PDB-8u12: Crystal Structure of Antitoxin Protein Rv0298 of Type II Toxin-an...

ID or keywords:

Entry

Database: PDB / ID: 8u12

Title

Crystal Structure of Antitoxin Protein Rv0298 of Type II Toxin-antitoxin Systems from Mycobacterium tuberculosis

Components

Antitoxin Rv0298

Keywords

ANTITOXIN / Toxin antitoxin modules / Type II TA system / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID

Function / homology

positive regulation of growth / Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / regulation of DNA-templated transcription / Antitoxin Rv0298

Function and homology information

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.6 Å

Authors

Kim, Y. / Tesar, C. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of Antitoxin Protein Rv0298 of Type II Toxin-antitoxin Systems from Mycobacterium tuberculosis
Authors: Kim, Y. / Tesar, C. / Endres, M. / Joachimiak, A.

History

Deposition	Aug 30, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 27, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8u12.cif.gz	220.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8u12.ent.gz	147.6 KB	Display	PDB format
PDBx/mmJSON format	8u12.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8u12_validation.pdf.gz	465.2 KB	Display	wwPDB validaton report
Full document	8u12_full_validation.pdf.gz	466 KB	Display
Data in XML	8u12_validation.xml.gz	19.2 KB	Display
Data in CIF	8u12_validation.cif.gz	29.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u1/8u12 ftp://data.pdbj.org/pub/pdb/validation_reports/u1/8u12	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: IDP97382

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Antitoxin Rv0298

B: Antitoxin Rv0298

C: Antitoxin Rv0298

D: Antitoxin Rv0298

E: Antitoxin Rv0298

F: Antitoxin Rv0298

G: Antitoxin Rv0298

H: Antitoxin Rv0298

hetero molecules

66.3 kDa, 8 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)	141.237, 141.237, 86.677
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3
Space group name Hall	R3
Symmetry operation	#1: x,y,z #2: -y,x-y,z #3: -x+y,-x,z #4: x+1/3,y+2/3,z+2/3 #5: -y+1/3,x-y+2/3,z+2/3 #6: -x+y+1/3,-x+2/3,z+2/3 #7: x+2/3,y+1/3,z+1/3 #8: -y+2/3,x-y+1/3,z+1/3 #9: -x+y+2/3,-x+1/3,z+1/3

#1: Protein	Antitoxin Rv0298 Mass: 8234.988 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: Rv0298 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: P9WJ09
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.55 Å³/Da / Density % sol: 51.85 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 1.0 M magnesium sulfate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jul 25, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 84954 / % possible obs: 99.4 % / Redundancy: 9 % / B_iso Wilson estimate: 20.78 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.112 / R_pim(I) all: 0.038 / R_rim(I) all: 0.118 / Net I/σ(I): 18.9
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.901 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 3917 / CC_1/2: 0.411 / R_pim(I) all: 0.556 / R_rim(I) all: 0.968 / % possible all: 91.1

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MLPHARE		phasing
MOLREP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.6→22.36 Å / SU ML: 0.2121 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 17.5181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.186	4094	4.84 %
R_work	0.1655	80479	-
obs	0.1664	84573	98.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 27.21 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→22.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3032	0	20	414	3466

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0127	3233
X-RAY DIFFRACTION	f_angle_d	1.2305	4371
X-RAY DIFFRACTION	f_chiral_restr	0.0773	527
X-RAY DIFFRACTION	f_plane_restr	0.0165	574
X-RAY DIFFRACTION	f_dihedral_angle_d	13.9216	1253

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 (%)
1.6-1.62	0.3398	124	0.3465	2373	X-RAY DIFFRACTION	85.43
1.62-1.64	0.3221	136	0.3387	2664	X-RAY DIFFRACTION	93.83
1.64-1.66	0.3094	184	0.2735	2627	X-RAY DIFFRACTION	95.58
1.66-1.68	0.2697	113	0.2524	2713	X-RAY DIFFRACTION	96.25
1.68-1.7	0.2557	175	0.2184	2709	X-RAY DIFFRACTION	97.01
1.7-1.73	0.2283	140	0.2168	2809	X-RAY DIFFRACTION	99.8
1.73-1.75	0.2582	134	0.1994	2796	X-RAY DIFFRACTION	99.97
1.75-1.78	0.1751	137	0.1913	2794	X-RAY DIFFRACTION	100
1.78-1.81	0.1856	121	0.1848	2820	X-RAY DIFFRACTION	100
1.81-1.84	0.2406	156	0.1756	2838	X-RAY DIFFRACTION	100
1.84-1.87	0.2006	142	0.1795	2782	X-RAY DIFFRACTION	100
1.87-1.91	0.1997	116	0.1784	2882	X-RAY DIFFRACTION	100
1.91-1.95	0.2044	124	0.1914	2765	X-RAY DIFFRACTION	100
1.95-1.99	0.2396	170	0.2005	2773	X-RAY DIFFRACTION	100
1.99-2.04	0.2096	189	0.1623	2745	X-RAY DIFFRACTION	100
2.04-2.09	0.2212	139	0.1538	2839	X-RAY DIFFRACTION	100
2.09-2.14	0.1895	115	0.1469	2845	X-RAY DIFFRACTION	100
2.14-2.21	0.1695	146	0.1368	2830	X-RAY DIFFRACTION	100
2.21-2.28	0.1789	201	0.1475	2746	X-RAY DIFFRACTION	100
2.28-2.36	0.1703	141	0.1625	2783	X-RAY DIFFRACTION	100
2.36-2.45	0.1394	102	0.1472	2804	X-RAY DIFFRACTION	100
2.45-2.56	0.1877	132	0.1569	2864	X-RAY DIFFRACTION	100
2.56-2.7	0.1571	158	0.159	2784	X-RAY DIFFRACTION	100
2.7-2.87	0.2028	162	0.1649	2802	X-RAY DIFFRACTION	100
2.87-3.09	0.2109	112	0.1645	2818	X-RAY DIFFRACTION	100
3.09-3.4	0.1472	150	0.1505	2814	X-RAY DIFFRACTION	100
3.4-3.89	0.1455	122	0.1387	2819	X-RAY DIFFRACTION	100
3.89-4.89	0.165	116	0.144	2825	X-RAY DIFFRACTION	100
4.89-22.36	0.175	137	0.1787	2816	X-RAY DIFFRACTION	99.97

