PDB-5t2f: Structure of the FHA1 domain of Rad53 bound to the BRCT domain of Dbf4

ID or keywords:

Entry

Database: PDB / ID: 5t2f

Title

Structure of the FHA1 domain of Rad53 bound to the BRCT domain of Dbf4

Components

DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein

Keywords

CELL CYCLE / FHA / BRCT / protein chimera

Function / homology

Function and homology information

positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / positive regulation of DNA replication initiation / negative regulation of exit from mitosis / Dbf4-dependent protein kinase complex / deoxyribonucleoside triphosphate biosynthetic process / positive regulation of meiosis I / positive regulation of nuclear cell cycle DNA replication / meiotic recombination checkpoint signaling / regulation of cell cycle phase transition ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.66 Å

Authors

Guarne, A. / Almawi, A.W. / Matthews, L.A.

Funding support

Canada, 1items

Citation

Journal: Sci Rep / Year: 2016
Title: 'AND' logic gates at work: Crystal structure of Rad53 bound to Dbf4 and Cdc7.
Authors: Almawi, A.W. / Matthews, L.A. / Myrox, P. / Boulton, S. / Lai, C. / Moraes, T. / Melacini, G. / Ghirlando, R. / Duncker, B.P. / Guarne, A.

History

Deposition	Aug 23, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 22, 2017	Group: Structure summary
Revision 1.2	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5t2f.cif.gz	554.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5t2f.ent.gz	467.1 KB	Display	PDB format
PDBx/mmJSON format	5t2f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5t2f_validation.pdf.gz	460.4 KB	Display	wwPDB validaton report
Full document	5t2f_full_validation.pdf.gz	460.6 KB	Display
Data in XML	5t2f_validation.xml.gz	35.1 KB	Display
Data in CIF	5t2f_validation.cif.gz	48.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t2/5t2f ftp://data.pdbj.org/pub/pdb/validation_reports/t2/5t2f	HTTPS FTP

-
Related structure data

Related structure data	5t2sC 1g6gS 3qbzS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1l0s-5 6z30-d 6q9m-1 5t69-d 1gqb-d 2ppt-d 3ps8-1 6hkw-2 6hkw-5 4yyx-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) 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

Related structure data

5t2sC

1g6gS

3qbzS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#168 - Dec 2013 DNA Helicase similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (2) #55 - Jul 2004 DNA Ligase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1)

Deposited unit

A: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein

B: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein

C: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein

D: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein

hetero molecules

125 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein

hetero molecules

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

2

B: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein

hetero molecules

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

3

C: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein

hetero molecules

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

4

D: DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	57.775, 66.527, 86.520
Angle α, β, γ (deg.)	109.24, 90.88, 90.30
Int Tables number	1
Space group name H-M	P1

#1: Protein	DDK kinase regulatory subunit DBF4,Serine/threonine-protein kinase RAD53 chimeric protein / Dumbbell forming protein 4 / CHEK2 homolog / Serine-protein kinase 1 Mass: 30930.336 Da / Num. of mol.: 4 Fragment: UNP P32325 residues 105-220 linked to UNP P22216 residues 22-161 via LINKER residues: VDSGASGGS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c Gene: DBF4, DNA52, YDR052C, D4205, YD9609.07C, RAD53, MEC2, SAD1, SPK1, YPL153C, P2588 Plasmid: pET15b Details (production host): includes a 6xHis-SUMO tag removable with TEV protease Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P32325, UniProt: P22216, dual-specificity kinase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.55 Å³/Da / Density % sol: 51.77 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50 mM sodium cacodylate pH 6.5 12% PEG 4000 (v/v) 250 mM MgCl2

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1.1 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2013

Radiation

Monochromator: double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.1 Å / Relative weight: 1

