PDB-8ylh: Crystal structure of Pectobacterium atrosepticum PecS

ID or keywords:

Entry

Database: PDB / ID: 8ylh

Title

Crystal structure of Pectobacterium atrosepticum PecS

Components

Regulatory protein

Keywords

TRANSCRIPTION / Transcription factor

Function / homology

MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / DNA-binding transcription factor activity / Winged helix-like DNA-binding domain superfamily / Regulatory protein

Function and homology information

Biological species

Pectobacterium atrosepticum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Song, W.S. / Yoon, S.I.

Funding support

Korea, Republic Of, 2items

Citation

Journal: Nucleic Acids Res. / Year: 2024
Title: Structural basis of transcriptional regulation by UrtR in response to uric acid.
Authors: Song, W.S. / Ki, D.U. / Cho, H.Y. / Kwon, O.H. / Cho, H. / Yoon, S.I.

History

Deposition	Mar 6, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 13, 2024	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ylh.cif.gz	170.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8ylh.ent.gz	111.2 KB	Display	PDB format
PDBx/mmJSON format	8ylh.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/yl/8ylh ftp://data.pdbj.org/pub/pdb/validation_reports/yl/8ylh	HTTPS FTP

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Related structure data

Related structure data	8ylfSC 8ylgC 8yliC 8yljC 8ylkC 8yllC 8ylmC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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

Deposited unit

A: Regulatory protein

B: Regulatory protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	52.350, 76.367, 78.651
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 16 through 33 or resid 35...
d_2	ens_1	(chain "B" and (resid 16 through 21 or (resid 22...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	ALA	ALA	ALA	ALA	A	A	16 - 33	7 - 24
d_1	2	PRO	PRO	LEU	LEU	A	A	35 - 53	26 - 44
d_1	3	CYS	CYS	PHE	PHE	A	A	56 - 57	47 - 48
d_1	4	PHE	PHE	PHE	PHE	A	A	60	51
d_1	5	LEU	LEU	SER	SER	A	A	62 - 63	53 - 54
d_1	6	GLU	GLU	HIS	HIS	A	A	66 - 80	57 - 71
d_1	7	LEU	LEU	PHE	PHE	A	A	82 - 88	73 - 79
d_1	8	THR	THR	LYS	LYS	A	A	90 - 103	81 - 94
d_1	9	LEU	LEU	THR	THR	A	A	105 - 128	96 - 119
d_1	10	SER	SER	ASP	ASP	A	A	130 - 162	121 - 153
d_1	11	ASN	ASN	HIS	HIS	A	A	164 - 175	155 - 166
d_2	1	ALA	ALA	ALA	ALA	B	B	16 - 33	7 - 24
d_2	2	PRO	PRO	LEU	LEU	B	B	35 - 53	26 - 44
d_2	3	CYS	CYS	PHE	PHE	B	B	56 - 57	47 - 48
d_2	4	PHE	PHE	PHE	PHE	B	B	60	51
d_2	5	LEU	LEU	SER	SER	B	B	62 - 63	53 - 54
d_2	6	GLU	GLU	HIS	HIS	B	B	66 - 80	57 - 71
d_2	7	LEU	LEU	PHE	PHE	B	B	82 - 88	73 - 79
d_2	8	THR	THR	LYS	LYS	B	B	90 - 103	81 - 94
d_2	9	LEU	LEU	THR	THR	B	B	105 - 128	96 - 119
d_2	10	SER	SER	ASP	ASP	B	B	130 - 162	121 - 153
d_2	11	ASN	ASN	HIS	HIS	B	B	164 - 175	155 - 166

NCS oper: (Code: givenMatrix: (-0.999943632064, 0.000882539458852, -0.0105808231166), (-0.00195028645092, 0.964316386382, 0.264745355651), (0.0104369093357, 0.264751068138, -0.964260308653)Vector: -0. ...

