFFRACTION	4	chain 'I' and (resid -13 through 16 )
5	X-RAY DIFFRACTION	5	chain 'I' and (resid 17 through 36 )
6	X-RAY DIFFRACTION	6	chain 'I' and (resid 37 through 46 )
7	X-RAY DIFFRACTION	7	chain 'I' and (resid 47 through 73 )
8	X-RAY DIFFRACTION	8	chain 'J' and (resid -73 through -54 )
9	X-RAY DIFFRACTION	9	chain 'J' and (resid -53 through -34 )
10	X-RAY DIFFRACTION	10	chain 'J' and (resid -33 through -14 )
11	X-RAY DIFFRACTION	11	chain 'J' and (resid -13 through 16 )
12	X-RAY DIFFRACTION	12	chain 'J' and (resid 17 through 26 )
13	X-RAY DIFFRACTION	13	chain 'J' and (resid 27 through 46 )
14	X-RAY DIFFRACTION	14	chain 'J' and (resid 47 through 56 )
15	X-RAY DIFFRACTION	15	chain 'J' and (resid 57 through 73 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 39 through 56 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 57 through 77 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 78 through 120 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 121 through 134 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 25 through 49 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 50 through 75 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 76 through 102 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 15 through 44 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 45 through 72 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 73 through 79 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 80 through 89 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 90 through 96 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 97 through 101 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 102 through 111 )
30	X-RAY DIFFRACTION	30	chain 'C' and (resid 112 through 120 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 28 through 52 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 53 through 81 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 82 through 121 )
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 39 through 56 )
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 57 through 78 )
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 79 through 85 )
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 86 through 120 )
38	X-RAY DIFFRACTION	38	chain 'E' and (resid 121 through 130 )
39	X-RAY DIFFRACTION	39	chain 'E' and (resid 131 through 135 )
40	X-RAY DIFFRACTION	40	chain 'F' and (resid 19 through 24 )
41	X-RAY DIFFRACTION	41	chain 'F' and (resid 25 through 49 )
42	X-RAY DIFFRACTION	42	chain 'F' and (resid 50 through 82 )
43	X-RAY DIFFRACTION	43	chain 'F' and (resid 83 through 102 )
44	X-RAY DIFFRACTION	44	chain 'G' and (resid 14 through 26 )
45	X-RAY DIFFRACTION	45	chain 'G' and (resid 27 through 36 )
46	X-RAY DIFFRACTION	46	chain 'G' and (resid 37 through 46 )
47	X-RAY DIFFRACTION	47	chain 'G' and (resid 47 through 72 )
48	X-RAY DIFFRACTION	48	chain 'G' and (resid 73 through 80 )
49	X-RAY DIFFRACTION	49	chain 'G' and (resid 81 through 89 )
50	X-RAY DIFFRACTION	50	chain 'G' and (resid 90 through 101 )
51	X-RAY DIFFRACTION	51	chain 'G' and (resid 102 through 111 )
52	X-RAY DIFFRACTION	52	chain 'G' and (resid 112 through 119 )
53	X-RAY DIFFRACTION	53	chain 'H' and (resid 29 through 34 )
54	X-RAY DIFFRACTION	54	chain 'H' and (resid 35 through 52 )
55	X-RAY DIFFRACTION	55	chain 'H' and (resid 53 through 81 )
56	X-RAY DIFFRACTION	56	chain 'H' and (resid 82 through 87 )
57	X-RAY DIFFRACTION	57	chain 'H' and (resid 88 through 100 )
58	X-RAY DIFFRACTION	58	chain 'H' and (resid 101 through 121 )

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DNA chain , 2 types, 2 molecules IJ

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Protein , 4 types, 8 molecules AEBFCGDH

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

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Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

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DNA chain , 2 types, 2 molecules IJ

-
Protein , 4 types, 8 molecules AEBFCGDH

-
Non-polymers , 3 types, 111 molecules

-
Details

-
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

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Yorodumi