Reflection

Resolution: 2.3→35 Å / Num. obs: 48005 / % possible obs: 87.2 % / Redundancy: 1.6 % / CC_1/2: 0.97 / R_merge(I) obs: 0.043 / Net I/σ(I): 13.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	CC_1/2	Diffraction-ID	% possible all
2.3-2.34	1.4	0.167	3.2	0.925	1	57.3
2.34-2.38	1.4	0.16	3.6	0.935	1	64.6
2.38-2.43	1.5	0.169	3.5	0.931	1	70.4
2.43-2.48	1.5	0.145	4	0.952	1	75.6
2.48-2.53	1.6	0.137	4.3	0.945	1	79.8
2.53-2.59	1.5	0.127	5	0.955	1	81.4
2.59-2.66	1.6	0.115	5.4	0.964	1	87.1
2.66-2.73	1.6	0.11	6.3	0.961	1	88.8
2.73-2.81	1.6	0.096	7	0.972	1	91.5
2.81-2.9	1.7	0.094	7.9	0.976	1	94.8
2.9-3	1.7	0.079	9.7	0.981	1	94.8
3-3.12	1.6	0.073	9.7	0.981	1	95.8
3.12-3.26	1.7	0.062	11.4	0.983	1	95.5
3.26-3.43	1.7	0.053	12.4	0.987	1	95.7
3.43-3.65	1.7	0.044	13.7	0.991	1	95.8
3.65-3.93	1.7	0.039	14.1	0.991	1	95.8
3.93-4.33	1.7	0.036	16.1	0.993	1	95.4
4.33-4.95	1.7	0.032	16.6	0.992	1	94.6
4.95-6.23	1.7	0.03	16.6	0.995	1	95.8
6.23-35					1

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1G6G, 3QBZ

1g6g

3qbz

Resolution: 2.66→34.965 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 25.53 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2373	2258	7.1 %
R_work	0.2059	-	-
obs	0.2081	31802	91.11 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.66→34.965 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7510	0	56	153	7719

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7662
X-RAY DIFFRACTION	f_angle_d	0.728	10324
X-RAY DIFFRACTION	f_dihedral_angle_d	13.526	2756
X-RAY DIFFRACTION	f_chiral_restr	0.026	1202
X-RAY DIFFRACTION	f_plane_restr	0.002	1302

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 (%)
2.66-2.7178	0.2761	134	0.2626	1752	X-RAY DIFFRACTION	88
2.7178-2.781	0.3598	140	0.2526	1797	X-RAY DIFFRACTION	88
2.781-2.8505	0.312	147	0.2602	1828	X-RAY DIFFRACTION	91
2.8505-2.9276	0.2678	134	0.2593	1836	X-RAY DIFFRACTION	90
2.9276-3.0137	0.2751	154	0.2339	1842	X-RAY DIFFRACTION	90
3.0137-3.1109	0.2743	144	0.2416	1817	X-RAY DIFFRACTION	91
3.1109-3.222	0.2552	127	0.238	1869	X-RAY DIFFRACTION	91
3.222-3.3509	0.2591	152	0.2254	1843	X-RAY DIFFRACTION	92
3.3509-3.5033	0.2973	137	0.2238	1875	X-RAY DIFFRACTION	92
3.5033-3.6878	0.2115	147	0.211	1880	X-RAY DIFFRACTION	93
3.6878-3.9186	0.2517	148	0.1988	1910	X-RAY DIFFRACTION	93
3.9186-4.2206	0.2323	128	0.1842	1840	X-RAY DIFFRACTION	91
4.2206-4.6445	0.1628	142	0.155	1874	X-RAY DIFFRACTION	92
4.6445-5.3146	0.1966	133	0.1748	1901	X-RAY DIFFRACTION	93
5.3146-6.6881	0.2523	140	0.2145	1871	X-RAY DIFFRACTION	92
6.6881-34.9679	0.1983	151	0.1822	1809	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	0.1064	0.0859	0.0523	0.079	-0.0835	0.0888	0.0139	0.1923	0.2663	0.0827	0.1664	-0.0148	0.0029	0.1273	0	0.3694	-0.029	0.0619	0.3763	-0.0178	0.2375	20.0859	-12.4677	26.8233
2	-0.0014	0.006	0.0086	0.1189	-0.0253	0.057	0.2171	-0.0417	0.1134	-0.1856	0.0511	-0.2703	-0.0189	-0.3892	0	0.3318	0.0221	-0.1672	0.4181	0.0084	0.3964	1.0519	-27.9561	25.3805
3	0.0089	0.016	0.0259	0.0071	0.0098	0.0461	0.0547	0.097	-0.0287	-0.2003	0.0597	0.0586	-0.1767	-0.2469	-0	-0.7948	0.0206	-1.0698	0.766	0.1617	-0.6608	0.0666	-21.0372	17.5587
4	0.099	0.1673	0.0653	0.1116	-0.0756	0.1041	-0.1417	0.0997	-0.0856	-0.0665	0.0757	0.0505	0.1001	-0.1119	0	0.3179	-0.0636	-0.0141	0.3325	-0.0407	0.2655	4.5416	-29.4758	29.7281
5	0.0365	0.0567	0.113	-0.0095	0.0844	0.1932	-0.0329	-0.1085	0.231	0.2584	0.0587	0.0649	-0.0373	-0.0997	0	0.2222	-0.0004	-0.0156	0.2414	0.0433	0.3232	7.6626	-21.7724	29.6128
6	0.0002	-0.0196	-0.0297	0.0045	-0.0189	-0.0032	-0.1702	0.1335	-0.0873	-0.1156	-0.0305	0.0827	-0.1478	0.1228	-0	0.8951	0.1304	-0.3426	0.5292	-0.0294	0.1869	8.7191	9.7835	16.0261
7	-0.0176	0.0071	-0.0218	0.011	0.0236	0.0136	-0.0996	0.0833	-0.3883	-0.2131	-0.2641	-0.0189	-0.1382	-0.0786	-0	0.8328	0.0679	-0.3611	0.4633	-0.1333	0.6481	5.2435	5.6311	19.2699
8	-0.0052	-0.0215	-0.0013	-0.0078	-0.0022	0.0034	-0.1388	0.0748	-0.0258	-0.0394	0.0078	-0.025	-0.0532	-0.0577	-0	1.6955	0.38	-0.1419	0.8882	0.2267	0.1685	1.8699	24.458	6.2791
9	-0.0086	-0.0009	0.0097	-0.0001	-0.0018	0.0031	0.2031	0.1255	0.14	-0.0675	-0.1353	0.1224	-0.0323	-0.1545	-0	0.8247	0.5296	-1.1847	0.2437	0.2962	-0.7737	-0.6922	17.3493	15.3723
10	0.0022	0.0003	0.001	0.0078	0.0069	-0.0107	-0.0048	-0.0201	-0.0568	0.0702	-0.1883	0.1169	-0.0525	0.0121	-0	0.3754	-0.3882	-1.1994	-0.0676	-0.7572	0.7072	-5.8756	6.4861	20.3875
