PDB-6qfd: The complex structure of hsRosR-S4 (vng0258/RosR-S4)

ID or keywords:

Entry

Database: PDB / ID: 6qfd

Title

The complex structure of hsRosR-S4 (vng0258/RosR-S4)

Components

(DNA (28-MER)) x 2
DNA-binding protein

Keywords

DNA BINDING PROTEIN / Halophiles / wHTH DNA binding protein / RosR / High salt medium / Protein-DNA interactions

Function / homology

Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / metal ion binding / : / DNA / DNA (> 10) / PadR family transcription regulator RosR

Function and homology information

Biological species

Halobacterium salinarum NRC-1 (Halophile)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.133 Å

Authors

Shaanan, B. / Kutnowski, N.

Funding support

Israel, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2019
Title: Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR.
Authors: Kutnowski, N. / Shmulevich, F. / Davidov, G. / Shahar, A. / Bar-Zvi, D. / Eichler, J. / Zarivach, R. / Shaanan, B.

History

Deposition	Jan 10, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 10, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jul 24, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Oct 23, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 24, 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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6qfd.cif.gz	440.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6qfd.ent.gz	362.9 KB	Display	PDB format
PDBx/mmJSON format	6qfd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6qfd_validation.pdf.gz	485.3 KB	Display	wwPDB validaton report
Full document	6qfd_full_validation.pdf.gz	491.5 KB	Display
Data in XML	6qfd_validation.xml.gz	22.3 KB	Display
Data in CIF	6qfd_validation.cif.gz	31.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qf/6qfd ftp://data.pdbj.org/pub/pdb/validation_reports/qf/6qfd	HTTPS FTP

-
Related structure data

Related structure data	6qh0C 6qilC 6quaC 4fx4S 6fdhS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6qh0-1 6qh0-2 6qil-2 6qua-1 6qua-2 5szi-d 6qil-1 4aby-4 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: DNA-binding protein

B: DNA-binding protein

C: DNA-binding protein

D: DNA-binding protein

E: DNA (28-MER)

F: DNA (28-MER)

G: DNA (28-MER)

H: DNA (28-MER)

hetero molecules

90.2 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DNA-binding protein

B: DNA-binding protein

E: DNA (28-MER)

F: DNA (28-MER)

hetero molecules

defined by author
Evidence: SAXS, SAXS results indicating that one protein dimer bound a single sequence., gel filtration, The elution volume of the complex indicated that hsRosR binds one DNA molecule as a dimer., ...Evidence: SAXS, SAXS results indicating that one protein dimer bound a single sequence., gel filtration, The elution volume of the complex indicated that hsRosR binds one DNA molecule as a dimer., isothermal titration calorimetry, The binding stoichiometry was approximately one, indicating that one protein dimer bound a single sequence.
45.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: DNA-binding protein

D: DNA-binding protein

G: DNA (28-MER)

H: DNA (28-MER)

hetero molecules

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

Unit cell

Length a, b, c (Å)	46.805, 83.995, 88.876
Angle α, β, γ (deg.)	81.530, 86.180, 74.480
Int Tables number	1
Space group name H-M	P1

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	DNA-binding protein Mass: 13179.443 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: hsRosR-DNA binding protein Source: (gene. exp.) Halobacterium salinarum NRC-1 (Halophile) Gene: VNG_0258H / Variant: NRC-1 / Production host: Haloferax volcanii (archaea) / References: UniProt: Q9HSF4

-
DNA chain , 2 types, 4 molecules EGFH

#2: DNA chain	DNA (28-MER) Mass: 8525.505 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA sequence (28-MER) / Source: (synth.) Halobacterium salinarum NRC-1 (Halophile)
#3: DNA chain	DNA (28-MER) Mass: 8685.601 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA sequence (28-MER) / Source: (synth.) Halobacterium salinarum NRC-1 (Halophile)

-
Non-polymers , 3 types, 151 molecules

#4: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 27 Source method: isolated from a genetically manipulated source Formula: SO₄
#5: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Formula: Mn
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.74 Å³/Da / Density % sol: 60 %
Crystal grow	Temperature: 293 K Details: The complex crystallized from a buffer containing 20 mM HEPES, pH 7, 2 M KCl and 0.02% azide. Crystals grown with S4 (DNA/hsRosR ratio = 1.45) appeared after 3 days in wells containing 2.94 ...Details: The complex crystallized from a buffer containing 20 mM HEPES, pH 7, 2 M KCl and 0.02% azide. Crystals grown with S4 (DNA/hsRosR ratio = 1.45) appeared after 3 days in wells containing 2.94 M (NH4)2SO4, 40 mM MnCl2 and 0.02% azide. Method: vapor diffusion, sitting drop / pH: 7 Details: The complex crystallized from a buffer containing 20 mM HEPES, pH 7, 2 M KCl and 0.02% azide. Crystals grown with S4 (DNA/hsRosR ratio = 1.45) appeared after 3 days in wells containing 2.94 ...Details: The complex crystallized from a buffer containing 20 mM HEPES, pH 7, 2 M KCl and 0.02% azide. Crystals grown with S4 (DNA/hsRosR ratio = 1.45) appeared after 3 days in wells containing 2.94 M (NH4)2SO4, 40 mM MnCl2 and 0.02% azide.

Crystal

Density Matthews: 2.74 Å³/Da / Density % sol: 60 %

Crystal grow

Temperature: 293 K
Details: The complex crystallized from a buffer containing 20 mM HEPES, pH 7, 2 M KCl and 0.02% azide. Crystals grown with S4 (DNA/hsRosR ratio = 1.45) appeared after 3 days in wells containing 2.94 ...
Method: vapor diffusion, sitting drop / pH: 7
Details: The complex crystallized from a buffer containing 20 mM HEPES, pH 7, 2 M KCl and 0.02% azide. Crystals grown with S4 (DNA/hsRosR ratio = 1.45) appeared after 3 days in wells containing 2.94 ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 17, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 2.133→44.585 Å / Num. obs: 45836 / % possible obs: 89.4 % / Redundancy: 3.7 % / R_pim(I) all: 0.037 / Net I/σ(I): 10
Reflection shell	Resolution: 2.133→2.356 Å

-
Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
XDS		data reduction
Aimless		data scaling
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: The starting model for molecular replacement was VNG0258H/RosR (from KCl; PDB code 6FDH) and a DNA model derived from Mycobacterium tuberculosis MosR (PDB code 4FX4).

6fdh

4fx4

Resolution: 2.133→44.585 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.55

	R_factor	Num. reflection	% reflection
R_free	0.2318	2308	5.04 %
R_work	0.2099	-	-
obs	0.211	45794	63.76 %

Solvent computation

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

Displacement parameters

B_iso max: 801.25 Å² / B_iso mean: 77.923 Å² / B_iso min: 20.41 Å²

Refinement step

Cycle: final / Resolution: 2.133→44.585 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3667	2296	143	116	6222
B_iso mean	-	-	127.74	42.28	-
Num. residues	-	-	-	-	570

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 16

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1331-2.1795	0.3421	3	0.3456	126	129	3
2.1795-2.2302	0.3951	25	0.3346	291	316	7
2.2302-2.286	0.3707	42	0.3279	568	610	14
2.286-2.3478	0.3728	54	0.3172	1131	1185	26
2.3478-2.4168	0.3166	101	0.3108	1516	1617	37
2.4168-2.4948	0.3265	115	0.3139	2017	2132	48
2.4948-2.584	0.3444	126	0.3276	2488	2614	58
2.584-2.6874	0.3499	155	0.3296	2953	3108	69
2.6874-2.8097	0.3231	181	0.3031	3597	3778	84
2.8097-2.9578	0.3305	229	0.2921	4122	4351	97
2.9578-3.1431	0.2914	236	0.2778	4161	4397	98
3.1431-3.3857	0.275	223	0.2343	4101	4324	97
3.3857-3.7263	0.2108	235	0.1952	4144	4379	98
3.7263-4.2651	0.2013	192	0.1692	4219	4411	97
4.2651-5.3722	0.1805	181	0.1623	4063	4244	95
5.3722-44.5945	0.1677	210	0.1631	3989	4199	93

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	3.4678	5.0077	-3.5948	7.3572	-4.6484	5.1663	-0.2099	1.7747	-1.9256	-2.0649	-1.0123	-2.6276	1.6576	0.9788	1.4112	1.2614	0.386	0.3156	1.0734	-0.0555	1.0461	16.8559	-14.7448	-23.7103
2	2.4843	-6.1956	7.283	2.2063	-5.1737	4.1504	-0.4831	-0.1422	-0.2496	0.0215	0.4562	-0.2111	-0.0221	-0.2582	0.2543	0.4442	-0.013	0.0354	0.3689	-0.0687	0.457	10.9788	-18.121	-11.222
3	4.9377	-5.1472	-2.4095	6.2066	0.7805	5.0247	-0.1489	-0.604	-0.2945	0.0289	0.5568	0.1887	0.6404	-0.026	-0.4261	0.3448	-0.0622	-0.0942	0.3034	0.0002	0.5332	3.5463	-19.5605	-6.0478
4	7.4727	0.6054	3.6854	9.8149	-1.4166	7.1757	-0.5859	-0.3252	0.1889	-0.996	-0.211	1.3612	0.5218	-0.753	0.7235	0.4299	-0.1523	-0.2887	0.4128	-0.1115	0.631	-2.541	-21.0085	-12.7177
5	2.1312	-3.1517	-3.5058	0.9189	1.0826	3.0509	-0.1476	0.9175	-1.2835	-1.4549	0.3646	-0.6543	1.2081	-0.3553	-0.2495	1.0153	-0.0542	0.0101	0.4965	-0.2374	0.7314	8.7935	-25.3782	-19.4057
6	1.8338	0.9136	0.3228	3.3625	-1.0862	2.813	-0.2843	0.1486	-1.4186	-0.9334	0.0703	-0.5825	1.3835	0.3158	0.2999	0.8286	0.1236	0.1194	0.3789	-0.1047	1.0129	13.1837	-29.3691	-11.9641
7	4.3817	0.4898	2.8014	4.8588	2.4497	8.2513	-0.3033	0.5377	0.0242	-0.5724	0.2702	-0.2133	-0.288	0.8548	0.0549	0.2865	-0.0214	0.0866	0.4199	0.0696	0.4438	22.2247	-2.3308	-12.5314
8	7.2757	5.2992	-3.3595	5.9914	-2.1262	8.0808	-0.2234	-0.4763	-0.5854	0.4979	-0.499	-1.4078	0.0101	0.0752	0.4607	0.1348	0.0719	-0.0299	0.3888	0.001	0.428	21.2489	-6.435	1.6737
9	8.5587	-4.0393	1.2862	2.1175	-8.7546	8.261	0.0568	-0.0752	0.3409	0.8356	1.1084	0.9936	-0.7467	-2.1093	-0.566	0.3887	0.0404	0.1047	0.6092	0.1692	0.499	2.7344	-2.6102	-8.5448
10	2.3048	7.0548	6.4541	8.2992	8.1021	2.3288	-0.8235	1.0211	0.4407	-1.4211	0.744	-0.2803	-0.4143	0.4173	0.1277	0.4162	-0.031	0.0359	0.4286	0.0972	0.3992	12.297	0.0245	-19.1923
11	5.9349	-2.63	3.5602	8.6822	-3.1913	3.8187	0.1741	1.4836	0.1513	-2.075	-0.2206	-0.6034	0.1838	0.7459	-0.0124	0.9312	-0.0545	0.1167	0.7123	0.0153	0.366	13.0069	0.1162	-29.0895