#1: Protein	Regulatory protein Mass: 19064.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Gene: pecS, ECA2036 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6D5K4
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.34 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Hepes, magnesium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 7, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.55→30 Å / Num. obs: 46157 / % possible obs: 99.5 % / Redundancy: 5.2 % / CC_1/2: 0.995 / Net I/σ(I): 28.9
Reflection shell	Resolution: 1.55→1.58 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2313 / CC_1/2: 0.768 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8YLF

8ylf

Resolution: 1.55→28.72 Å / SU ML: 0.1519 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0113
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.218	2245	4.87 %
R_work	0.2005	43831	-
obs	0.2014	46076	99.31 %

Solvent computation

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

Displacement parameters

B_iso mean: 17.69 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→28.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2484	0	2	152	2638

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0056	2586
X-RAY DIFFRACTION	f_angle_d	0.7791	3527
X-RAY DIFFRACTION	f_chiral_restr	0.0434	422
X-RAY DIFFRACTION	f_plane_restr	0.0098	460
X-RAY DIFFRACTION	f_dihedral_angle_d	10.7327	990

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.68749453932 Å

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 (%)
1.55-1.58	0.2544	120	0.2488	2669	X-RAY DIFFRACTION	97.18
1.58-1.62	0.2279	150	0.2319	2712	X-RAY DIFFRACTION	99.93
1.62-1.66	0.2202	142	0.2133	2712	X-RAY DIFFRACTION	99.89
1.66-1.71	0.2631	140	0.2133	2710	X-RAY DIFFRACTION	99.96
1.71-1.76	0.2469	130	0.2118	2731	X-RAY DIFFRACTION	99.9
1.76-1.81	0.2358	140	0.21	2716	X-RAY DIFFRACTION	99.86
1.81-1.88	0.2636	187	0.2089	2690	X-RAY DIFFRACTION	99.93
1.88-1.95	0.2566	147	0.2218	2736	X-RAY DIFFRACTION	99.9
1.95-2.04	0.2301	152	0.19	2698	X-RAY DIFFRACTION	99.93
2.04-2.15	0.1918	122	0.1814	2772	X-RAY DIFFRACTION	99.93
2.15-2.29	0.2047	130	0.1804	2760	X-RAY DIFFRACTION	99.93
2.29-2.46	0.2054	123	0.1944	2772	X-RAY DIFFRACTION	99.76
2.46-2.71	0.225	170	0.2074	2713	X-RAY DIFFRACTION	99.14
2.71-3.1	0.2399	109	0.21	2812	X-RAY DIFFRACTION	99.08
3.1-3.91	0.2132	158	0.1894	2767	X-RAY DIFFRACTION	98.72
3.91-28.72	0.1742	125	0.1976	2861	X-RAY DIFFRACTION	96.32