11	-0.0013	-0.0031	-0.006	-0.0018	-0.0013	0.002	-0.2939	-0.1192	0.0348	0.0109	-0.1104	0.0765	-0.0232	0.1494	0	0.5439	0.0949	-0.1821	0.4982	-0.0861	1.0822	-8.6062	7.6582	27.6223
12	0.0019	0.015	-0.0029	-0.0154	-0.0067	-0.0013	0.262	0.3282	0.2448	-0.2937	-0.0108	-0.1556	-0.2864	0.1757	0	0.7069	0.4029	-0.6475	0.276	0.1401	0.217	2.2736	20.8796	17.9193
13	0.0179	-0.0011	0.054	0.0247	0.0341	0.0324	0.0558	0.0937	0.059	-0.0818	-0.3364	0.3806	-0.2248	-0.0735	0	0.4492	-0.2225	-0.368	-0.2223	-0.2488	0.5448	-1.7194	17.7285	28.1055
14	0.0072	-0.0086	0.023	0.0043	0.0197	-0.0135	0.1255	-0.0845	0.0139	-0.0577	-0.137	0.0797	-0.2165	-0.0828	0	0.4062	0.0513	-0.1045	0.3976	-0.0314	0.4383	-0.9579	20.8618	32.4185
15	0.0198	-0.0228	-0.0219	-0.0018	0.0053	-0.0069	0.206	0.133	-0.3172	-0.0921	-0.0258	0.0095	-0.2914	0.061	-0	0.5825	-0.0098	-0.2003	0.5398	-0.0359	0.4776	6.613	17.2801	27.2937
16	-0.0025	0.0032	-0.001	0.0064	0.0023	0.0004	0.0467	0.0155	0.0055	-0.0329	0.0432	0.0093	-0.0232	0.0431	0	0.8681	0.069	-0.2162	0.5942	-0.0451	1.1195	-1.8612	4.8723	36.6499
17	-0.0031	0.0022	-0.0138	0.0043	-0.0066	-0.0049	0.0878	-0.0038	-0.0068	-0.0354	-0.0588	-0.019	-0.0238	-0.1126	-0	0.9614	0.438	-0.2252	0.2781	-0.2061	0.5671	8.4451	10.3372	25.1
18	0.0002	0.001	-0.0006	0.0112	-0.0064	0.0033	-0.0237	0.0753	0.024	0.0196	-0.0423	0.0031	0.0029	0.0257	0.0001	1.4912	0.3056	-0.1563	0.9945	-0.1146	0.7698	14.5246	19.3045	11.2042
19	0.1248	0.007	-0.0755	0.0677	-0.1708	0.2515	-0.0685	-0.0431	-0.0628	0.138	0.0258	0.0165	0.0612	0.0876	0	0.2181	0.0247	-0.0548	0.3253	-0.0169	0.2272	-9.4535	5.6242	-5.3048
20	0.0026	0.0054	0.0107	0.0003	-0.0104	-0.0027	0.1684	-0.0164	0.0024	-0.034	0.187	0.0721	0.0865	-0.3665	0	0.2329	0.0006	-0.0505	0.4028	0.0058	0.47	-36.3652	16.6705	-6.125
21	0.0315	0.0376	-0.0531	-0.0085	-0.0335	0.0067	-0.2624	-0.2236	-0.1077	0.2367	-0.0592	0.2834	0.1558	-0.7256	-0	0.0994	-0.0385	0.3599	0.745	0.0782	-0.0138	-28.3165	9.8703	2.5117
22	0.0096	-0.0037	0.0103	-0.0082	-0.0365	0.0111	-0.0809	-0.1162	0.2502	0.313	0.1655	-0.0551	-0.3405	0.1968	-0	0.2905	-0.0206	-0.0035	0.2974	0.0226	0.3456	-16.6432	20.837	-1.991
23	0.0436	-0.0078	-0.0264	0.0019	-0.0369	0.0692	-0.0209	-0.1581	0.1411	-0.0311	0.0446	0.1775	-0.0234	-0.1692	-0	0.1844	0.0184	0.019	0.2626	-0.004	0.2578	-27.9371	18.2338	-14.0154
24	0.0165	-0.0031	-0.0076	0	0.0079	0.0192	0.0258	-0.0247	-0.1025	-0.2359	0.4079	-0.0202	-0.1334	0.0729	-0	0.2492	0.0326	0.071	0.2454	0.0019	0.2865	-19.8926	21.532	-15.2191
25	0.0139	-0.0139	-0.0081	0.0368	0.0133	0.02	0.2263	0.2059	-0.1822	0.0226	-0.1888	0.0171	0.2254	-0.0343	0	0.1325	-0.0582	0.0165	0.2142	0.0501	0.3324	-19.9526	5.9608	-5.2923
26	0.0679	0.0334	0.0126	0.0187	0.0095	0.0104	-0.0337	-0.2481	0.5178	0.4258	-0.0484	0.183	0.0139	-0.254	-0	0.5824	-0.0207	0.144	0.4589	-0.0786	0.4119	-20.2214	-20.4863	6.1412
