PDB-7s2j: Crystal structure of sulfonamide resistance enzyme Sul2 apoenzyme

ID or keywords:

Entry

Database: PDB / ID: 7s2j

Title

Crystal structure of sulfonamide resistance enzyme Sul2 apoenzyme

Components

Sul2

Keywords

TRANSFERASE / TIM barrel / alpha beta protein / antibiotic resistance / sulfonamides / structural genomics / CSGID / Center for Structural genomics of infectious diseases / NIAID / National Institute of Allergy and Infectious Diseases

Function / homology

Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Stogios, P.J. / Skarina, T. / Michalska, K. / Venkatesan, M. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID) / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: Molecular mechanism of plasmid-borne resistance to sulfonamide antibiotics.
Authors: Venkatesan, M. / Fruci, M. / Verellen, L.A. / Skarina, T. / Mesa, N. / Flick, R. / Pham, C. / Mahadevan, R. / Stogios, P.J. / Savchenko, A.

History

Deposition	Sep 3, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 3, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jul 19, 2023	Group: 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	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7s2j.cif.gz	488.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7s2j.ent.gz	354.9 KB	Display	PDB format
PDBx/mmJSON format	7s2j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7s2j_validation.pdf.gz	488.2 KB	Display	wwPDB validaton report
Full document	7s2j_full_validation.pdf.gz	501 KB	Display
Data in XML	7s2j_validation.xml.gz	51.7 KB	Display
Data in CIF	7s2j_validation.cif.gz	76.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s2/7s2j ftp://data.pdbj.org/pub/pdb/validation_reports/s2/7s2j	HTTPS FTP

-
Related structure data

Related structure data	7s2iC 7s2kC 7s2lC 7s2mC 7tq1C 8scdC 1aj0S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: IDP91800

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Sul2

B: Sul2

C: Sul2

D: Sul2

hetero molecules

116 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Sul2

hetero molecules

C: Sul2

hetero molecules

defined by author&software
Evidence: gel filtration
57.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Sul2

D: Sul2

hetero molecules

defined by author&software
Evidence: gel filtration
57.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	39.819, 143.293, 85.893
Angle α, β, γ (deg.)	90.000, 90.506, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Sul2 Mass: 28501.510 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: Sul2 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold

-
Non-polymers , 5 types, 1149 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1127 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.77 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.6 M ammonium sulfate, 2% hexanediol, 0.1 M HEPES, pH 7.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97951 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97951 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. obs: 81585 / % possible obs: 99.4 % / Redundancy: 6.6 % / B_iso Wilson estimate: 25.63 Å² / R_merge(I) obs: 0.105 / R_pim(I) all: 0.043 / Net I/σ(I): 19.34
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.69 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 4084 / CC_1/2: 0.711 / R_pim(I) all: 0.328 / % possible all: 99.3

-
Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1AJ0

1aj0

Resolution: 1.85→42.94 Å / SU ML: 0.2244 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6769
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2069	3896	2.43 %
R_work	0.1612	156647	-
obs	0.1623	81545	98.64 %

Solvent computation

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

Displacement parameters

B_iso mean: 36.8 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→42.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7920	0	89	1127	9136

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0062	8179
X-RAY DIFFRACTION	f_angle_d	0.8952	11105
X-RAY DIFFRACTION	f_chiral_restr	0.0572	1270
X-RAY DIFFRACTION	f_plane_restr	0.0084	1470
X-RAY DIFFRACTION	f_dihedral_angle_d	14.1721	2990