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	3.03373335888	1.0764394968	1.69840103667	1.76624200312	-0.819097099526	8.13811361488	0.106954428807	-0.00379391657343	-0.183849026646	-0.0304572036323	-0.0415246173333	-0.08594396477	0.337212499408	0.256365279281	-0.057026719566	0.10861165312	0.0295548628274	0.0087974136429	0.0640388140187	-0.00114011897961	0.11065756108	16.636054253	-17.8948355043	30.6625319084
2	1.83782538431	-3.40790185498	3.46433638274	5.20901525274	-6.1388088934	5.47017952967	0.0522009689349	0.0639808613488	0.141399062525	-0.0224513550053	-0.106159480234	-0.20461354709	0.0148852682934	0.147792474876	0.136325358369	0.121930826473	-0.000758154091212	0.0067888977402	0.115682907943	-0.00762454749856	0.131800005965	2.94697787655	-9.23032299082	14.3798252659
3	3.24565410303	-0.0205566937554	-1.04122077452	3.0727986222	-0.103366188666	2.47772630864	-0.0397884146196	-0.216315937223	0.023998964483	0.104132183154	0.00699044078067	-0.00813433210762	0.05136728519	0.0352680723026	0.0303545315259	0.0833458860005	0.00141641286643	-0.0111607860786	0.0793129852995	0.0144140186895	0.0791548692202	-15.8311609884	-2.16055193073	11.98374233
4	0.51535563615	1.42203101707	-1.69826383628	6.16406783782	-3.59443225829	6.05416896616	0.180541880495	-0.260299328593	0.128897989775	0.358380957284	-0.16804859839	-0.0674600137198	-0.431754453345	0.0123112180421	-0.0225060435507	0.146505941225	-0.0305107040552	-0.0463072114384	0.157163010111	0.00669488775638	0.266682942708	-13.321098329	8.88131092647	14.2611047138
5	5.34937925843	1.21201772535	-4.52023842061	1.36562924536	-0.61392232943	5.77303690381	0.114482689211	0.409003751402	0.527630183162	0.449941367208	0.361539116315	0.46093848988	-0.455269832249	-1.08709084074	-0.288832554677	0.185545538155	0.0785592527771	0.0533648960844	0.232496330066	0.07131593093	0.255698506332	-23.3988311867	7.82420718468	10.3625342194
6	7.36186054524	-1.4334071831	-5.78115422787	3.08134037348	0.416013483844	8.42789717477	0.14469906812	-0.304007039049	0.393768956006	0.145360066404	0.243429034469	0.494723068473	-0.430481134956	0.0711478052626	-0.341966463356	0.138050443993	0.0053994821732	0.016772939012	0.136119176969	0.0113752109471	0.258269536473	-26.5289845857	5.52832183278	12.9947657681
7	7.54632542486	-5.69838671811	2.11750652937	6.057999956	-1.99646456322	2.1771844033	0.0868020808895	0.542801425152	0.00847407586226	-0.28297125532	-0.18889742812	-0.0783648268755	0.0968652826809	0.168156509102	0.0944052859568	0.157350048505	-0.0238128887377	0.0114726483675	0.124321546893	-0.00525122709738	0.0732994417567	-7.58950046694	-7.11583814808	0.798278255263
8	5.29566188252	1.31166342888	-2.1203605942	2.26480343405	-0.489153243825	7.73997843561	0.127839818425	-0.202731772687	-0.0834742089178	0.0773739852549	0.0169536264984	0.108450631623	0.204860566884	-0.41989962036	-0.10848544457	0.109082784879	-0.0150859038192	-0.046169029855	0.0771053930124	0.0429266757848	0.142385106923	-5.42170524545	-21.5570212461	18.0298969835
9	2.59391033302	-1.05372479073	0.380847569353	2.20219731267	0.248876828583	6.69513824407	0.0752452296423	0.0269339352503	-0.209747919496	-0.239311122953	0.0819645558141	0.191767901396	0.346127605333	-0.252574964897	-0.132689232741	0.165276801282	-0.0345850948903	-0.0315131773339	0.0877048743256	-0.00702218754506	0.122311353465	-17.1115474333	-14.1901776779	4.44496138888
10	2.39413732161	1.59869328856	3.66306200827	1.63131277604	3.16518091924	6.82538213045	0.00791038957591	-0.137275888406	0.0847239946487	-0.0245481076212	-0.00913236568444	0.080025803549	-0.15671253612	-0.171424744188	0.0292936821218	0.0994688814437	0.0117491300719	0.0171079602137	0.107497648764	0.00277828051922	0.10875068076	-3.63537596538	-10.9359430232	23.4249122666
11	3.38996814524	-0.37737262212	0.774671187763	2.09787990647	-0.748443767826	1.6164549127	0.0598405533448	0.0384108253176	0.143203694068	0.0988551610261	-0.0595728859512	0.0204528898227	-0.0726044527926	0.0122251623881	-0.00374957117662	0.0956243185976	-0.0168337107553	0.00742471354631	0.104655736829	-0.0308945890543	0.0958665982106	14.2006831974	-4.80308371434	31.6913037104
12	2.77665900799	3.0197539979	-1.3336531752	6.50661921235	-0.395067553477	5.89297550385	-0.189542543138	0.423264096839	0.0194903800637	-0.317963153049	0.0585679733551	0.21530955406	-0.0520156105891	-0.138028884649	0.120602624426	0.114379286863	0.0168136461548	0.00630433973193	0.15607275747	-0.0217579622893	0.110833601748	17.2310867137	-3.50953235321	22.3512766017
13	2.47887471294	-0.879253729757	0.759796424999	7.07309381512	3.19288790445	2.71523005979	0.218389612072	0.267365803159	0.735505408051	-0.0244164685261	-0.0428484825436	0.0596756171602	0.108070350392	-0.218577139559	-0.153834247018	0.119707541758	-0.0033246058667	0.0183683258004	0.175542721283	0.00266637326008	0.211043953392	12.8704793601	7.06973536253	28.5448157239
14	8.25413155289	-2.0451760531	-4.96618191995	2.42058002292	1.67753000067	7.07361141222	0.310200146975	-0.366341821828	0.545573943645	0.0107634019366	0.00403167555845	-0.0688401726559	-0.343739371463	0.462247406014	-0.27346010192	0.186739937352	-0.0196941277409	0.0139108050651	0.167489073671	-0.0822297349906	0.201695273737	19.8752536174	5.30663262214	32.9132012818
15	4.32452390385	1.30908729168	-6.39202730347	4.27452824792	-2.11345292114	9.61091775013	0.191538960992	-0.159595603799	0.569792807334	-0.235327778468	0.127447735222	-0.385031128919	-0.186641593333	0.393719266377	-0.374878281642	0.148821558872	-0.016156113162	0.0289449962156	0.203718626898	-0.04618593834	0.213891746863	27.8704063879	3.49403063542	27.1921543603
16	5.75022546354	4.58585005039	3.34104064799	4.85557485165	2.63426299728	2.89454135109	0.246918021698	-0.608264841861	0.0192434241907	0.322352756229	-0.330267017688	0.0935471986709	0.0859244608464	-0.182661255661	0.0830757544413	0.136416063623	0.00419313021425	0.0229743497651	0.172455064182	-0.0158346315332	0.0798332434234	7.42002284819	-12.2351448029	37.3276378426
17	7.53490135682	3.63476138999	-4.70031520667	7.52620460971	-5.42944310871	7.78187529042	0.0816386851396	0.275277781346	0.0691914561282	-0.3170738361	0.0929187034071	-0.0220026589502	0.286856996392	0.2395024743	-0.141505755381	0.115981628099	0.0148199104218	-0.0446965454108	0.110667008531	-0.0452741744243	0.11972238093	5.01634770099	-21.6709043495	16.8302687837

