PDB-4f43: Protelomerase TelA mutant R255A complexed with CAAG hairpin DNA

ID or keywords:

Entry

Database: PDB / ID: 4f43

Title

Protelomerase TelA mutant R255A complexed with CAAG hairpin DNA

Components

DNA hairpinStem-loop
ProtelomeraseTelomere resolvase

Keywords

RECOMBINATION/DNA / RECOMBINATION-DNA complex

Function / homology

Function and homology information

Helix Hairpins - #1780 /

Telomere resolvase / Telomere resolvase ResT / Telomere resolvase ResT superfamily /

Telomere resolvase / hpI Integrase; Chain A / Helix Hairpins / Helix non-globular / Special / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology

Biological species

Agrobacterium tumefaciens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.354 Å

Authors

Shi, K. / Aihara, H.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Linear Chromosome-generating System of Agrobacterium tumefaciens C58: PROTELOMERASE GENERATES AND PROTECTS HAIRPIN ENDS.
Authors: Huang, W.M. / Dagloria, J. / Fox, H. / Ruan, Q. / Tillou, J. / Shi, K. / Aihara, H. / Aron, J. / Casjens, S.

History

Deposition	May 10, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 13, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 29, 2012	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4f43.cif.gz	184.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4f43.ent.gz	145 KB	Display	PDB format
PDBx/mmJSON format	4f43.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f4/4f43 ftp://data.pdbj.org/pub/pdb/validation_reports/f4/4f43	HTTPS FTP

-
Related structure data

Related structure data	4f41C C: citing same article (ref.)
Similar structure data	4e10-d 4e0y-d 4e0j-d 4f41-d 5eqg-d 4e0g-d 5eqi-d 5eqh-d 6tha-d 4e0z-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&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) #91 - Jul 2007 Thymine Dimers similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #253 - Jan 2021 Expressome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #227 - Nov 2018 Telomerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #135 - Mar 2011 Integrase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #23 - Nov 2001 DNA similarity (1) #190 - Oct 2015 Two-component Systems 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)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Protelomerase

C: DNA hairpin

45.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	118.123, 121.258, 58.124
Angle α, β, γ (deg.)	90.00, 111.30, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Protelomerase / Telomere resolvase Mass: 36070.121 Da / Num. of mol.: 1 / Fragment: UNP residues 102-421 / Mutation: R255A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58/ATCC 33970 / Gene: telA, Atu2523 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CWV1
#2: DNA chain	DNA hairpin / Stem-loop Mass: 9845.414 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 204 / 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: 4.22 Å³/Da / Density % sol: 70.88 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 5% (w/v) PEG 4000, 10mM Tris-HCl, 300mM NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 96 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2010
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.35→50 Å / Num. all: 22687 / Num. obs: 22687 / % possible obs: 73.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2.35→2.39 Å / % possible all: 45.1

-
Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.354→40.388 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 34.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2898	900	4.93 %	Random
R_work	0.2366	-	-	-
all	0.2394	18266	-	-
obs	0.2394	18266	57.86 %	-

Solvent computation

Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 36.735 Å² / k_sol: 0.338 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.0482 Å²	0 Å²	7.3734 Å²
2-	-	-2.0557 Å²	-0 Å²
3-	-	-	-19.5753 Å²

Refinement step

Cycle: LAST / Resolution: 2.354→40.388 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2532	651	0	204	3387

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3412
X-RAY DIFFRACTION	f_angle_d	0.709	4772
X-RAY DIFFRACTION	f_dihedral_angle_d	18.189	1264
X-RAY DIFFRACTION	f_chiral_restr	0.045	523
X-RAY DIFFRACTION	f_plane_restr	0.003	496

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 (%)
2.354-2.5017	0.6123	38	0.3951	826	X-RAY DIFFRACTION	17
2.5017-2.6948	0.399	90	0.3311	1657	X-RAY DIFFRACTION	33
2.6948-2.9659	0.299	123	0.3215	2386	X-RAY DIFFRACTION	48
2.9659-3.3949	0.3424	158	0.2655	3239	X-RAY DIFFRACTION	64
3.3949-4.2765	0.2688	234	0.2098	4367	X-RAY DIFFRACTION	87
4.2765-40.388	0.2595	257	0.213	4891	X-RAY DIFFRACTION	97