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	7.19771736016	0.664610777624	-0.335089570988	2.47307400285	0.780271810291	1.48232472461	0.0212119078456	-0.320633779256	-0.0101307673914	0.108420362422	-0.0332118123902	0.247243680215	-0.0486668410081	-0.216259288025	-0.0119902227242	0.15393631036	0.0114078550498	-0.0312406696383	0.24530315167	0.0185888494221	0.174208793469	1.85712048237	36.5137520892	30.925709394
2	4.56700635782	0.649773182691	3.22324451485	3.27356077949	2.62851752646	6.52922153609	-0.0562784054458	0.0345507503537	0.242692950725	-0.0435021329337	0.0193854523656	0.0834741122285	-0.0245608937889	-0.0263300388739	0.0739284828827	0.118281638176	-0.0076531633995	0.00357651819933	0.168520190398	0.0454834244055	0.178908011794	-0.6892051649	36.8039157738	18.3508818129
3	5.70906287996	-5.08108390239	5.90641341502	4.85826806154	-5.54165956239	6.55321343593	-0.149718141834	-0.776732157325	-0.239890448534	-0.326061171574	-0.152623319597	-0.950555142511	0.607200366147	0.0299988371174	0.273947596248	0.357862355508	0.0591087548019	0.0422327269515	0.478009581069	0.11735922173	0.454370905884	-2.32177118816	31.6817709465	33.570782563
4	3.44643030098	-3.15279035558	-1.5307823633	3.03603220051	1.07401740555	2.23265287806	0.0930236766993	0.262201626019	0.040977952109	-0.217371476436	-0.151393497871	0.161668159765	-0.0540243518104	-0.345389234955	0.104677968108	0.176891079599	-0.0124288110602	-0.0319183334704	0.265889563463	0.0238511145515	0.197633830159	-8.93697450503	30.2843528595	20.0081472441
5	8.63325095798	4.9536415331	-1.84875875723	3.94384906802	-1.08481344857	2.29977421328	0.131512607693	-0.317579711616	-0.073388646943	0.13518389081	-0.127872468705	-0.0281981857894	0.0508978587916	0.00373983577561	-0.00841554624844	0.123202769117	0.0039774479394	-0.00895960762767	0.157335816479	0.0217102855399	0.129958720754	3.69085287764	30.7715655092	22.6527996415
6	4.51458635761	4.07355240543	-2.31935703127	5.04707170379	-0.726400623661	3.19797571262	-0.184329387707	0.320329327713	-0.421838594474	1.11834062179	0.292164644984	0.0455160850044	0.232289666337	-0.769446664024	-0.366328356578	0.473107731753	-0.053318286141	0.0599809859492	0.364730434669	-0.0139153931885	0.360554193985	-53.4941927203	-0.54305365097	28.9019991853
7	1.08263408945	-0.802607925503	1.97219050203	5.76419757813	-5.25094672833	6.82084008645	0.00322432333932	0.226500584868	0.00222805350933	-0.123118405934	-0.100422942238	-0.166391341991	-0.04725097979	0.32392348104	0.067376422915	0.168013719255	-0.0134178951559	0.052983257764	0.211086565725	-0.0326079322156	0.194389881493	-38.2394021867	2.45676251546	28.6407138147
8	3.88739752636	-3.15902886234	-2.11690029647	7.0983960536	4.05269751224	3.66420500445	-0.0240507720132	0.0685924480631	-0.250664101669	-0.058281408033	-0.062875889865	0.203478895321	0.0612472126962	-0.072894657341	0.0772876439094	0.131630717985	-0.0145981372699	0.0237746148574	0.126971145931	-0.00900730921679	0.129813802919	-47.3440165782	5.57246282883	37.9222781511
9	5.24323052474	0.339957666822	-0.274489848335	6.80528835751	6.19347496959	5.71815639694	0.406416719648	-0.239644142012	0.76232155462	-0.0917332379374	-0.784333492053	0.783940359634	-0.658953032027	-0.689237921706	0.341616165727	0.239950083376	0.0116222125059	0.0489520939923	0.207524865777	-0.0679224885603	0.30706552343	-52.3735433945	24.9241276967	46.9304462163
10	6.43760152091	0.362974272017	-2.92110989491	9.23362641708	-6.64796639357	9.89800477615	-0.0113617412608	0.607817345992	0.153660630278	-0.104555499795	-0.42699596675	-0.00782898746455	-0.0856171805666	0.184386280978	0.437148979004	0.266105019812	-0.024290208987	0.0221016948647	0.251904360743	-0.050585178909	0.248820154941	-50.316034203	3.19817174114	24.5560437199
11	6.35181666833	0.0385234104564	-1.69975768836	1.32521761668	0.0291729268952	1.61748039585	0.0322614932923	0.227334905777	0.0706660736379	-0.0524834441401	-0.000558965340737	-0.0375898850482	-0.0988939450319	-0.0824029960457	-0.0287118689277	0.165657639651	-0.00669979339568	0.0367057498567	0.141894640143	-0.0121294502041	0.131764843018	-48.697658439	10.2708264629	34.0938198835
12	9.01024660239	5.42223724133	-2.55820658479	7.68389580773	-2.40607897886	5.01379378764	0.244895921823	0.672754440094	-0.125083763484	0.0352064795141	0.213445687383	-0.940007543729	-0.365475913214	0.344170052403	-0.476229076726	0.29906767578	-0.00720918427482	0.0976225637748	0.281803245004	-0.0533034333479	0.42863813427	-28.671798052	47.9791025833	32.7950264488