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 15 through 32 )	A	A	15 - 32	1 - 18
2	2	chain 'A' and (resid 33 through 60 )	A	A	33 - 60	19 - 46
3	3	chain 'A' and (resid 61 through 98 )	A	A	61 - 98	47 - 84
4	4	chain 'A' and (resid 99 through 107 )	A	A	99 - 107	85 - 93
5	5	chain 'A' and (resid 108 through 118 )	A	A	108 - 118	94 - 104
6	6	chain 'A' and (resid 119 through 128 )	A	A	119 - 128	105 - 114
7	7	chain 'A' and (resid 129 through 152 )	A	A	129 - 152	115 - 138
8	8	chain 'A' and (resid 153 through 175 )	A	A	153 - 175	139 - 161
9	9	chain 'B' and (resid 16 through 32 )	B	C	16 - 32	1 - 17
10	10	chain 'B' and (resid 33 through 60 )	B	C	33 - 60	18 - 45
11	11	chain 'B' and (resid 61 through 80 )	B	C	61 - 80	46 - 65
12	12	chain 'B' and (resid 81 through 98 )	B	C	81 - 98	66 - 83
13	13	chain 'B' and (resid 99 through 107 )	B	C	99 - 107	84 - 92
14	14	chain 'B' and (resid 108 through 115 )	B	C	108 - 115	93 - 100
15	15	chain 'B' and (resid 116 through 128 )	B	C	116 - 128	101 - 113
16	16	chain 'B' and (resid 129 through 152 )	B	C	129 - 152	114 - 137
17	17	chain 'B' and (resid 153 through 175 )	B	C	153 - 175	138 - 160

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+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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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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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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi