PDB-5j5q: AMP-PNP-stabilized ATPase domain of topoisomerase IV from Strepto...

ID or keywords:

Entry

Database: PDB / ID: 5j5q

Title

AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type II

Components

DNA (5'-D(*GP*CP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*GP*C)-3')
DNA topoisomerase 4 subunit B

Keywords

ISOMERASE/DNA / Streptococcus PNEUMONIAE / TOPOISOMERASE IV / DNA BINDING / ISOMERASE-DNA COMPLEX / ATPase domain / T-segment

Function / homology

Function and homology information

DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / metal ion binding
Similarity search - Function

Biological species

Streptococcus pneumoniae (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.83 Å

Authors

Laponogov, I. / Pan, X.-S. / Skamrova, G. / Umrekar, T. / Fisher, L.M. / Sanderson, M.R.

Funding support

United Kingdom, 1items

Citation

Journal: Nat Commun / Year: 2018
Title: Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase.
Authors: Laponogov, I. / Pan, X.S. / Veselkov, D.A. / Skamrova, G.B. / Umrekar, T.R. / Fisher, L.M. / Sanderson, M.R.

History

Deposition	Apr 3, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 26, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jul 18, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 10, 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.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_label_asym_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5j5q.cif.gz	644.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5j5q.ent.gz	527.2 KB	Display	PDB format
PDBx/mmJSON format	5j5q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5j5q_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	5j5q_full_validation.pdf.gz	2 MB	Display
Data in XML	5j5q_validation.xml.gz	67.8 KB	Display
Data in CIF	5j5q_validation.cif.gz	89.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j5/5j5q ftp://data.pdbj.org/pub/pdb/validation_reports/j5/5j5q	HTTPS FTP

-
Related structure data

Related structure data	5j5pC 1ei1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5j5p-d 3zkb-4 4wuc-1 3zkb-5 3zkb-3 1s16-d 3zkb-2 5zxm-d 3zkb-8 4wud-1 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 (4) #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) #73 - Jan 2006 Topoisomerase similarity (16) #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) #87 - Mar 2007 Zinc Fingers similarity (1) #131 - Nov 2010 Inteins similarity (3) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses 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) #108 - Dec 2008 Hsp90 similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters 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 (4)
#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)
#73 - Jan 2006
Topoisomerase
similarity (16)
#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)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#131 - Nov 2010
Inteins
similarity (3)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#125 - May 2010
Parvoviruses
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)
#108 - Dec 2008
Hsp90
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: DNA topoisomerase 4 subunit B

B: DNA topoisomerase 4 subunit B

C: DNA topoisomerase 4 subunit B

D: DNA topoisomerase 4 subunit B

E: DNA (5'-D(*GP*CP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*GP*C)-3')

F: DNA (5'-D(*GP*CP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*GP*C)-3')

hetero molecules

191 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DNA topoisomerase 4 subunit B

B: DNA topoisomerase 4 subunit B

E: DNA (5'-D(*GP*CP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*GP*C)-3')

F: DNA (5'-D(*GP*CP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*GP*C)-3')

hetero molecules

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

2

C: DNA topoisomerase 4 subunit B

D: DNA topoisomerase 4 subunit B

hetero molecules

defined by author&software
91.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	124.950, 72.740, 222.960
Angle α, β, γ (deg.)	90.00, 91.89, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	DNA topoisomerase 4 subunit B / Topoisomerase IV subunit B Mass: 45032.457 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: parE, SP_0852 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q59961, EC: 5.99.1.3
#2: DNA chain	DNA (5'-D(GPCPAPTPAPTPAPTPAPTPAPTPGPC)-3') Mass: 4278.815 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.16 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / Details: 5 mM MgCl2, 50 mM HEPES, 25% PEG MME 550 / PH range: 7 / Temp details: Incubator

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 2.83→60.759 Å / Num. obs: 48001 / % possible obs: 99.67 % / Redundancy: 3.31 % / CC_1/2: 0.9745 / R_merge(I) obs: 0.047 / Net I/σ(I): 2.5
Reflection shell	Resolution: 2.83→2.92 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.466 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: derived from 1EI1

1ei1

Resolution: 2.83→60.759 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.71

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.263	2338	4.87 %	RANDOM
R_work	0.1837	-	-	-
obs	0.1876	48001	99.67 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.83→60.759 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11393	568	151	0	12112