12	2.0164	-1.3606	0.242	2.0577	7.1301	8.1449	-0.5448	0.0591	0.2567	-1.1416	-0.3894	1.4108	-0.2708	-1.6762	0.5817	0.5531	0.0007	-0.199	0.6834	0.1022	0.6203	1.5862	3.8828	-20.0573
13	8.1836	2.9216	-6.3709	9.5662	-7.5627	8.0277	-0.0831	0.9924	1.4253	-0.37	0.2247	-0.1266	-1.3115	-0.2489	-0.3259	0.944	-0.0078	-0.1402	0.5727	0.1424	0.5751	7.9095	14.3776	-25.1075
14	3.3476	-6.8958	7.9545	9.6563	-4.4006	7.0332	-0.3159	0.031	0.2301	-0.6171	0.1941	-0.4644	-0.2781	-0.2173	0.1137	0.2852	-0.0687	0.0333	0.331	0.0386	0.3135	10.6785	3.2717	-11.1814
15	4.1443	4.1758	1.6617	4.4672	2.9696	7.1445	-0.2871	-0.62	-0.5747	-0.1182	0.1529	-0.1596	0.2007	0.0867	0.0907	0.2278	0.0595	-0.0144	0.3526	0.0292	0.4834	18.4118	-14.0384	-4.7089
16	6.0663	-3.8148	1.4105	6.5869	-0.8565	9.698	0.1776	0.2542	-0.041	-0.2992	-0.5617	-1.3207	-0.504	1.3965	0.5666	0.2771	-0.0328	0.1317	0.738	-0.0553	0.5991	29.7676	-5.0388	-9.2192
17	8.5847	2.0177	8.5926	2.0102	1.9156	8.7754	-1.2883	1.9793	-1.655	-1.9554	1.6911	-2.9047	-1.1219	3.2275	-0.63	0.531	-0.0249	0.2742	0.9066	-0.207	0.3798	8.9032	-9.6279	15.1835
18	8.6836	5.1928	-3.2694	9.393	-2.216	6.9091	0.1817	0.0463	0.4683	0.5139	0.5878	1.1299	-0.7043	-0.6796	-0.7088	0.2146	0.0477	0.0508	0.2322	-0.0032	0.3155	3.4403	2.0767	9.6893
19	2.4981	4.1617	-7.3118	2.2034	-3.4226	6.8195	0.7352	-0.6888	1.0733	1.2478	-0.0662	0.7812	-1.079	-0.2226	-0.6472	0.6412	0.0132	0.1644	0.4965	-0.053	0.5451	1.1861	10.1381	14.9222
20	6.7273	1.5836	1.9014	5.4723	4.6421	8.7859	0.3731	-0.9357	-0.318	1.0107	-0.3094	-0.6492	-0.7487	0.5483	-0.2923	0.4672	-0.1529	-0.0205	0.4654	-0.0833	0.2289	12.5295	3.9138	14.2874
21	7.1802	5.2709	0.9354	2.3748	1.7874	4.8826	-0.3943	0.9559	0.0327	-0.7524	0.527	-0.6302	-0.7415	0.7218	-0.1663	0.3582	-0.0964	0.044	0.5305	0.0369	0.3896	12.1421	5.4148	3.3204
22	6.0459	2.6149	-8.4818	9.9188	-3.628	1.9863	0.5862	-1.1803	-2.1186	1.5836	0.2967	-2.0877	1.6632	1.8626	-0.6326	0.4182	0.1692	-0.212	0.6398	-0.0057	0.7134	2.041	-10.0958	7.8083