13	2.43663356825	-0.834249888074	1.58863873391	2.34753346641	-0.124245942954	1.16575885998	-0.0724074696364	-0.322632790424	-0.20438302605	0.275677627863	0.0882290490024	0.176647176091	-0.0386201445813	-0.165304391455	-0.0129130189927	0.261950277298	-0.017393420967	0.0517451502584	0.231779852115	0.0025401849828	0.190123010813	-30.6815105471	37.3130114615	43.3228853533
14	1.18547512756	0.340817269757	0.44821175216	4.75792297558	4.23711568188	9.13648248888	-0.0258335576367	0.0149849660287	0.0441943662672	-0.0560806577811	-0.0138420879131	-0.0224163474845	-0.271779158841	0.137054112977	-0.00485991917959	0.141250844783	-0.0146103470082	0.0235361860063	0.129429871547	-0.00176615983384	0.129574425431	-24.7920251674	36.0789103913	31.8756651187
15	6.40886365739	-2.9482134095	-2.93426212956	4.6286328405	2.33661097615	7.86137019294	0.0476356437284	0.435889577953	-0.159372246258	-1.26334762332	-0.389049883067	-0.0372545714438	-0.111929061109	-0.942979232776	0.311871083291	0.330153040712	-0.0394516472815	0.0292730725075	0.213862733914	-0.0195127832224	0.199072686484	-28.3806520389	22.1637242928	16.2082468272
16	3.81321076073	-1.58432626619	-4.96106513739	3.50243377622	0.597997983239	7.79218949656	-0.0758619752757	-0.31130574372	-0.119595986732	-0.129795596989	0.274619882734	0.301118706247	-0.356060493199	-0.290624396169	-0.209495592354	0.298678413259	-0.0154150947868	0.0432300222079	0.253626257007	-0.0385364879153	0.281266482679	-34.4736328166	45.841918137	34.9610981726
17	1.37225056318	0.772086714928	-1.23747111468	2.42917545114	-2.18241295866	5.03922534399	0.0400396145919	0.0615599688034	0.0191597862445	0.0649161683867	0.00680251165013	0.094229854837	-0.0715395234972	-0.195086257095	-0.0707397709934	0.173533936982	-0.0135725694914	0.0331701953691	0.184408514134	-0.0246406223984	0.162717281742	-30.623403911	35.5339230207	29.8121475121
18	6.07835128424	2.81880486909	-2.08064334704	8.07797431954	-7.18185325914	7.19443676009	0.0776227161905	-0.316999523711	-0.522586709704	0.654136264909	0.198320875866	0.00244651734555	-0.790937851454	0.0734261279177	-0.275601135161	0.417928932962	-0.0540414050781	0.0317195408873	0.239103421696	-0.046060145325	0.278466753438	-20.112364979	4.27634117651	23.0163997578
19	3.18384625431	0.632143575108	1.65221955448	2.31481267677	-0.865112007841	4.68198659415	0.0474625249039	0.00654577451343	-0.366154696179	-0.109487171231	0.154326173909	-0.144819066392	0.218326445914	-0.141926488858	-0.176534188526	0.174721406515	-0.0407493030466	0.0149621396484	0.198215357783	0.00637568285487	0.236691208458	-12.0793078535	16.9475393786	23.7710958614
20	5.65359629784	-1.46336888509	-0.47847386545	4.2827771685	-0.307553181087	2.05363663172	0.0268769111363	-0.0456478943619	0.00814941813482	0.187441853676	-0.0827074491283	0.0216534053569	0.0393483402297	-0.0866025081519	0.0611223399754	0.18883351683	-0.0413045707137	0.0281040508443	0.151167027318	-0.0175398500927	0.139654755582	-27.2422992457	14.9993358098	27.871311466
21	3.52060049148	3.06506013443	-3.95312611505	7.05039622742	-4.97548358584	5.32423087978	-0.254150365596	0.336566958033	-0.359309362559	-0.807441176896	-0.174355830961	-0.716434206745	-0.670240622703	0.25424538369	0.416378942608	0.460924615262	-0.0385114842857	0.0780247195772	0.359374308764	-0.0106100205561	0.353956311559	-17.142799439	7.16224660017	17.9805729152
22	1.64797288312	-2.4357181745	1.81291751547	5.70993794376	-4.28698005525	3.34114160338	-0.021573014754	-0.0720790606643	-0.336328424107	0.179982187933	0.145918233304	0.419619341687	0.018915169272	-0.291197177105	-0.158216872376	0.188455880541	-0.0410028634682	0.0322106426862	0.208868635415	-0.0215440050509	0.244392272718	-31.9060823772	8.10027482311	21.1443174773
23	4.02091277818	3.53615206023	2.68314648212	7.81839205221	4.92346768141	4.53876419959	-0.0821292302252	0.242243915873	-0.0934249623576	-0.179377526534	0.16148490959	-0.179518543656	-0.0754650270756	0.148193901325	-0.0722149092881	0.126516753853	-0.0165910905471	0.0269935556473	0.129128551813	-0.0072088965452	0.133845916757	-23.2956210813	17.7214709821	20.7347765532
24	2.32988787566	-1.55180563508	-1.26328676275	4.62624921283	5.5004039224	6.69977901484	0.322512846533	-0.640457802939	0.571911783771	0.345573837463	0.190365276355	-0.73278638373	-0.276432611609	0.484269322543	-0.439460904409	0.236955250272	-0.0475132483582	0.0156617508227	0.237369531228	-0.0831909083693	0.24204022734	-18.2516934103	32.6819977506	35.9504735007
25	4.40698328654	1.92939322408	-0.322004786869	4.5718306774	-2.90965796493	8.75936917318	0.217251969845	-0.392047069565	0.946977360187	0.0803335685254	-0.386451163831	0.0247954305007	-0.730550762699	1.23092237225	0.0196522496624	0.203565582067	-0.083391603329	0.00355672220297	0.279686389746	0.0360049654303	0.234945573634	19.1731838435	44.1084757055	14.6246511735

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 1 through 28 )	A	A	1 - 28	1 - 28
2	2	chain 'A' and (resid 29 through 50 )	A	A	29 - 50	29 - 50
3	3	chain 'B' and (resid 2 through 11 )	B	B	2 - 11	1 - 10
4	4	chain 'B' and (resid 12 through 28 )	B	B	12 - 28	11 - 27
5	5	chain 'B' and (resid 29 through 45)	B	B	29 - 45	28 - 44
6	6	chain 'C' and (resid 2 through 11 )	C	C	2 - 11	1 - 10
7	7	chain 'C' and (resid 12 through 28 )	C	C	12 - 28	11 - 27
8	8	chain 'C' and (resid 29 through 45 )	C	C	29 - 45	28 - 44
9	9	chain 'C' and (resid 46 through 50 )	C	C	46 - 50	45 - 49
10	10	chain 'D' and (resid 1 through 11 )	D	D	1 - 11	1 - 11
11	11	chain 'D' and (resid 12 through 50 )	D	D	12 - 50	12 - 50
12	12	chain 'E' and (resid 2 through 11 )	E	E	2 - 11	1 - 10
13	13	chain 'E' and (resid 12 through 28 )	E	E	12 - 28	11 - 27
14	14	chain 'E' and (resid 29 through 45 )	E	E	29 - 45	28 - 44
15	15	chain 'E' and (resid 46 through 50 )	E	E	46 - 50	45 - 49
16	16	chain 'F' and (resid 1 through 11 )	F	F	1 - 11	1 - 11
17	17	chain 'F' and (resid 12 through 50 )	F	F	12 - 50	12 - 50
18	18	chain 'G' and (resid 1 through 11 )	G	G	1 - 11	1 - 11
19	19	chain 'G' and (resid 12 through 28 )	G	G	12 - 28	12 - 28
20	20	chain 'G' and (resid 29 through 50 )	G	G	29 - 50	29 - 50
21	21	chain 'H' and (resid 2 through 11 )	H	H	2 - 11	1 - 10
22	22	chain 'H' and (resid 12 through 28 )	H	H	12 - 28	11 - 27
23	23	chain 'H' and (resid 29 through 45 )	H	H	29 - 45	28 - 44
24	24	chain 'H' and (resid 46 through 50 )	H	H	46 - 50	45 - 49
25	25	Chain 'B' and (resid 46 through 50)	B	B	46 - 50	45 - 49

-
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://pdbjlvh1.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