PDB-6emy: Structure of the Tn1549 transposon Integrase (aa 82-397, Y379F) i...

ID or keywords:

Entry

Database: PDB / ID: 6emy

Title

Structure of the Tn1549 transposon Integrase (aa 82-397, Y379F) in complex with transposon right end DNA

Components

DNA (20-MER)
DNA (26-MER)
Int protein

Keywords

RECOMBINATION /

transposase protein-DNA complex / tyrosine recombinase / Y-transposase / Tn916-like conjugative transposon / antibiotic resistance transfer

Function / homology

Function and homology information

integrase activity / viral genome integration into host DNA / establishment of integrated proviral latency / DNA recombination / symbiont entry into host cell /

Biological species

Enterococcus faecalis (bacteria)

Clostridioides difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.5 Å

Authors

Schulz, E.C. / Rubio-Cosials, A. / Barabas, O.

Citation

Journal: Cell / Year: 2018
Title: Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance.
Authors: Rubio-Cosials, A. / Schulz, E.C. / Lambertsen, L. / Smyshlyaev, G. / Rojas-Cordova, C. / Forslund, K. / Karaca, E. / Bebel, A. / Bork, P. / Barabas, O.

History

Deposition	Oct 4, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 4, 2018	Provider: repository / Type: Initial release
Revision 1.1	Sep 19, 2018	Group: Data collection / Category: diffrn_radiation_wavelength / Item: _diffrn_radiation_wavelength.wavelength

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6emy.cif.gz	362.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6emy.ent.gz	306 KB	Display	PDB format
PDBx/mmJSON format	6emy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/em/6emy ftp://data.pdbj.org/pub/pdb/validation_reports/em/6emy	HTTPS FTP

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Related structure data

Related structure data	6emzC 6en0C 6en1C 6en2C C: citing same article (ref.)
Similar structure data	7e3j-d 1m0t-d 6nob-2 4dlo-d 4i7z-d 2aus-1 4eb5-d 14 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
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) #84 - Dec 2006 Transposase similarity (10) #253 - Jan 2021 Expressome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #135 - Mar 2011 Integrase similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #73 - Jan 2006 Topoisomerase similarity (2) #87 - Mar 2007 Zinc Fingers 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) #160 - Apr 2013 Actinomycin similarity (2) #39 - Mar 2003 lac Repressor similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase 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) #23 - Nov 2001 DNA similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #131 - Nov 2010 Inteins similarity (1) #125 - May 2010 Parvoviruses similarity (1) #119 - Nov 2009 Designed DNA Crystal 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)
#84 - Dec 2006
Transposase
similarity (10)
#253 - Jan 2021
Expressome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (2)
#87 - Mar 2007
Zinc Fingers
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)
#160 - Apr 2013
Actinomycin
similarity (2)
#39 - Mar 2003
lac Repressor
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
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)
#23 - Nov 2001
DNA
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Int protein

B: Int protein

C: DNA (20-MER)

E: DNA (20-MER)

F: DNA (26-MER)

D: DNA (26-MER)

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

1

Idetical with deposited unit
defined by software
Evidence: equilibrium centrifugation, gel filtration

Unit cell

Length a, b, c (Å)	77.230, 121.681, 77.234
Angle α, β, γ (deg.)	90.00, 118.12, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Int protein / Integrase Mass: 36270.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: int / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q7BP35
#2: DNA chain	DNA (20-MER) Mass: 6050.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Transposon right end DNA / Source: (synth.) Clostridioides difficile (bacteria)
#3: DNA chain	DNA (26-MER) Mass: 8030.223 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Transposon right end DNA with 6nt single stranded 5' overhang in the crossover region Source: (synth.) Clostridioides difficile (bacteria)
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	3.18	61.3
2

Crystal grow

Temperature (K)	Crystal-ID	Method	Details
293	1	vapor diffusion	13% (v/v) PEG 3350, 0.25 M NaCl
293	2	vapor diffusion	13% (v/v) PEG 3350, 0.25 M NaCl

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	2

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	PETRA III, EMBL c/o DESY	P13 (MX1)	1	0.977315
SYNCHROTRON	PETRA III, EMBL c/o DESY	P13 (MX1)	2	0.977315

Detector

Type	ID	Detector	Date
DECTRIS PILATUS3 S 6M	1	PIXEL	Sep 28, 2013
DECTRIS PILATUS3 S 6M	2	PIXEL	Sep 28, 2013

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.977315	1
2	0.977315	1

Reflection

B_iso Wilson estimate: 57.351 Å² / Entry-ID: 6EMY

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	CC_1/2	R_merge(I) obs	R_pim(I) all	Diffraction-ID	Net I/σ(I)	R_sym value
2.5-45.38	41916	96.5	3.8	0.999	0.065	0.039	1	11.7
2.8-50	61251	97.1	3.5	0.994			2	8.79	0.109

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	Diffraction-ID	% possible all	R_sym value
2.5-2.64	3.8	0.835	1.6	6187	0.659	0.493	1	98
2.8-2.87	3.5		1.35	4618	0.547		2	98.2	0.988

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
Coot		model building
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.5→38.597 Å / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 23.58

	R_factor	Num. reflection	% reflection
R_free	0.1839	4185	5.24 %
R_work	0.1605	-	-
obs	0.1625	41894	93.03 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→38.597 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5038	1791	0	234	7063

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7141
X-RAY DIFFRACTION	f_angle_d	0.767	10006
X-RAY DIFFRACTION	f_dihedral_angle_d	21.746	2814
X-RAY DIFFRACTION	f_chiral_restr	0.033	1106
X-RAY DIFFRACTION	f_plane_restr	0.004	984

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 (%)
2.5001-2.5432	0.3029	205	0.2984	3834	X-RAY DIFFRACTION	91
2.5432-2.5894	0.3092	207	0.2925	3926	X-RAY DIFFRACTION	90
2.5894-2.6392	0.324	201	0.284	3858	X-RAY DIFFRACTION	90
2.6392-2.6931	0.2861	202	0.2744	3780	X-RAY DIFFRACTION	88
2.6931-2.7516	0.275	188	0.2738	3617	X-RAY DIFFRACTION	84
2.7516-2.8156	0.2971	207	0.26	3945	X-RAY DIFFRACTION	92
2.8156-2.886	0.2903	203	0.2595	3888	X-RAY DIFFRACTION	91
2.886-2.9639	0.272	209	0.2466	3900	X-RAY DIFFRACTION	91
2.9639-3.0511	0.2592	202	0.2408	3876	X-RAY DIFFRACTION	91
3.0511-3.1495	0.2487	206	0.2188	3899	X-RAY DIFFRACTION	90
3.1495-3.262	0.2056	205	0.1915	3846	X-RAY DIFFRACTION	90
3.262-3.3925	0.2391	197	0.1774	3711	X-RAY DIFFRACTION	86
3.3925-3.5467	0.1997	199	0.16	3884	X-RAY DIFFRACTION	92
3.5467-3.7335	0.1701	205	0.1615	3909	X-RAY DIFFRACTION	91
3.7335-3.9671	0.1568	208	0.135	3899	X-RAY DIFFRACTION	90
3.9671-4.2729	0.1534	202	0.1291	3751	X-RAY DIFFRACTION	87
4.2729-4.7019	0.1572	185	0.1216	3567	X-RAY DIFFRACTION	84
4.7019-5.3799	0.1293	196	0.1227	3758	X-RAY DIFFRACTION	88
5.3799-6.7694	0.1586	184	0.1353	3486	X-RAY DIFFRACTION	81
6.7694-34.0598	0.1378	184	0.1107	3454	X-RAY DIFFRACTION	80