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.026	12452
X-RAY DIFFRACTION	f_angle_d	2.33	17107
X-RAY DIFFRACTION	f_dihedral_angle_d	20.148	7151
X-RAY DIFFRACTION	f_chiral_restr	0.111	1993
X-RAY DIFFRACTION	f_plane_restr	0.012	2135

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 (%)
2.83-2.8878	0.4079	119	0.3055	2701	X-RAY DIFFRACTION	100
2.8878-2.9506	0.3738	125	0.2788	2629	X-RAY DIFFRACTION	100
2.9506-3.0192	0.3652	118	0.2554	2734	X-RAY DIFFRACTION	100
3.0192-3.0947	0.3168	139	0.248	2618	X-RAY DIFFRACTION	100
3.0947-3.1784	0.3623	146	0.2383	2674	X-RAY DIFFRACTION	100
3.1784-3.2719	0.3281	160	0.2391	2672	X-RAY DIFFRACTION	100
3.2719-3.3775	0.2979	119	0.227	2668	X-RAY DIFFRACTION	100
3.3775-3.4982	0.3095	147	0.2085	2682	X-RAY DIFFRACTION	100
3.4982-3.6383	0.2869	121	0.1912	2707	X-RAY DIFFRACTION	100
3.6383-3.8038	0.2941	147	0.1823	2695	X-RAY DIFFRACTION	100
3.8038-4.0043	0.2344	181	0.1724	2621	X-RAY DIFFRACTION	100
4.0043-4.2551	0.2601	121	0.1474	2707	X-RAY DIFFRACTION	100
4.2551-4.5836	0.2341	128	0.1386	2690	X-RAY DIFFRACTION	100
4.5836-5.0446	0.1888	140	0.1358	2681	X-RAY DIFFRACTION	100
5.0446-5.7741	0.2137	129	0.1613	2695	X-RAY DIFFRACTION	100
5.7741-7.2729	0.2838	133	0.1913	2747	X-RAY DIFFRACTION	99
7.2729-60.7725	0.232	165	0.1732	2742	X-RAY DIFFRACTION	98