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	4.182	-4.3367	-1.0471	5.7002	-0.164	1.5618	-0.1166	-0.0583	0.2005	0.0457	-0.0113	-0.3661	-0.0927	0.0114	0.0336	0.1942	0.0759	0.0753	0.1921	0.0077	0.7461	33.9722	-31.1707	0.7396
2	0.3496	-0.3971	0.0741	0.5261	-0.1479	0.1773	-0.1142	-0.0766	-0.0493	0.0976	-0.0123	-0.1367	0.0024	0.0361	-0.38	-0.1551	0.2985	-0.1357	-0.3142	0.2164	0.4739	21.2899	-33.5024	6.2763
3	0.4549	-1.1866	-0.2131	3.8521	0.504	0.3192	-0.1233	-0.1248	-0.1826	0.3719	0.1895	0.0691	0.0731	0.018	-0.0327	0.1014	0.0298	-0.0018	0.0447	0.0176	0.3003	4.8656	-14.2847	10.2045
4	0.0127	-0.0392	-0.0171	0.1479	0.0636	0.002	0.102	0.0092	0.2794	-0.0594	0.1415	-0.4024	-0.0331	0.1845	0.8211	-0.1866	-0.2175	0.0116	-0.844	0.0927	0.5273	20.2978	0.5977	-3.065
5	0.9398	-1.8592	-1.3086	4.1273	1.7337	3.4561	0.0895	-0.0371	0.1189	0.2531	-0.2253	0.5751	-0.5313	-0.3004	0.2183	0.5122	0.0534	-0.0911	0.2801	-0.2717	0.7687	2.1103	14.9979	8.1837
6	1.271	-1.7091	0.8939	8.0253	-6.297	6.327	0.1253	0.0416	0.3025	-0.8344	-0.4473	-2.2914	-0.5158	0.3155	0.3258	0.4332	0.0433	-0.1037	0.2122	-0.0567	0.8382	10.0392	-15.545	-5.0237
7	3.3477	0.008	-0.8665	0.1226	-0.1275	0.3527	0.0248	-0.2973	0.3558	0.0166	-0.28	0.31	-0.0433	-0.4178	0.2536	0.5047	-0.0869	-0.344	0.5387	-0.0703	1.2129	6.5804	-18.371	-5.7662
8	6.4829	-1.7778	-0.7146	0.5083	0.1039	0.4867	0.0339	-0.2726	-0.414	-0.0001	0.0191	0.1027	0.1163	-0.1584	-0.049	0.436	-0.0791	-0.1952	0.6806	0.1335	1.5375	2.8556	-21.7916	-2.9764
9	7.2894	1.3013	-0.0934	1.9259	0.5984	0.8354	0.1844	-0.1081	-0.6387	0.0447	-0.0779	0.1191	0.2858	-0.4227	-0.1516	0.4951	-0.156	-0.3965	0.946	0.1529	1.0623	6.0389	-24.1003	0.5917
10	6.7597	-0.586	1.6278	6.0726	1.862	3.4905	0.3491	-0.3078	-0.8833	0.0907	-0.1932	0.2707	0.423	-0.1463	-0.1873	0.3023	-0.075	-0.2565	0.3555	0.0043	0.8149	10.5844	-24.1128	1.7638
11	2.1598	0.009	0.3768	1.479	1.2884	1.1852	-0.0024	0.0027	0.0039	-0.0558	0.0369	-0.2754	-0.0208	0.0488	-0.0755	0.1994	-0.0842	-0.0598	0.2385	0.075	0.627	15.2377	-22.1419	0.4143
12	1.0577	-0.2205	-0.2428	0.5012	0.52	0.8428	0.0378	0.0968	-0.1449	0.0147	0.0848	-0.1603	0.077	0.1344	-0.1183	0.1897	0.046	-0.1662	0.2054	-0.1878	0.5181	18.5844	-18.2142	-0.3099
13	3.4458	1.9924	0.7913	1.8776	0.7233	2.2319	0.1381	-0.4101	0.3585	0.0318	-0.2511	0.3286	-0.0039	-0.1649	0.1169	0.2742	-0.093	-0.1971	0.2897	0.1258	0.7486	21.068	-14.2505	0.3892
14	2.6982	2.0515	1.7933	2.2746	1.3107	3.385	0.0932	-0.0145	-0.2719	0.0435	-0.0007	-0.1543	0.0903	0.0852	-0.0807	0.2011	-0.0288	-0.137	0.217	-0.0967	0.4665	22.2161	-10.5308	4.1861
15	6.397	2.6317	1.7605	3.1699	0.1847	2.8128	0.108	-0.0196	-0.2631	0.0345	-0.0146	-0.0911	0.0935	0.0715	-0.0767	0.2805	-0.0904	-0.1748	0.3288	-0.1129	0.5778	22.822	-9.8237	9.7023
16	7.1635	0.8686	3.0308	1.215	0.5747	4.9447	0.0012	-0.1424	0.0431	0.035	0.0489	-0.0755	0.0373	-0.1638	-0.0112	0.3991	0.0475	-0.3198	0.3897	-0.1252	0.9556	24.3653	-10.0779	14.4525
17	0.7655	0.6317	0.1941	0.5486	0.203	0.6301	-0.025	-0.0989	0.2611	-0.0643	-0.0253	0.2095	0.0018	-0.2241	0.0788	0.5287	-0.1274	-0.3473	0.7006	-0.1479	0.9221	26.8245	-12.2693	18.5475
18	4.8598	3.4394	-4.6357	7.7517	-1.6771	4.9056	-0.0221	-1.4773	0.5168	-0.4289	0.2468	1.0802	0.0904	-1.899	-0.2552	0.4903	0.0484	-0.4049	0.8498	-0.0416	0.7199	29.5464	-16.2065	21.1804
19	8.9879	1.4412	-3.0751	8.1805	-4.8744	7.6439	0.5659	-0.2026	-1.5743	0.0268	-0.237	-0.0895	0.9605	0.4404	-0.3749	0.6407	0.1683	-0.4559	0.9695	0.1658	0.9503	33.2153	-19.5226	21.8288
20	2	-4.7245	4.7853	6.8477	-3.9559	9.9571	1.2439	0.1652	-3.5861	-0.5072	-0.3905	0.7817	1.3352	-0.546	-0.8989	0.4912	0.1343	-0.3562	0.8196	0.0593	1.1949	37.7935	-21.0655	20.5482
21	7.3916	-2.2892	3.8237	6.9561	-1.024	9.3954	0.7304	0.3928	-2.013	-0.0818	-0.1783	0.1038	0.9952	-0.4288	-0.6221	0.4714	-0.0436	-0.4048	0.8843	-0.0443	0.9427	42.9781	-20.6008	19.7696
22	2.2691	-2.5839	-3.3742	8.7529	3.6696	6.4056	0.3261	0.9587	-1.243	0.0739	0.2238	-0.646	0.447	1.1243	-0.584	0.5476	-0.0382	-0.4748	1.1334	-0.0696	1.0703	47.0934	-18.343	19.7321
23	8.1517	0.7513	-0.3586	8.9422	-5.3162	4.309	0.6217	2.5908	-2.2819	-0.6682	0.5076	0.1251	1.7827	0.0322	-1.1393	0.9031	-0.0531	-0.6417	1.4335	-0.164	1.2838	49.7912	-14.3964	20.9979
24	4.7074	0.8713	-0.0029	3.5687	1.8726	2.6958	-0.8949	-0.4891	2.8712	-0.1296	0.1393	0.5896	-0.9413	-0.2959	0.7826	0.8799	0.0171	-0.6375	1.399	-0.1527	1.4389	44.7198	-11.8787	29.611
25	9.7565	-6.9747	2.3418	7.9794	-6.255	7.5728	-0.8463	-2.3315	2.7236	0.3856	-0.4531	0.1991	-1.3646	-0.2489	1.3291	0.9361	0.0699	-0.6717	1.6585	-0.1382	1.5828	42.526	-9.2908	26.8297
26	2	3.3733	-8.4395	1.2333	-1.9645	2	-1.276	-3.244	5.4329	0.2809	-0.5247	1.0293	-2.9855	0.6959	1.8157	0.9452	-0.042	-0.6496	1.2457	-0.2501	1.6088	41.9615	-8.6592	22.0593
27	2.7313	4.9543	-0.6799	8.9867	-1.2468	8.4842	-0.7999	-1.272	4.4598	-0.2812	-0.2615	1.0464	-1.6666	0.4374	1.0885	0.6573	-0.0665	-0.4966	0.7899	-0.0198	1.4592	40.8075	-9.7631	17.6791
28	9.1971	-5.6881	1.2407	4.581	1.4726	4.8866	-0.7387	1.0494	2.4704	0.4437	0.4156	-0.9894	-0.7975	1.1782	0.3369	0.6135	-0.0395	-0.4805	0.5938	-0.0096	1.0655	39.687	-12.8518	14.0151
29	5.9031	-6.6231	1.2312	8.6336	1.5012	7.1641	0.0955	1.2355	0.912	0.5864	0.1504	-1.6387	0.3197	1.6583	-0.2659	0.4191	0.0344	-0.3489	0.7202	-0.0279	0.9279	37.0873	-16.1816	11.8619
30	1.0327	-1.1703	-0.4138	1.7857	0.2698	0.2522	0.1253	0.1256	-0.2897	0.1257	0.0458	-0.3796	0.1946	0.1096	-0.1919	0.3492	-0.0313	-0.2986	0.5844	-0.0928	0.9013	32.9176	-19.0063	11.144
31	6.3762	0.012	2.7226	1.6826	-0.0306	3.3049	-0.2017	-0.1968	0.6987	-0.0196	0.0544	0.0556	-0.2695	-0.0174	0.127	0.3816	0.0362	-0.3024	0.4325	0.0178	1.0499	28.5012	-20.9415	13.1993
32	8.1904	1.6881	0.9424	1.8912	-0.1849	3.3799	0.2655	-0.3791	-1.0746	0.0633	0.0119	-0.1885	0.3813	0.0072	-0.2901	0.3137	-0.0196	-0.2086	0.5031	-0.0149	1.1024	24.4556	-20.4373	15.2062
33	4.7209	1.826	1.3791	1.4505	1.0529	3.2677	0.2201	-0.2781	-0.5048	0.1624	-0.0516	-0.1334	0.2974	-0.0565	-0.1866	0.3033	-0.0965	-0.269	0.4445	0.0235	0.5521	20.2939	-17.4352	14.0227
34	5.993	-2.4455	-3.359	0.9997	1.3035	4.2759	-0.0836	-0.9239	-0.767	0.0762	-0.1347	0.4951	0.2061	0.0076	0.2321	0.1749	-0.0662	-0.0672	0.3982	0.175	0.7069	16.7322	-14.6426	11.8484
35	3.3086	0.3348	0.8961	0.2593	0.4822	1.0403	-0.0269	-0.0555	0.2169	-0.0066	-0.0098	0.0069	-0.0423	-0.049	0.0794	0.2094	-0.0848	-0.1621	0.278	0.1975	0.5345	14.2372	-11.9884	8.6102
36	8.0649	0.9817	3.3879	3.7339	-0.2633	4.0002	-0.1316	-0.2548	0.287	0.099	0.0858	-0.0435	-0.1328	-0.1297	0.0679	0.3255	0.1211	-0.258	0.2748	-0.1546	0.4905	12.9178	-11.0391	3.5858
37	0.1232	0.0533	-0.0489	0.0593	0.0169	0.0592	-0.0012	-0.0055	-0.0181	0.0003	0.0077	0.0186	0.0039	-0.0117	-0.0179	0.162	0.0083	-0.1494	0.3824	0.0073	0.2854	11.3474	-13.4271	-1.0873

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and resid 103:122
2	X-RAY DIFFRACTION	2	chain A and resid 124:195
3	X-RAY DIFFRACTION	3	chain A and resid 197:219
4	X-RAY DIFFRACTION	4	chain A and resid 220:409
5	X-RAY DIFFRACTION	5	chain A and resid 410:421
6	X-RAY DIFFRACTION	6	chain C and resid 15:15
7	X-RAY DIFFRACTION	7	chain C and resid 16:16
8	X-RAY DIFFRACTION	8	chain C and resid 17:17
9	X-RAY DIFFRACTION	9	chain C and resid 18:18
10	X-RAY DIFFRACTION	10	chain C and resid 19:19
11	X-RAY DIFFRACTION	11	chain C and resid 20:20
12	X-RAY DIFFRACTION	12	chain C and resid 21:21
13	X-RAY DIFFRACTION	13	chain C and resid 22:22
14	X-RAY DIFFRACTION	14	chain C and resid 23:23
15	X-RAY DIFFRACTION	15	chain C and resid 24:24
16	X-RAY DIFFRACTION	16	chain C and resid 25:25
17	X-RAY DIFFRACTION	17	chain C and resid 26:26
18	X-RAY DIFFRACTION	18	chain C and resid 27:27
19	X-RAY DIFFRACTION	19	chain C and resid 28:28
20	X-RAY DIFFRACTION	20	chain C and resid 29:29
21	X-RAY DIFFRACTION	21	chain C and resid 30:30
22	X-RAY DIFFRACTION	22	chain C and resid 31:31
23	X-RAY DIFFRACTION	23	chain C and resid 32:32
24	X-RAY DIFFRACTION	24	chain C and resid 1:1
25	X-RAY DIFFRACTION	25	chain C and resid 2:2
26	X-RAY DIFFRACTION	26	chain C and resid 3:3
27	X-RAY DIFFRACTION	27	chain C and resid 4:4
28	X-RAY DIFFRACTION	28	chain C and resid 5:5
29	X-RAY DIFFRACTION	29	chain C and resid 6:6
30	X-RAY DIFFRACTION	30	chain C and resid 7:7
31	X-RAY DIFFRACTION	31	chain C and resid 8:8
32	X-RAY DIFFRACTION	32	chain C and resid 9:9
33	X-RAY DIFFRACTION	33	chain C and resid 10:10
34	X-RAY DIFFRACTION	34	chain C and resid 11:11
35	X-RAY DIFFRACTION	35	chain C and resid 12:12
36	X-RAY DIFFRACTION	36	chain C and resid 13:13
37	X-RAY DIFFRACTION	37	chain C and resid 14:14

-
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