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.0464	-0.3312	0.163	4.3636	-0.575	1.6716	0.2244	0.5069	-0.0466	-0.5617	-0.1538	0.7469	-0.0946	-0.3575	-0.0242	0.4455	0.0891	-0.0801	0.5059	-0.0167	0.5412	-96.3363	37.4367	65.3926
2	1.463	-0.2546	0.6562	1.699	-0.3894	0.1464	-0.1343	0.0462	0.3409	-0.0111	-0.0856	-0.1481	-0.5345	0.2585	0.2578	0.5045	-0.0271	-0.0297	0.5508	0.0631	0.8033	-89.7587	46.4805	73.6051
3	2.742	0.6984	0.6405	2.7375	0.554	2.1775	0.1551	-0.1739	-0.2343	0.4797	-0.1782	-0.2987	0.0288	0.0183	0.0591	0.4514	0.0057	-0.002	0.3118	0.0325	0.3451	-79.6816	18.2384	91.7899
4	1.2202	1.207	-0.5232	1.3176	-0.5744	2.193	0.1583	-0.0739	0.2453	0.3712	-0.1491	0.1457	-0.3129	-0.1347	0.0287	0.5257	0.0079	0.0312	0.4045	-0.0601	0.4322	-77.2894	37.3948	91.8429
5	3.3227	3.8151	6.0846	4.3179	6.915	2.0729	-0.4634	0.3342	0.7916	-0.8581	-0.5385	0.994	-0.5669	-0.252	1.1844	0.6856	0.0011	-0.0823	0.8076	0.0528	0.6605	-72.9718	54.3297	47.4679
6	0.828	-0.1777	-0.6001	3.4571	0.6479	1.3605	0.1026	0.6435	-0.2951	-0.7296	-0.1064	0.2778	0.3164	-0.0343	0.0805	0.6344	0.0228	-0.0274	0.5992	-0.15	0.4907	-63.4158	44.726	45.8377
7	8.9786	-1.3374	2.4518	3.4858	-0.7381	3.4875	-0.0056	0.6093	-0.1629	-0.0947	-0.2764	0.5752	0.2937	-0.1128	0.282	0.6963	-0.0885	0.1359	0.5868	-0.1107	0.4088	-69.9695	43.6858	53.4314
8	0.0172	0.4448	-0.0957	1.0436	0.3843	3.1294	-0.3441	0.0778	-0.103	-0.107	0.0189	0.1125	-0.1401	-0.2387	0.4081	0.6425	0.0138	-0.0321	0.4743	-0.0748	0.7417	-63.3345	38.9337	58.1793
9	4.3369	0.0252	-0.0407	2.1427	0.7183	1.7508	-0.1354	-0.3872	0.5401	0.6375	0.3004	-0.5612	-0.1256	0.482	-0.106	0.5542	0.0256	-0.1277	0.4861	-0.0217	0.8334	-40.2605	58.8387	77.3807
10	1.7329	-0.1114	-0.5812	1.5711	-2.0448	6.5122	0.0141	-0.156	-0.0113	0.2718	-0.0278	-0.0034	-0.5362	-0.2964	0.0898	0.503	0.0461	0.0847	0.3695	-0.0136	0.4712	-59.314	64.9298	74.186
11	3.407	0.2426	-0.7134	2.2381	-0.1403	3.722	-0.1695	-0.299	0.6988	0.4688	0.0949	-0.4602	-0.167	0.3862	-0.0994	0.4815	0.0108	-0.0807	0.3747	-0.0129	0.5426	-49.9161	72.0442	74.2764
12	4.6529	-3.6513	4.3659	4.5999	-3.9502	4.3131	0.4504	-0.3828	-0.4804	-0.2606	-0.299	-0.1964	0.2237	0.2463	-0.0116	0.4012	-0.0128	0.0509	0.4875	0.0705	0.9001	-39.3572	56.5853	67.3041
13	1.5322	1.2219	-0.8645	2.3253	-1.1413	1.5624	0.1422	-0.1111	-0.3511	0.1695	-0.357	-0.2878	-0.1487	0.0863	0.2119	0.4597	-0.0214	0.004	0.4293	0.015	0.5549	-56.7787	43.4628	80.3628
14	2.0351	-1.8509	-3.6337	5.7549	0.434	8.902	-0.1416	-0.9115	0.4916	-0.3384	0.2841	0.1151	0.3329	-0.7621	-0.3514	0.9934	-0.1695	0.1603	1.1312	-0.0779	1.1845	-110.5239	20.0739	109.7095
15	3.7234	1.6941	-1.4645	3.4356	-0.1802	0.7102	0.1906	-0.2761	0.0178	0.3298	-0.3416	0.4098	0.185	-0.0521	0.0887	0.4681	-0.0521	0.1245	0.4811	0.0109	0.5956	-94.9051	27.7678	83.858
16	2.011	0.8124	-5.0848	6.3078	-2.7051	2.0138	-1.2266	0.2031	-0.2278	-0.7032	-0.5989	-0.491	0.0978	1.0345	1.5493	0.9312	-0.0016	0.3298	1.5124	0.6977	1.9451	-21.808	62.9557	53.0647
17	2.0277	0.3052	0.8946	1.8445	-0.3849	0.6376	-0.1826	0.4956	0.5221	-0.2849	-0.0442	-0.3658	0.2457	0.2626	0.151	0.5513	0.0037	0.1948	0.502	0.0374	0.8037	-49.0625	57.1161	58.4558
18	3.8002	2.631	-2.7944	1.9327	-2.0333	2.0755	0.232	-0.0424	-0.457	0.7143	-0.3096	0.6484	0.0807	-0.3184	-0.0172	0.5679	-0.1434	0.2318	0.5031	-0.1254	0.8354	-72.3202	48.779	64.5208
19	5.8187	2.2031	-0.4694	0.9863	-0.3941	0.3807	-0.8506	0.2455	-0.0082	-0.7558	0.264	-1.5186	0.2654	0.3124	0.4659	0.5858	0.0857	0.2886	0.8795	0.2367	1.4628	-34.7359	60.9053	56.7192
20	7.7918	3.7857	-0.747	1.8474	-0.3492	0.0469	0.4868	0.4208	-0.2726	-0.7205	0.32	-1.9162	-1.2466	2.1538	-0.5897	0.7272	-0.3483	0.2513	1.2083	-0.0793	1.1926	-77.8003	37.0643	66.9669
21	3.944	0.8096	-0.522	2.6824	-0.8818	2.0191	0.0861	-0.4434	0.0274	0.3377	0.0543	0.8684	0.196	-0.5055	-0.1976	0.5038	0.0039	0.1645	0.5356	0.0505	0.716	-96.7021	27.5343	85.4248
22	3.97	-0.3301	-1.9216	1.2902	0.7468	4.5386	0.1815	-0.7682	0.4415	0.5543	0.5139	-0.3308	0.756	-1.0205	-0.6939	1.3172	-0.1518	0.1813	0.8829	0.0514	1.2112	-108.9412	19.8382	108.2672

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 82 through 165 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 166 through 192 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 193 through 314 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 315 through 397 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 82 through 99 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 100 through 144 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 145 through 164 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 165 through 194 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 195 through 222 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 223 through 275 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 276 through 314 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 315 through 332 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 333 through 397 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid -19 through -12 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid -11 through -1 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid -18 through -14 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid -13 through -1 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 0 through 9 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 10 through 24 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 0 through 7 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 8 through 16 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 17 through 25 )

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News

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

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