27	0.103	0.0666	0.0646	0.0378	0.0985	0.0278	-0.0122	-0.2885	0.0297	0.2208	-0.3208	0.6545	0.0571	-0.7122	0	0.3823	-0.0071	0.2058	0.3737	-0.0472	0.6219	-31.0042	-23.3339	1.1628
28	0.0422	-0.0183	-0.0616	0.0648	0.0092	0.0509	0.3129	-0.1495	0.3642	-0.06	-0.2694	0.2452	0.2621	0.0293	0	0.3165	-0.0259	0.1328	0.3333	-0.0381	0.428	-25.0726	-29.3828	-6.7534
29	0.1049	-0.0246	-0.146	0.0742	0.11	0.0846	-0.158	-0.1261	0.1041	0.0512	0.0471	0.1239	0.1338	-0.1405	0	0.3957	0.0385	0.0286	0.4455	0.0013	0.4878	-19.024	-22.8914	-1.6786
30	0.02	0.0439	0.0453	0.0569	0.0864	0.0494	-0.1725	-0.2393	0.1227	-0.1708	0.1422	0.0763	-0.0391	-0.0507	-0	0.3775	0.0013	0.0126	0.2897	-0.0166	0.5794	-9.4235	-15.1084	-4.1034
31	0.0053	0.0068	-0.0071	0.018	-0.0074	0.0072	-0.1599	-0.3043	-0.221	0.2986	0.1377	-0.1557	0.0058	0.0503	0	0.4907	0.0426	0.1096	0.3372	0.1248	0.508	-4.3962	-31.2119	-12.6234
32	-0.0094	-0.0007	0.0017	-0.0086	-0.0169	0.0003	0.0095	0.2149	-0.0282	-0.149	0.0332	0.0025	-0.1487	-0.0341	-0	0.5147	-0.0537	0.0841	0.5445	0.034	0.4316	-6.0486	-30.758	-31.7905
33	0.026	0.001	0.0074	0.0376	-0.0293	0.0138	-0.233	0.1007	0.4467	-0.2201	0.1497	-0.2702	-0.1243	-0.0863	0	0.2803	-0.188	0.4714	0.376	0.0669	0.6946	1.2962	-24.465	-23.0734
34	0.0166	-0.0177	0.019	0.0104	0.0188	0.0048	-0.171	-0.1874	-0.0469	0.2732	-0.2357	-0.1536	0.5652	0.1543	-0	0.5492	0.0289	0.1604	0.3131	0.0084	0.5276	-3.6865	-34.2048	-12.2826
35	0.0185	-0.0112	0.0236	0.0156	-0.012	0.0271	0.1586	0.1715	0.1207	-0.4262	0.0339	0.0617	0.0809	0.0204	0	0.4529	0.0182	0.08	0.3375	0.0701	0.416	-15.0722	-31.8044	-25.0062
36	0.0211	-0.0441	0.1107	0.0537	0.0094	0.0155	-0.0229	0.0575	0.2006	-0.0893	-0.002	0.3146	0.0735	0.0306	0	0.3544	-0.0264	0.1139	0.1906	0.0621	0.4008	-11.3722	-25.652	-16.9927
37	0.0065	0.0037	-0.0019	0.0026	0.0054	-0.0011	0.0149	-0.0012	-0.0103	-0.0713	-0.0059	-0.0724	-0.0286	0.0231	0	0.5694	-0.0278	-0.0797	0.5457	0.0718	1.1061	3.4746	-13.8584	-14.65
38	0.0244	-0.0458	-0.0341	0.081	-0.0015	0.102	-0.1028	-0.1292	-0.275	-0.3852	-0.025	-0.1464	0.0983	0.137	-0	0.2782	0.0401	-0.004	0.3313	-0.0433	0.311	1.1471	4.4008	-16.1555
39	0.0095	0.0514	-0.0327	-0.0171	0.0222	-0.0474	0.072	0.3014	0.24	-0.1429	-0.1574	-0.1728	-0.3713	0.3678	-0	-2.1963	-0.7645	1.8343	0.1893	0.3873	-0.9417	9.4443	17.9966	-20.8717
40	0.0146	-0.0447	0.0258	0.0175	0.0259	0.0187	0.0828	0.2119	-0.0348	0.0105	-0.0434	-0.1251	0.0318	-0.0074	-0	0.2056	0.005	0.0159	0.3677	-0.0223	0.2378	-4.076	3.7529	-30.9373
41	0.0931	-0.0729	-0.0988	0.0946	0.0097	0.0287	-0.1316	0.0713	0.4875	-0.2845	0.0755	-0.0133	-0.4937	-0.0512	-0	0.1783	0.0541	0.0046	0.2089	0.0066	0.2217	-6.8602	16.9718	-23.7243
42	-0.0096	-0.0151	0.0147	-0.0098	0.0166	0.0176	-0.2241	-0.096	0.0821	0.3113	0.1661	0.0296	-0.0183	-0.2825	-0	0.1958	-0.0092	-0.0036	0.3043	-0.0319	0.2626	-9.2835	11.541	-16.326