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 (%)
1.85-1.87	0.3439	128	0.2568	5360	X-RAY DIFFRACTION	94.69
1.87-1.89	0.2512	143	0.2473	5628	X-RAY DIFFRACTION	98.45
1.89-1.92	0.3112	139	0.2365	5371	X-RAY DIFFRACTION	95.51
1.92-1.95	0.2763	136	0.2231	5574	X-RAY DIFFRACTION	98.4
1.95-1.97	0.2438	149	0.215	5648	X-RAY DIFFRACTION	99.14
1.97-2	0.2433	144	0.2051	5682	X-RAY DIFFRACTION	99.13
2-2.03	0.2369	133	0.1988	5490	X-RAY DIFFRACTION	99.22
2.03-2.07	0.2635	140	0.1983	5680	X-RAY DIFFRACTION	99.08
2.07-2.1	0.248	144	0.2015	5691	X-RAY DIFFRACTION	99.1
2.1-2.14	0.2182	137	0.1747	5540	X-RAY DIFFRACTION	99.14
2.14-2.18	0.2282	148	0.1756	5566	X-RAY DIFFRACTION	98.4
2.18-2.23	0.2139	134	0.1706	5667	X-RAY DIFFRACTION	98.57
2.23-2.27	0.2648	149	0.1771	5471	X-RAY DIFFRACTION	98.39
2.28-2.33	0.2583	138	0.1706	5622	X-RAY DIFFRACTION	97.51
2.33-2.39	0.1833	141	0.1733	5580	X-RAY DIFFRACTION	99.39
2.39-2.45	0.2267	143	0.1652	5623	X-RAY DIFFRACTION	99.17
2.45-2.52	0.2234	141	0.1761	5668	X-RAY DIFFRACTION	99.32
2.52-2.6	0.2103	136	0.1617	5663	X-RAY DIFFRACTION	99.54
2.6-2.7	0.2383	136	0.1653	5637	X-RAY DIFFRACTION	99.43
2.7-2.81	0.2343	143	0.1607	5602	X-RAY DIFFRACTION	99.07
2.81-2.93	0.219	133	0.1693	5555	X-RAY DIFFRACTION	98.36
2.93-3.09	0.1963	138	0.1621	5582	X-RAY DIFFRACTION	98.23
3.09-3.28	0.1711	142	0.1532	5655	X-RAY DIFFRACTION	99.57
3.28-3.53	0.1828	140	0.1377	5619	X-RAY DIFFRACTION	99.46
3.53-3.89	0.2032	145	0.1353	5667	X-RAY DIFFRACTION	99.64
3.89-4.45	0.1602	134	0.1216	5570	X-RAY DIFFRACTION	97.96
4.45-5.61	0.164	136	0.1415	5643	X-RAY DIFFRACTION	99.66
5.61-42.94	0.1901	126	0.1569	5593	X-RAY DIFFRACTION	98.48

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	1.79701147101	0.902709857174	-0.219837695251	1.17145248234	0.825907883837	1.25899818037	-0.134036009614	-0.745285714193	-0.429329382494	1.06885510791	0.285708164859	0.157162845821	0.50112709047	-0.27672615968	0.0030639227103	0.672504815158	0.0152041137698	0.0498487932709	0.391665963282	0.0903868893983	0.307741630449	13.1854446255	6.4830474189	11.3048003126
2	1.28613155943	0.688721176279	-0.0659048843532	3.27085593192	1.70242869891	2.35948001531	0.0815321119534	-0.184552782704	-0.174856321124	0.880653813272	-0.216716815093	0.276101920895	0.603835705451	-0.131803867987	0.0120417762689	0.354494795917	-0.05573368322	0.0764818791665	0.248562548623	-0.0135908170116	0.253035987864	7.49734638765	3.22146000509	2.21232050165
3	0.827082443091	-0.254357244229	0.0278293177993	0.514027265362	0.378731530538	0.38238264133	-0.181022413586	0.127081391751	-0.730615489686	-0.296664498549	-0.0248278941311	-0.32437883945	0.444784601469	0.452942634075	-0.0075565503837	0.30581599259	0.0545417003919	0.0566273266587	0.370761678444	0.00458021689528	0.418463274142	27.7838537578	3.22665079967	-10.2667243189
4	0.655081127339	0.446772497885	0.499860405579	2.19684043818	1.89488656399	2.26465148645	-0.0212682109263	-0.0927020838366	0.140363577519	0.0539865917278	0.0565514195111	-0.0312498760103	-0.0944206112829	0.19024383261	0.0105088936591	0.167769929491	-0.0195633979802	0.00553010124405	0.235649908162	-0.00713853063305	0.16107595385	19.0316175124	17.7687039812	-3.61599549952
5	1.31981894704	-0.617861167004	0.551216883583	1.02824868823	0.451324876375	1.35119877582	0.0827034302371	0.157198871938	-0.018353143872	-0.108668301861	-0.0702149893776	-0.129776556363	-0.137906883505	-0.0160431360541	3.29372706982E-7	0.198368116441	0.0341821666033	0.0136556048553	0.207408904796	-0.0022936779745	0.20806769903	2.02087723176	12.737773219	-55.3215224218
6	0.382663349168	-0.591397104218	-0.186080460379	1.28811568103	0.13648923747	0.931596738466	0.122762187418	0.100519694114	-0.146470982909	-0.0970652016344	-0.00199180238331	-0.505706716793	0.0088152082716	0.0899401423034	1.02400273703E-7	0.234380470014	0.00678990054908	-0.0344934423499	0.232343835663	0.0060817089288	0.253925380461	0.295321922729	13.3856231586	-54.3348817359
7	0.837263376089	-0.429764432354	-0.455758203871	1.3272865558	-0.504601823218	0.729555894376	0.0384782818543	-0.0367471298491	-0.0490142068598	0.103931788252	0.0375392204859	0.158936602276	-0.155345359549	-0.204913270042	1.01135356735E-7	0.257086372701	0.0232518444803	-0.0154952664706	0.25615470473	0.0191346260366	0.229150488464	-6.46977931424	20.1432114216	-49.0323205627
8	0.461185063611	-0.206525785623	-0.0341369396555	0.217870835744	-0.200711085391	0.688492870511	0.00703834824622	-0.0743703908002	0.334201611356	0.138640476765	0.0637466362058	0.0720179990489	-0.176084361146	-0.0505862630806	1.66541600558E-8	0.240720670918	0.0321589577522	0.0138998802789	0.271956121017	-0.00932670668533	0.274571016184	-5.83661182475	16.6617573653	-36.6291269986
9	4.05337177567	0.00331223871614	0.085940008057	0.000483648442501	-0.00807754790699	0.715059504122	-0.00276569046126	-0.355367865606	0.861831261404	0.240537160391	0.0786027505231	-0.162499879288	-0.455786328255	0.180843550656	-0.0138200823372	0.30547304299	-0.0116668323981	-0.0172993164257	0.266857908521	-0.0280273826019	0.322249023616	14.3596964207	13.431691688	-31.6558763377
10	0.776309620597	0.133686847123	0.708163755011	1.39512000858	-0.289332838067	1.32362700034	0.00464072581472	-0.03966891477	-0.11885990144	0.110661763296	0.0503747813808	0.00316328326582	0.115087006643	0.0439434285455	-4.97986290736E-8	0.202623250066	0.0131024199825	-0.0203127044793	0.239151472984	0.000239884604234	0.210496880365	3.7598111996	5.41462948684	-31.7664144658
11	1.44189188712	-0.148141427487	1.24563535277	1.50801131558	0.395108540646	1.23986966231	-0.0487517391535	0.553113324962	0.0930207692206	-0.236183904149	0.0674880336234	-0.383320675312	0.132711474595	0.237710762918	1.14791800702E-6	0.245607375055	0.0209058347945	0.0102028040139	0.240068303874	0.020180916715	0.283148347882	11.5791938534	2.07694236928	-46.5858504715
12	0.384386547299	-0.188180123997	0.157326044648	0.202381812363	0.0317175160514	0.121503678763	0.0175934324851	-0.0535511601956	-0.137305088957	-0.120728015249	-0.0263037487075	-0.0313374640475	0.169649410175	0.0215960206701	-3.28139463869E-6	0.240367070894	0.0084874383617	0.00406257101279	0.218363622875	-0.0144223409093	0.258097778114	4.29033530328	-1.76866250648	-46.9063428021
13	0.711889108424	-0.19665705971	-0.07767876928	0.713516255346	0.606186982658	0.503563739183	-0.271187326904	-0.389967885057	-0.2966640961	0.0188919483095	0.154198048064	0.667283069839	0.265336613085	-0.321866172666	0.00545612651564	0.313062958282	0.0181437425963	0.0416531037575	0.311536834573	0.0211085192748	0.345424172967	-1.88325131332	-12.019930557	-49.9906236968
14	1.84218326443	0.190699274874	0.87839392234	2.23345852216	-0.176795057683	0.464690358209	0.121869316717	-0.0158952217695	-0.00119375329759	-0.129752135854	-0.0453817078035	-0.138011243946	-0.660135310828	-0.0607509243765	-0.00211582036941	0.24116766226	-0.0165438577696	-0.0122333941021	0.205747382121	0.00058525941665	0.168915397699	6.68328554363	-34.4800251249	-23.8254663168
15	0.892040695536	0.017143964856	-0.0149381426746	3.13092566045	1.22591863628	1.84591093463	0.0264092238553	0.0476175343457	0.142706870697	-0.375218645921	-0.177559244527	0.181949654471	-0.120267544254	-0.0575311049509	-0.00181382610927	0.154534103765	0.0136724047627	-0.0357978688098	0.180819585954	-0.00611542782592	0.194702017905	1.58991095068	-25.9876943536	-23.9430026763
16	1.3650920976	-0.376122111885	-0.252595499978	0.428654031993	0.440882745555	0.489937552237	-0.141863040594	0.677210882583	1.00637480849	0.0680757500664	0.353353903274	-1.31326359651	-0.532955057864	1.02415876442	0.0956263866672	0.40609192603	-0.191807959816	-0.0846523013519	0.547481393672	0.0842538559822	0.793392931592	22.028578495	-15.5043703626	-16.7388070685
17	0.760626996859	0.813033622684	0.20836211839	2.34250444476	-0.712376735473	1.61303517366	-0.0334406854735	-0.141272685746	0.0313555949972	0.730395436506	-0.150989079472	-0.482651303735	-0.20139256867	0.227023986705	-0.00874850515847	0.261745548464	-0.0569658361215	-0.0943075238004	0.215990440846	-0.00742044853168	0.28761375906	13.1906205571	-19.6300049699	-8.05116133126
18	0.972172266584	0.372234110578	0.32406465471	1.01269179103	-0.686761445901	0.839543733118	0.0373245992302	0.0716549925486	-0.605654322499	0.0914077788213	-0.384676809933	-0.20130265294	0.0679540014024	0.331480409216	-0.000433981529361	0.268697369662	-0.0158096164405	-0.011282887388	0.370746870721	0.0632396414085	0.362677229438	19.8721226682	-34.6326395421	-14.3863730499
19	0.522994493138	0.219052688577	0.119657552915	0.362256007718	-0.262830316842	0.334389174002	-0.0192459426674	-0.141882670018	-0.118335535701	0.199254410907	-0.146579139395	-0.210657254588	-0.0455362748065	0.108481509521	-1.39139868691E-7	0.275082965315	-0.00532572039721	-0.0300595703543	0.301872979228	0.0519065740646	0.236980870952	12.7283002479	-36.2340617269	-10.2278700075
20	0.552097410815	-0.0435620393684	0.0905558346315	1.19070159697	0.115417227888	0.325249268641	-0.133007655301	-0.639914086874	0.0574566514298	0.380634772929	0.38129629029	0.74625862273	0.215722711934	-0.411052648403	-0.0180777963734	0.2880393927	0.069419347748	0.0412082333937	0.40935762395	0.0715131727768	0.376515956995	7.37928958854	-44.8977494293	-1.55551044967
21	1.63798920368	0.469723096359	-0.815421827116	4.84446253736	0.650235610605	2.00052619959	0.0256476634917	0.297820369934	0.147078568623	-0.75416468123	0.102322240389	-0.174287520794	-0.135890772922	-0.030715004007	0.000425630019356	0.430152859095	0.0559764570735	0.0837818140573	0.339939695753	0.0136546137938	0.310262176075	19.7862756404	-26.6167310086	-68.4123923382
22	0.445643260526	-0.240675872177	0.0123293989266	0.236771327062	-0.0666302788449	0.29298965215	0.00870781260169	0.589017726679	-1.15102763474	-0.194332574307	-0.0381499861546	1.72371626108	0.678477224853	-1.27812287815	0.0335537253466	0.823742995448	-0.0732476774171	0.00424215752036	0.662119459233	-0.130641412752	0.860399601927	-0.209964158735	-36.4377555558	-60.7861546366
23	1.15455130725	-0.863409151959	-0.0967396814079	3.9631791423	1.14499214535	1.34039815874	-0.0499406040143	-0.0843832872413	0.010682603169	-0.0029538484229	0.0298287815192	0.124098121399	0.132037137375	-0.0281534231292	0.0011201672528	0.278449658306	0.0270561123983	0.0109195885988	0.226321645895	0.0159901235294	0.200248465088	10.2688677795	-24.0064824628	-52.9798791