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	3.8885	0.3736	0.2506	-0.0996	-0.1525	0.164	0.0404	-0.0531	0.8988	0.2192	-0.091	0.2736	-0.0229	-0.203	0.1223	0.5628	-0.1169	0.0808	0.3861	-0.0477	0.7102	-12.8382	9.4809	82.4841
2	2.1594	0.6815	-0.2203	3.947	-1.077	3.6363	-0.1378	0.1097	0.2343	0.3772	-0.1134	-0.533	-0.4973	0.4626	0.2025	0.3548	-0.1289	-0.0979	0.408	-0.0208	0.5099	8.9315	8.1097	80.0151
3	2.6273	1.0839	-0.7196	3.6279	-0.7051	1.6059	-0.0293	-0.0779	0.5866	0.011	0.0924	-0.3021	-0.403	0.3396	-0.0447	0.3882	-0.1262	-0.0251	0.4085	-0.0112	0.5945	3.296	11.6795	79.995
4	6.6239	0.7851	0.9595	7.992	3.3575	7.2467	-0.0592	-0.9058	-0.4246	0.38	-0.4312	-0.6649	-0.4145	0.5595	0.2759	0.4343	-0.1458	-0.1178	0.496	-0.0169	0.5934	9.4809	-3.5763	92.4595
5	6.9424	-3.0421	-0.1012	7.2985	-2.362	6.6308	1.0958	-1.2808	0.0211	0.7392	-0.573	-1.7129	0.7855	0.3827	-0.3314	0.6901	-0.0821	-0.2451	0.54	-0.0181	0.737	8.8265	-21.0837	91.3109
6	2.9278	-0.3378	-0.7072	6.0852	-1.5773	1.3407	-0.0591	0.0938	-0.5097	0.2288	0.1288	0.0574	0.3347	-0.1204	-0.0371	0.4219	-0.0105	-0.0272	0.3419	-0.0606	0.4381	-4.274	-26.8666	83.0729
7	4.662	-3.0537	2.624	9.8041	-7.8488	6.8945	0.3612	-0.0863	-0.3419	-0.0452	0.2491	0.6802	0.2736	-0.4795	-0.4896	0.3487	-0.0883	-0.0091	0.285	-0.0337	0.3624	-5.3149	-11.3702	76.6576
8	3.7017	2.7312	1.1158	7.3019	-6.2042	9.8456	-0.2921	0.6562	-0.9008	-2.0825	-0.0426	-1.4359	2.0961	0.3491	0.1602	0.6716	-0.0182	-0.0279	0.5837	-0.0752	0.2629	-0.3017	-29.785	75.3676
9	8.3812	-1.6938	-6.5141	2.9681	0.9248	8.0591	-0.6432	-0.0419	-1.8509	0.6104	0.1536	0.2052	0.8048	-0.8499	0.4058	0.7832	-0.1314	0.0402	0.5725	0.2328	0.6428	-12.8064	-36.8565	95.6674
10	8.4762	-0.3895	-2.7296	2.8533	-0.738	6.2624	1.3835	-0.6482	0.4117	0.9112	-1.2071	-1.2101	-0.2579	-0.2757	-0.4309	0.3838	-0.1264	0.0321	0.4284	-0.0584	0.4257	1.1227	4.3123	75.4408
11	6.1267	-0.3469	1.2627	2.957	1.0024	0.1419	-0.0749	0.1441	0.3418	-0.2348	-0.0087	0.0307	-0.184	0.2532	0.0529	0.3711	-0.0073	0.0852	0.3923	0.1168	0.518	-14.7612	1.2693	70.1561
12	2.5185	2.1618	-1.2661	7.0394	-0.034	3.15	0.2281	0.265	1.185	-0.0079	0.0986	0.4544	-0.5148	-0.3919	-0.3471	0.3681	0.0768	-0.0199	0.4418	0.1248	0.8002	-35.7855	7.6277	69.1687
13	3.1919	-0.088	-0.7664	3.0329	1.2049	4.3103	0.1064	0.2748	0.6772	-0.2327	0.0012	0.4828	-0.3675	-0.2325	-0.0877	0.3299	-0.0404	-0.0094	0.3361	0.1429	0.5505	-29.5667	7.4535	66.7194
14	4.3535	-0.953	-4.0368	3.4655	-1.6002	9.7273	-0.0626	-0.0447	-0.3212	0.2289	-0.1157	0.9627	0.1934	-0.2958	0.1168	0.3565	-0.1273	0.0266	0.3814	0.0311	0.6647	-40.26	-8.2024	74.8421
15	8.0855	2.0957	-0.5072	6.8378	-5.2327	4.1174	0.1265	-0.4191	-0.3268	-0.5667	0.1945	0.3136	1.0991	-0.9123	-0.2686	0.8089	-0.1976	0.2752	0.646	-0.0137	0.6406	-43.4109	-12.6958	91.6214
16	1.1657	0.0758	0.8112	4.669	-4.3678	5.2153	0.313	-0.9291	-0.0293	0.5833	0.1199	0.601	-0.0269	0.0619	-0.3667	0.657	-0.0681	0.2863	0.8108	-0.0198	0.5122	-30.9893	-9.6419	101.9268
17	5.049	3.1836	-3.272	6.5697	-2.8128	7.479	0.2663	-0.5842	0.1067	-0.1824	-0.1625	-1.3814	-1.0247	0.5782	-0.1467	0.4416	-0.0944	0.0819	0.4312	-0.0652	0.6507	-25.7391	1.37	90.4274
18	5.1865	1.4371	-2.6341	4.3305	-5.1896	6.6948	-1.1154	-1.4886	0.5387	1.6911	0.4475	-0.0146	-1.8662	-0.2587	0.0525	0.869	-0.0912	0.2794	1.0801	-0.2663	0.6376	-33.8386	-2.6788	106.1884
19	1.263	-1.2305	0.9787	4.6809	-0.285	0.6617	-0.1209	-1.0803	0.1921	-0.0647	0.2895	-0.6921	0.1049	-0.0166	0.031	0.7366	-0.195	0.0901	0.8435	0.0304	0.4741	-25.7437	-25.9596	108.2236
20	9.5089	-0.9445	-6.7474	2.0154	1.6972	5.3314	0.3247	-1.0433	-0.1515	0.2263	0.8976	1.6869	-0.6478	-1.1694	-1.2115	0.3082	0.0426	0.0534	0.6195	0.071	0.6001	-28.3107	8.9589	75.4999
21	3.4692	-1.3013	-0.2136	3.3562	-0.1712	1.7808	-0.1694	0.3189	0.4645	-0.2957	0.2497	0.0606	-0.4927	-0.2591	-0.1284	0.7088	0.0474	-0.3083	0.5126	0.0316	1.1173	-4.7613	-3.4736	25.2272