43	0.0396	0.0173	-0.0658	-0.0109	-0.0017	0.0324	-0.1298	-0.0034	0.1408	-0.0472	0.0133	0.1359	0.0486	-0.2111	-0	0.1583	-0.0349	0.0162	0.297	0.0218	0.3815	-10.5785	5.2113	-20.1445
44	-0.0016	-0.0027	0.0204	0.0033	-0.0097	0.0047	0.1593	-0.1744	0.046	0.2087	0.2699	-0.0162	-0.276	-0.1163	-0	0.477	-0.0421	0.1319	0.8414	-0.2256	0.17	8.2309	19.6473	-7.729
45	0.0508	-0.0901	-0.0582	0.0775	0.0671	0.0744	-0.2143	0.4223	-0.0139	0.0994	0.1594	0.4213	-0.0144	0.2363	0	0.668	-0.0076	-0.0066	0.2463	-0.0285	0.4739	17.5833	4.9792	24.6732
46	0.0013	-0.0196	0.0105	0.0089	0.0004	0.0001	-0.1512	0.1327	0.1758	-0.243	0.122	0.0065	0.0387	0.0032	-0	0.5742	-0.0468	0.0139	0.2894	0.1064	0.4192	22.6489	20.9889	34.1816
47	0.0103	0.0211	-0.0134	0.0266	0.0072	0.0108	-0.1524	-0.247	-0.3891	0.076	0.1399	-0.3285	0.075	-0.1206	-0	0.5024	0.0795	-0.1488	0.3581	0.0385	0.5508	26.7176	15.6631	45.9982
48	-0.0002	-0.0024	-0.0103	0.0003	0.0198	0.01	-0.2383	0.1757	0.1773	-0.3397	-0.049	-0.1977	-0.1558	-0.2633	-0	0.5864	-0.0927	-0.1227	0.4016	0.0132	0.4758	23.2939	23.7768	33.2315
49	0.0137	0.0092	0.0493	0.0034	0.0165	0.0099	0.4845	-0.0394	-0.1165	0.7576	0.0153	-0.205	0.2215	-0.3618	0	0.5691	0.0013	-0.3285	0.3476	0.0853	0.4427	12.0057	21.2006	45.7996
50	0.0044	-0.0019	0.0192	0.0045	0.0065	0.0132	0.1115	0.0156	0.1323	0.1446	-0.0668	0.1632	-0.0118	0.1512	-0	0.4481	-0.0115	-0.1392	0.3556	-0.0155	0.3378	9.9817	24.7476	38.1979
51	-0.0003	-0.003	-0.0067	0.0126	0.0249	0.0477	-0.1235	0.0856	-0.1342	-0.0361	0.0523	0.1238	0.2214	-0.1053	-0	0.6854	0.0498	-0.0901	0.2627	0.0544	0.4495	20.9081	8.4818	37.292
52	0.0027	0.0115	-0.0062	0.039	-0.0164	0.0245	-0.0153	0.1475	0.2275	0.1882	-0.0683	0.0417	-0.0812	0.0159	0	0.2709	-0.0952	0.0259	0.405	-0.0522	0.2118	30.4238	-16.8357	34.5359
53	0.0161	0.0191	0.0282	0.0383	0.0223	0.0433	-0.1014	0.1855	0.0018	0.0579	0.0373	-0.1229	-0.2708	0.2021	-0	0.2808	-0.0648	-0.0187	0.3618	0.0059	0.4017	26.8132	-12.8264	38.6842
54	0.008	-0.0058	-0.0036	-0.0036	-0.0209	0.0008	-0.0145	-0.1788	-0.049	0.1853	0.0898	-0.1632	0.0186	0.1055	0	0.4332	0.155	-0.0674	0.5657	0.0148	0.6024	41.2741	-30.6705	39.7912
55	0.0145	0.0089	0.064	-0.0243	0.179	0.054	-0.0404	-0.2854	0.1161	0.058	0.1047	0.0197	0.0308	0.0674	-0	0.2316	-0.0181	-0.0081	0.3433	-0.0208	0.1643	25.8045	-17.0307	49.4784
56	0.0832	0.1009	0.0695	0.1134	0.04	0.0691	0.1228	-0.1116	-0.3443	0.1553	-0.044	-0.058	0.3453	-0.0775	0	0.2308	-0.0142	-0.0163	0.2768	0.0028	0.1759	20.8607	-26.0483	44.1585
57	0.1279	0.0729	0.1215	0.0962	-0.0241	0.1247	0.0424	-0.0529	-0.0901	0.2324	-0.1353	0.1868	0.0251	-0.0361	0	0.2802	-0.0381	-0.0261	0.3547	0.0446	0.1664	17.8581	-21.101	41.2094
58	-0.0021	-0.0049	-0.0087	0.0039	0.0028	0.0065	0.1187	0.0878	-0.0988	-0.0558	0.0027	0.018	0.1311	-0.0127	-0	0.416	0.0115	0.0193	0.8921	-0.2621	0.519	35.3893	-29.9723	29.0043