23	6.5162	2.8869	2.1379	1.9612	0.8418	7.8434	0.5741	-0.1438	-1.025	0.0843	0.2442	0.6182	0.3632	-0.7144	-0.814	0.3097	0.0117	0.0042	0.4122	0.187	0.6704	-10.4213	-15.1682	9.5636
24	2.3913	4.7077	-1.7124	2.2409	-6.5106	2.3439	-0.0813	0.1627	0.4987	0.4678	0.6241	0.1929	-0.9171	-1.6582	-0.5851	0.4089	0.124	0.1056	0.5638	0.1055	0.6276	-14.6789	-2.6432	2.823
25	6.5161	1.102	3.6293	1.0309	-0.0426	2.7726	0.1827	-0.4747	0.7663	1.15	-0.0997	0.9316	-0.9993	-0.9946	-0.108	0.5775	0.1277	0.23	0.8038	0.1241	0.618	-4.3605	-4.0759	22.5575
26	8.0292	1.169	-1.1918	7.9682	-5.778	6.2589	0.2974	-0.8861	-1.4284	0.4008	0.1691	0.6551	0.8335	-0.4839	-0.3386	0.4931	-0.0799	0.0468	0.6071	0.2382	0.6804	-3.6654	-20.8603	22.1037
27	2.1331	-2.4113	0.2382	8.9428	5.2603	2.1024	0.3297	-0.7138	-0.4475	0.3652	0.0089	-0.6411	0.8691	-0.453	-0.2986	0.4592	-0.0627	-0.0424	0.5847	0.2899	0.6985	6.9282	-18.623	18.9634
28	3.2066	-1.3818	-0.0073	6.8335	-1.8716	6.335	0.2873	-0.8976	-0.4808	1.558	0.1368	0.8656	-0.0267	-0.2521	-0.393	0.8072	-0.0682	0.1315	1.017	0.3276	0.5905	-5.292	-17.4311	32.1001
29	1.0689	0.4836	2.2599	9.8804	-6.1243	2.0897	0.3172	-1.525	-0.3614	1.1394	-0.5431	0.5972	-0.8036	-0.3498	0.1344	0.4465	0.0153	0.2327	0.7039	0.1006	0.6027	-12.437	-7.865	20.0739
30	0.7144	1.4244	0.692	3.0204	0.4045	9.3707	0.2275	0.1859	-0.2141	0.8864	0.1413	0.1509	-1.259	-0.0445	-0.3957	0.2714	0.0593	0.1356	0.3024	-0.0179	0.5005	-6.1538	-1.3757	8.1568
31	7.019	7.1238	0.7798	8.0935	-1.9495	9.0034	-0.3726	0.0209	-0.1817	-0.8228	-1.2793	-1.0493	-0.0304	0.2061	1.2627	0.2108	0.0179	0.0161	0.2154	0.1534	0.5832	-6.1348	-0.9202	-2.3573
32	8.6807	2.9446	-1.953	2.4002	-2.504	5.8347	0.1912	0.1652	-1.0336	-0.6835	0.0953	0.4246	0.6447	-0.2157	-0.3431	0.2446	0.0343	-0.0679	0.3295	-0.0036	0.6213	-7.9074	-14.1557	0.17
33	2.0056	4.6224	-0.6318	3.7278	1.4448	1.7462	0.9153	2.856	0.9198	-1.7328	-1.9317	1.8753	1.4994	0.9419	0.7836	2.3475	-0.2515	0.1699	1.5167	0.556	0.9301	12.2292	17.0269	-48.3521
34	1.033	-0.5181	0.429	6.697	-0.9433	4.7378	-0.5842	0.6711	0.4616	-2.1617	0.162	0.8737	0.8451	0.0268	0.3133	1.5062	-0.2324	-0.3429	0.8508	0.2639	0.5809	2.5633	6.2908	-35.1283
35	1.7557	1.3932	-1.1469	2.4959	2.2608	7.5756	-0.3031	0.7117	-0.6783	-0.1402	-0.0129	1.3827	0.2608	1.4446	0.2599	2.2205	-0.3451	-0.5976	1.1773	-0.0019	0.6191	-3.4058	-12.5483	-35.4727
36	6.4276	-1.0792	7.2173	9.7178	3.2276	2.0665	-0.4069	0.2855	-0.5987	-1.5313	0.5024	1.9428	1.5479	-0.4632	-0.2213	0.9053	-0.2826	-0.283	0.5711	-0.0159	0.7837	-5.4901	-18.8613	-20.8214
37	8.8698	7.8583	-1.4376	7.024	-0.6041	8.8857	0.657	0.3891	-0.7714	0.878	-0.088	3.5882	0.9947	-0.3699	-0.4958	1.2199	-0.3574	-0.4386	0.7016	0.1228	1.624	-11.5515	-32.0424	-16.0476
38	3.5998	-0.8489	1.3	0.8528	1.1213	4.1307	0.6199	-0.4465	-0.986	-0.3411	0.4691	0.7105	0.2407	0.1569	-1.1108	1.4197	-0.291	-0.0002	0.4991	0.1548	1.5379	-3.0414	-41.477	-2.7763
39	9.3335	2.5997	-6.1546	4.6095	-0.3013	5.1206	0.1977	0.6962	1.213	-0.0294	1.1588	3.5613	1.2169	-1.5772	-1.21	1.3128	-0.3848	-0.2199	0.8177	0.4661	1.6488	-10.0874	-39.1283	-1.4452
40	6.3185	1.9371	3.0698	1.9748	3.3405	5.7726	-0.1357	0.5537	-0.9095	-1.2138	0.163	0.4173	1.0872	-0.3183	0.1028	1.0683	-0.1677	-0.1912	0.3832	-0.1214	0.9338	-1.726	-32.0294	-13.765
41	9.688	-6.0162	2.8824	4.3527	-3.3773	4.7332	-0.1299	2.4494	0.5355	-1.6504	-0.3127	0.9541	1.6178	0.2052	0.1781	1.2572	-1.1287	-1.6088	0.6498	-0.403	0.7366	-10.2679	-23.452	-26.1177
42	8.5	-0.8656	4.0507	2.6314	0.6935	4.9048	1.259	-0.0317	0.3726	-2.473	-0.7042	1.5793	-0.3352	0.89	-0.4058	1.744	-0.1793	-0.3933	0.7409	0.1322	0.4959	-1.4015	-7.1366	-31.8007
43	8.3251	-1.4739	0.7204	5.7315	5.8944	7.6826	0.5414	1.3564	1.2451	-3.7864	-1.3754	0.3612	-0.0058	0.3844	0.7146	1.8895	-0.1656	-0.4266	1.153	0.4746	1.0622	0.9562	9.707	-41.7154
44	3.1711	-3.234	0.2334	4.2719	1.8141	4.5673	-0.3949	0.6202	1.4945	-0.9782	-0.0413	-0.4328	-0.014	0.9203	0.3173	1.6457	-0.112	-0.0583	1.0183	0.5834	0.9753	13.4571	20.1785	-39.7734
45	2.8297	0.4573	0.1442	4.5088	1.9287	1.0783	0.9503	-0.7832	1.9305	1.7759	-1.8935	-0.047	-2.4299	0.7806	0.5988	1.9293	-0.4008	-0.1177	0.5522	0.1726	1.3582	13.749	28.7564	11.5269
46	2.0903	7.3645	1.4984	2.1055	8.4742	2.0697	0.2237	0.0591	0.3853	1.6608	-0.0954	-0.0183	-0.5208	2.1343	-0.1414	0.8998	-0.2083	-0.1407	0.8017	-0.008	0.5956	18.5564	12.274	17.679
47	9.9572	8.8867	1.9215	2.2903	4.6139	2.2081	0.6206	-2.3188	1.282	1.0595	-1.2342	0.7958	-0.7125	0.6539	0.7175	1.164	-0.1951	-0.0443	0.9999	-0.0699	0.7154	13.6684	3.3465	33.0039
48	9.5327	0.2178	7.67	4.2825	-2.0032	7.4571	-0.7153	-1.2455	-1.4844	1.8129	-0.7595	-0.8225	0.5396	1.451	1.4194	0.9972	0.1128	0.0502	1.184	0.4325	0.6779	12.4433	-15.2869	33.0167
49	1.3665	2.7016	-1.3951	5.2741	-2.8213	5.4734	0.5342	-1.5893	-0.5925	0.8559	-0.6662	-0.5957	0.7636	0.6418	0.1935	1.7185	-0.4929	0.2075	0.7874	2.8323	-1.8578	6.1942	-25.1198	43.3579
50	4.6757	-0.3936	0.3561	0.212	-0.9323	4.1288	0.6281	-0.6064	-1.0512	0.3232	-0.7422	-0.77	1.6505	-0.2357	0.077	1.6555	-0.0697	-0.0114	1.3646	0.8076	1.3117	-3.7703	-37.8961	37.7259
51	8.2294	-4.4488	-0.5624	2.0335	-4.4677	5.759	1.5676	-0.009	0.1094	1.4714	-1.2597	-1.2014	-0.0181	2.3739	0.2522	1.8011	-0.2738	-0.104	1.2318	0.8108	1.6214	4.5722	-38.3921	38.2996
52	6.4708	5.7781	-4.2615	8.404	-5.4106	3.6209	1.7376	-1.9656	-0.4179	2.3238	-1.5375	-0.7081	-0.3744	-0.0575	-0.0173	1.1081	-0.1867	-0.0858	1.2262	0.4611	0.7507	3.7779	-18.8241	38.5704
53	6.734	-6.5667	-2.5011	6.5321	2.04	6.6565	2.0292	-1.4664	0.2738	0.0889	-0.8947	-0.0899	0.8687	1.0521	-1.2582	1.1265	-0.1823	-0.2642	1.1387	0.204	0.54	17.3332	-7.1835	33.7272
54	2.1649	3.835	4.179	6.5643	6.0845	10.0092	0.7874	-1.6405	0.2012	0.246	-0.9243	0.5408	-1.3497	0.421	0.0457	1.2193	-0.2875	0.0431	0.8008	-0.1	0.3717	11.7994	6.2213	26.6524
55	8.6592	-4.536	1.4323	3.4001	-1.4748	9.5352	-0.3555	-1.3373	2.5029	2.0525	-0.759	2.0693	-1.8305	2.7401	0.9968	1.6898	-0.5363	-0.0656	0.9211	-0.2458	1.1465	18.5293	19.2743	22.8997
56	3.3608	4.0787	0.3347	5.57	2.3561	8.1179	-0.6135	0.4889	0.2377	1.4077	0.2074	0.9621	-2.904	0.8789	0.4893	1.4738	-0.4078	-0.1265	0.6569	0.2954	1.2879	15.6437	26.0732	6.3447

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 7:16)	A	7 - 16
2	X-RAY DIFFRACTION	2	(chain A and resid 17:29)	A	17 - 29
3	X-RAY DIFFRACTION	3	(chain A and resid 30:46)	A	30 - 46
4	X-RAY DIFFRACTION	4	(chain A and resid 47:53)	A	47 - 53
5	X-RAY DIFFRACTION	5	(chain A and resid 54:66)	A	54 - 66
6	X-RAY DIFFRACTION	6	(chain A and resid 67:88)	A	67 - 88
7	X-RAY DIFFRACTION	7	(chain A and resid 89:106)	A	89 - 106
8	X-RAY DIFFRACTION	8	(chain A and resid 107:121)	A	107 - 121
9	X-RAY DIFFRACTION	9	(chain B and resid 6:15)	B	6 - 15
10	X-RAY DIFFRACTION	10	(chain B and resid 16:30)	B	16 - 30
11	X-RAY DIFFRACTION	11	(chain B and resid 31:55)	B	31 - 55
12	X-RAY DIFFRACTION	12	(chain B and resid 56:64)	B	56 - 64
13	X-RAY DIFFRACTION	13	(chain B and resid 65:76)	B	65 - 76
14	X-RAY DIFFRACTION	14	(chain B and resid 77:93)	B	77 - 93
15	X-RAY DIFFRACTION	15	(chain B and resid 94:105)	B	94 - 105
16	X-RAY DIFFRACTION	16	(chain B and resid 106:121)	B	106 - 121
17	X-RAY DIFFRACTION	17	(chain C and resid 11:16)	C	11 - 16
18	X-RAY DIFFRACTION	18	(chain C and resid 17:31)	C	17 - 31
19	X-RAY DIFFRACTION	19	(chain C and resid 32:47)	C	32 - 47
20	X-RAY DIFFRACTION	20	(chain C and resid 48:66)	C	48 - 66
21	X-RAY DIFFRACTION	21	(chain C and resid 67:87)	C	67 - 87
22	X-RAY DIFFRACTION	22	(chain C and resid 88:91)	C	88 - 91
23	X-RAY DIFFRACTION	23	(chain C and resid 92:107)	C	92 - 107
24	X-RAY DIFFRACTION	24	(chain C and resid 108:121)	C	108 - 121
25	X-RAY DIFFRACTION	25	(chain D and resid 7:22)	D	7 - 22
26	X-RAY DIFFRACTION	26	(chain D and resid 23:41)	D	23 - 41
27	X-RAY DIFFRACTION	27	(chain D and resid 42:48)	D	42 - 48
28	X-RAY DIFFRACTION	28	(chain D and resid 49:78)	D	49 - 78
29	X-RAY DIFFRACTION	29	(chain D and resid 79:92)	D	79 - 92
30	X-RAY DIFFRACTION	30	(chain D and resid 93:99)	D	93 - 99
31	X-RAY DIFFRACTION	31	(chain D and resid 100:103)	D	100 - 103
32	X-RAY DIFFRACTION	32	(chain D and resid 104:121)	D	104 - 121
33	X-RAY DIFFRACTION	33	(chain E and resid 1:4)	E	1 - 4
34	X-RAY DIFFRACTION	34	(chain E and resid 5:11)	E	5 - 11
35	X-RAY DIFFRACTION	35	(chain E and resid 12:15)	E	12 - 15
36	X-RAY DIFFRACTION	36	(chain E and resid 16:19)	E	16 - 19
37	X-RAY DIFFRACTION	37	(chain E and resid 20:23)	E	20 - 23
38	X-RAY DIFFRACTION	38	(chain E and resid 24:28)	E	24 - 28
39	X-RAY DIFFRACTION	39	(chain F and resid 1:5)	F	1 - 5
40	X-RAY DIFFRACTION	40	(chain F and resid 6:9)	F	6 - 9
41	X-RAY DIFFRACTION	41	(chain F and resid 10:13)	F	10 - 13
42	X-RAY DIFFRACTION	42	(chain F and resid 14:20)	F	14 - 20
43	X-RAY DIFFRACTION	43	(chain F and resid 21:24)	F	21 - 24
44	X-RAY DIFFRACTION	44	(chain F and resid 25:28)	F	25 - 28
45	X-RAY DIFFRACTION	45	(chain G and resid 1:6)	G	1 - 6
46	X-RAY DIFFRACTION	46	(chain G and resid 7:10)	G	7 - 10
47	X-RAY DIFFRACTION	47	(chain G and resid 11:16)	G	11 - 16
48	X-RAY DIFFRACTION	48	(chain G and resid 17:20)	G	17 - 20
49	X-RAY DIFFRACTION	49	(chain G and resid 21:24)	G	21 - 24
50	X-RAY DIFFRACTION	50	(chain G and resid 25:28)	G	25 - 28
51	X-RAY DIFFRACTION	51	(chain H and resid 1:5)	H	1 - 5
52	X-RAY DIFFRACTION	52	(chain H and resid 6:11)	H	6 - 11
53	X-RAY DIFFRACTION	53	(chain H and resid 12:15)	H	12 - 15
54	X-RAY DIFFRACTION	54	(chain H and resid 16:19)	H	16 - 19
55	X-RAY DIFFRACTION	55	(chain H and resid 20:23)	H	20 - 23
56	X-RAY DIFFRACTION	56	(chain H and resid 24:28)	H	24 - 28

-
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

-
Protein , 1 types, 4 molecules ABCD

-
DNA chain , 2 types, 4 molecules EGFH

-
Non-polymers , 3 types, 151 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

-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

-Protein , 1 types, 4 molecules ABCD

-DNA chain , 2 types, 4 molecules EGFH

-Non-polymers , 3 types, 151 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

-
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

-
Protein , 1 types, 4 molecules ABCD

-
DNA chain , 2 types, 4 molecules EGFH

-
Non-polymers , 3 types, 151 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