22	3.5577	0.331	0.4823	4.9494	1.6017	4.5512	0.3456	-0.7585	-1.2344	-0.2078	0.0819	1.9968	0.3759	-0.8745	-0.3002	0.6057	-0.0427	-0.1765	0.6809	0.2721	1.7969	-14.1289	-17.158	38.3855
23	4.8733	-0.389	0.9436	2.2049	-0.5967	3.3652	-0.2716	-0.5407	-0.3063	-0.0658	0.3179	0.9832	-0.0688	-0.8378	-0.096	0.5653	0.124	-0.1284	0.6765	0.1784	1.2997	-14.194	-11.838	34.0352
24	3.5727	1.1141	-1.5487	5.5065	1.1404	6.0532	-0.5466	0.1862	-0.9298	-0.2677	0.2114	0.4153	0.7624	-0.0747	0.1648	0.7705	-0.0556	-0.2232	0.5109	0.0895	1.5695	-4.149	-29.4275	32.1677
25	8.9416	-5.3628	1.6454	4.8443	-1.69	1.0142	-0.0784	0.0744	-2.3092	-0.1927	-0.0404	0.9998	1.3167	0.0141	-0.0974	0.835	0.1758	-0.1848	0.6934	0.1681	1.4421	11.5765	-34.2675	37.9554
26	6.9047	-2.143	2.8484	7.0366	-1.6003	3.9543	0.0413	0.1618	-0.642	-0.2711	0.0814	0.1091	0.4876	0.5546	-0.1725	0.5703	0.2078	-0.0484	0.5704	0.0673	0.5656	22.4638	-22.3849	38.7533
27	7.0887	-3.742	-2.9055	3.0859	3.394	5.6278	0.0936	-0.3454	-0.6905	-0.1563	0.2729	-0.1329	-0.2164	-0.0972	-0.3481	0.5423	0.1966	-0.1893	0.5146	0.1483	0.7707	9.5069	-12.1994	39.3468
28	5.5766	-1.0364	-1.3727	2.3545	2.5225	2.7185	0.6879	-0.6144	-0.5958	-0.4527	-0.6802	0.4737	0.5444	0.1846	0.0611	0.7496	0.2114	-0.0074	0.5283	0.1478	0.6543	23.8266	-21.7336	48.1647
29	5.8084	0.2377	-3.5211	1.0111	1.932	6.1927	0.4646	0.6649	-0.3187	-0.6304	0.0693	-0.0537	0.5764	1.0067	-0.2668	0.9448	0.5672	0.0978	1.3931	0.0347	0.7802	34.9495	-28.8133	28.3156
30	1.2566	-0.7034	2.6267	0.3936	-1.4175	7.1744	-0.5201	-0.3478	0.2788	0.7511	1.4257	1.2431	-0.1062	-0.6297	-0.3063	0.7478	0.0325	-0.1527	0.6701	0.2761	1.2698	-7.2357	-10.249	38.952
31	3.4823	1.5326	-2.7978	5.8223	-3.2618	4.5538	0.0628	-0.1217	0.094	0.1541	0.0715	0.3919	-0.4486	-0.2733	-0.1785	0.6182	0.124	-0.1541	0.5629	-0.0865	0.869	3.6804	3.6377	35.3199
32	3.5041	-2.3364	-1.2056	1.6897	0.8989	5.4995	0.2613	0.0937	0.2334	-0.7279	0.1146	1.0608	-1.8752	0.5253	-0.2071	1.2306	0.0025	-0.2976	0.2805	0.1434	1.6449	7.8556	20.9342	24.306
33	2.8983	-2.1261	-0.2158	5.8498	-1.8152	4.6319	0.1207	0.0672	1.0984	-0.3375	0.099	0.8059	-1.1341	-0.0407	-0.212	0.9872	0.0196	-0.0859	0.499	0.0156	1.2021	4.6387	17.3963	29.8738
34	8.4885	2.788	-1.3768	8.733	-0.0355	4.724	-0.3903	0.8736	1.2668	-1.629	-0.7472	-0.7821	-0.5591	1.9839	0.9453	1.2382	-0.1946	0.215	0.7196	0.2616	1.2984	23.1844	15.0395	21.4315
35	6.9565	3.7358	0.6638	6.5036	1.9124	8.6056	0.6401	0.5495	1.5835	-0.0062	-0.2419	-1.5623	-1.1975	1.476	-0.2458	1.2712	0.0004	0.6576	1.0542	0.1319	1.2085	29.2565	4.2757	8.1265
36	8.1322	-4.4384	-3.5526	4.1505	3.4961	5.9721	0.0774	0.6172	0.3297	-0.5445	-0.0988	-0.5155	0.8529	0.3948	0.0881	1.3079	0.2201	0.1522	0.7948	0.1507	0.5478	19.7458	-8.2865	5.6579
37	6.9342	-3.4352	-0.4171	6.3126	1.5513	8.8038	-0.1928	0.4373	1.0966	-1.4585	-0.3797	0.3385	0.1363	-0.4397	0.682	1.0292	0.1058	-0.253	0.5131	0.038	0.6555	8.5459	-1.4041	14.2713
38	8.0203	-1.5708	-1.4718	2.8008	-1.1002	5.3452	-0.3137	3.9449	0.0965	-0.5776	-0.5736	-0.5373	-0.9265	2.0503	0.5378	1.3609	-0.149	-0.1321	1.979	0.1083	0.53	14.8645	-6.2331	-1.9853
39	7.4123	-1.7892	0.866	6.6631	2.4593	1.2394	-0.445	0.8232	0.476	-1.8636	1.2362	-1.27	1.1847	-0.2483	-0.6443	1.2723	0.051	0.3513	1.4463	0.0449	0.7801	31.9487	-21.3785	6.155
40	6.8551	-0.1234	-0.4436	3.9137	-3.4143	4.5847	1.326	0.9122	0.7785	2.6708	-0.2135	0.5521	-1.7843	0.0432	-1.1252	1.0703	0.0386	0.0266	0.5916	0.1126	1.2613	2.8448	12.5233	22.8538
41	4.3422	0.4092	3.2384	6.7334	0.6382	5.8314	2.3766	1.5438	-1.7618	-1.7463	-0.5876	-1.0597	0.4868	-1.0949	-2.1701	2.638	0.442	-0.4736	2.3319	-0.145	1.6902	-22.8622	-25.8437	82.6756
42	3.087	-0.8552	4.5048	4.7544	0.3271	6.6613	1.6655	-0.1261	-0.5671	-0.3721	-0.8135	-0.6773	1.1993	-0.8125	-1.0853	1.6141	-0.0558	-0.0861	2.7179	0.332	2.8219	-22.9828	-24.1881	80.9555
43	4.59	-3.4518	0.8718	2.5924	-0.6396	1.3762	0.381	0.1414	0.1758	-0.0435	0.1073	0.4634	-0.1252	-0.6775	-0.3823	1.9744	-0.031	-0.8067	2.43	1.6278	3.337	-21.1733	-18.4337	94.7202

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 57 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 93 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 94 through 189 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 190 through 222 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 223 through 245 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 246 through 323 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 324 through 349 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 350 through 371 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 372 through 400 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 800 or resid 901)
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 5 through 57 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 58 through 93 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 94 through 189 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 190 through 222 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 223 through 245 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 246 through 323 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 324 through 349 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 350 through 371 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 372 through 400 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 800 or resid 901)
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 6 through 57 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 58 through 93 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 94 through 189 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 190 through 222 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 223 through 245 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 246 through 323 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 324 through 349 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 350 through 371 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 372 through 399 )
30	X-RAY DIFFRACTION	30	chain 'C' and resid 800:901
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 6 through 57 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 58 through 93 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 94 through 189 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 190 through 222 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 223 through 245 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 246 through 323 )
37	X-RAY DIFFRACTION	37	chain 'D' and (resid 324 through 349 )
38	X-RAY DIFFRACTION	38	chain 'D' and (resid 350 through 371 )
39	X-RAY DIFFRACTION	39	chain 'D' and (resid 372 through 399 )
40	X-RAY DIFFRACTION	40	chain 'D' and resid 800:901
41	X-RAY DIFFRACTION	41	chain E
42	X-RAY DIFFRACTION	42	chain F
43	X-RAY DIFFRACTION	43	chain A and resid 0

-
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