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 103 through 122 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 123 through 136 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 139 through 157 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 158 through 189 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 190 through 216 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 238 through 246 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 247 through 259 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 260 through 269 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 270 through 276 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 277 through 286 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 287 through 296 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 297 through 305 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 306 through 319 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 320 through 328 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 329 through 340 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 341 through 348 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 349 through 355 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 356 through 363 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 103 through 128 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 129 through 137 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 138 through 157 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 158 through 171 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 172 through 189 )
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 190 through 199 )
25	X-RAY DIFFRACTION	25	chain 'B' and (resid 200 through 216 )
26	X-RAY DIFFRACTION	26	chain 'B' and (resid 236 through 265 )
27	X-RAY DIFFRACTION	27	chain 'B' and (resid 266 through 301 )
28	X-RAY DIFFRACTION	28	chain 'B' and (resid 302 through 340 )
29	X-RAY DIFFRACTION	29	chain 'B' and (resid 341 through 365 )
30	X-RAY DIFFRACTION	30	chain 'C' and (resid 103 through 122 )
31	X-RAY DIFFRACTION	31	chain 'C' and (resid 123 through 128 )
32	X-RAY DIFFRACTION	32	chain 'C' and (resid 129 through 137 )
33	X-RAY DIFFRACTION	33	chain 'C' and (resid 138 through 157 )
34	X-RAY DIFFRACTION	34	chain 'C' and (resid 158 through 171 )
35	X-RAY DIFFRACTION	35	chain 'C' and (resid 172 through 189 )
36	X-RAY DIFFRACTION	36	chain 'C' and (resid 190 through 214 )
37	X-RAY DIFFRACTION	37	chain 'C' and (resid 215 through 219 )
38	X-RAY DIFFRACTION	38	chain 'C' and (resid 237 through 259 )
39	X-RAY DIFFRACTION	39	chain 'C' and (resid 260 through 276 )
40	X-RAY DIFFRACTION	40	chain 'C' and (resid 277 through 296 )
41	X-RAY DIFFRACTION	41	chain 'C' and (resid 297 through 331 )
42	X-RAY DIFFRACTION	42	chain 'C' and (resid 332 through 340 )
43	X-RAY DIFFRACTION	43	chain 'C' and (resid 341 through 356 )
44	X-RAY DIFFRACTION	44	chain 'C' and (resid 357 through 367 )
45	X-RAY DIFFRACTION	45	chain 'D' and (resid 103 through 122 )
46	X-RAY DIFFRACTION	46	chain 'D' and (resid 123 through 128 )
47	X-RAY DIFFRACTION	47	chain 'D' and (resid 129 through 157 )
48	X-RAY DIFFRACTION	48	chain 'D' and (resid 158 through 171 )
49	X-RAY DIFFRACTION	49	chain 'D' and (resid 172 through 189 )
50	X-RAY DIFFRACTION	50	chain 'D' and (resid 190 through 199 )
51	X-RAY DIFFRACTION	51	chain 'D' and (resid 200 through 218 )
52	X-RAY DIFFRACTION	52	chain 'D' and (resid 237 through 246 )
53	X-RAY DIFFRACTION	53	chain 'D' and (resid 247 through 259 )
54	X-RAY DIFFRACTION	54	chain 'D' and (resid 260 through 269 )
55	X-RAY DIFFRACTION	55	chain 'D' and (resid 270 through 296 )
56	X-RAY DIFFRACTION	56	chain 'D' and (resid 297 through 324 )
57	X-RAY DIFFRACTION	57	chain 'D' and (resid 325 through 356 )
58	X-RAY DIFFRACTION	58	chain 'D' and (resid 357 through 367 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
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

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
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