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 3 through 26 )	A	A	3 - 26	1 - 24
2	2	chain 'A' and (resid 27 through 128 )	A	A	27 - 128	25 - 126
3	3	chain 'A' and (resid 129 through 145 )	A	A	129 - 145	127 - 143
4	4	chain 'A' and (resid 146 through 269 )	A	A	146 - 269	144 - 267
5	5	chain 'B' and (resid 3 through 26 )	B	B	3 - 26	1 - 24
6	6	chain 'B' and (resid 27 through 60 )	B	B	27 - 60	25 - 58
7	7	chain 'B' and (resid 61 through 98 )	B	B	61 - 98	59 - 96
8	8	chain 'B' and (resid 99 through 128 )	B	B	99 - 128	97 - 126
9	9	chain 'B' and (resid 129 through 145 )	B	B	129 - 145	127 - 143
10	10	chain 'B' and (resid 146 through 202 )	B	B	146 - 202	144 - 200
11	11	chain 'B' and (resid 203 through 227 )	B	B	203 - 227	201 - 225
12	12	chain 'B' and (resid 228 through 250 )	B	B	228 - 250	226 - 248
13	13	chain 'B' and (resid 251 through 269 )	B	B	251 - 269	249 - 267
14	14	chain 'C' and (resid 1 through 26 )	C	C	1 - 26	1 - 26
15	15	chain 'C' and (resid 27 through 128 )	C	C	27 - 128	27 - 128
16	16	chain 'C' and (resid 129 through 145 )	C	C	129 - 145	129 - 145
17	17	chain 'C' and (resid 146 through 202 )	C	C	146 - 202	146 - 202
18	18	chain 'C' and (resid 203 through 227 )	C	C	203 - 227	203 - 227
19	19	chain 'C' and (resid 228 through 250 )	C	C	228 - 250	228 - 250
20	20	chain 'C' and (resid 251 through 270 )	C	C	251 - 270	251 - 270
21	21	chain 'D' and (resid 2 through 128 )	D	D	2 - 128	1 - 127
22	22	chain 'D' and (resid 129 through 145 )	D	D	129 - 145	128 - 144
23	23	chain 'D' and (resid 146 through 270 )	D	D	146 - 270	145 - 269

-
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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 1149 molecules

-
Details

-
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

-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 5 types, 1149 molecules

-Details

-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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 1149 molecules

-
Details

-
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