PDB-7lwz: Apo Structure of Vibrio cholerae dGTPase protein VC1979

ID or keywords:

Entry

Database: PDB / ID: 7lwz

Title

Apo Structure of Vibrio cholerae dGTPase protein VC1979

Components

Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1

Keywords

HYDROLASE / METALLOENZYME / METAL BINDING PROTEIN

Function / homology

Function and homology information

dGTPase activity / dGTP catabolic process
Similarity search - Function

Biological species

Vibrio cholerae serotype O1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.32 Å

Authors

Sikkema, A.P. / Horng, J. / Klemm, B.P. / Schaaper, R.M. / Hall, T.M.T.

Citation

Journal: To Be Published
Title: Structure of Vibrio cholerae dGTPase protein VC1979
Authors: Sikkema, A.P. / Horng, J. / Klemm, B.P. / Schaaper, R.M. / Hall, T.M.T.

History

Deposition	Mar 2, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 10, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7lwz.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb7lwz.ent.gz	767.4 KB	Display	PDB format
PDBx/mmJSON format	7lwz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7lwz_validation.pdf.gz	492.2 KB	Display	wwPDB validaton report
Full document	7lwz_full_validation.pdf.gz	525.9 KB	Display
Data in XML	7lwz_validation.xml.gz	78 KB	Display
Data in CIF	7lwz_validation.cif.gz	106.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lw/7lwz ftp://data.pdbj.org/pub/pdb/validation_reports/lw/7lwz	HTTPS FTP

-
Related structure data

Related structure data	2pgsS S: Starting model for refinement
Similar structure data	23355 4ry3-2 23356 5jsb-d 5hq2-d 4guv-d 2pgs-1 5fb3-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#152 - Aug 2012 cAMP-dependent Protein Kinase similarity (2)

Deposited unit

B: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1

A: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1

D: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1

C: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1

F: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1

E: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1

hetero molecules

301 kDa, 6 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)	105.003, 161.869, 184.773
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

#1: Protein	Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1 Mass: 50159.805 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_1979 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KQL9
#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.63 Å³/Da / Density % sol: 53.2 % Description: Crystal were approximately 200um with an orthorhombic pyramidal morphology. Grew under precipitate.
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Protein solution (15mg/mL dGTPase, 50mM Tris pH 7.9, 100mM NaCl, 10% glycerol) mixed 1:1 with well solution (0.95M NaCl, 7mM NiCl2, 0.06M Na Acetate). Cryo condition was well solution with ...Details: Protein solution (15mg/mL dGTPase, 50mM Tris pH 7.9, 100mM NaCl, 10% glycerol) mixed 1:1 with well solution (0.95M NaCl, 7mM NiCl2, 0.06M Na Acetate). Cryo condition was well solution with 30% ethylene glycol added.

Crystal

Density Matthews: 2.63 Å³/Da / Density % sol: 53.2 %
Description: Crystal were approximately 200um with an orthorhombic pyramidal morphology. Grew under precipitate.

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Protein solution (15mg/mL dGTPase, 50mM Tris pH 7.9, 100mM NaCl, 10% glycerol) mixed 1:1 with well solution (0.95M NaCl, 7mM NiCl2, 0.06M Na Acetate). Cryo condition was well solution with ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2019
Radiation	Monochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.32→37.86 Å / Num. obs: 270862 / % possible obs: 99.3 % / Redundancy: 5.7 % / B_iso Wilson estimate: 65.21 Å² / CC_1/2: 0.997 / R_rim(I) all: 0.088 / Net I/σ(I): 11.15
Reflection shell	Resolution: 2.32→2.46 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.06 / Num. unique obs: 42766 / CC_1/2: 0.481 / R_rim(I) all: 1.64 / % possible all: 98.3

-
Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2PGS

2pgs

Resolution: 2.32→37.86 Å / SU ML: 0.4081 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.1055
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2517	11887	4.58 %
R_work	0.2184	247401	-
obs	0.22	259288	98.59 %

Solvent computation

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

Displacement parameters

B_iso mean: 79.38 Å²

Refinement step

Cycle: LAST / Resolution: 2.32→37.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18255	0	6	132	18393

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0092	18654
X-RAY DIFFRACTION	f_angle_d	1.149	25280
X-RAY DIFFRACTION	f_chiral_restr	0.1524	2784
X-RAY DIFFRACTION	f_plane_restr	0.0084	3303
X-RAY DIFFRACTION	f_dihedral_angle_d	25.0187	6752

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 (%)
2.32-2.35	0.388	362	0.3992	7515	X-RAY DIFFRACTION	89.41
2.35-2.37	0.3701	394	0.3903	8212	X-RAY DIFFRACTION	98.56
2.37-2.4	0.3935	394	0.3772	8286	X-RAY DIFFRACTION	98.83
2.4-2.43	0.3874	400	0.367	8279	X-RAY DIFFRACTION	99.2
2.43-2.47	0.363	399	0.3608	8314	X-RAY DIFFRACTION	99.14
2.47-2.5	0.377	395	0.3436	8326	X-RAY DIFFRACTION	98.53
2.5-2.54	0.3536	391	0.3352	8107	X-RAY DIFFRACTION	98.21
2.54-2.57	0.3235	399	0.3154	8215	X-RAY DIFFRACTION	97.98
2.57-2.61	0.333	397	0.3137	8315	X-RAY DIFFRACTION	99.65
2.61-2.66	0.3498	398	0.3087	8347	X-RAY DIFFRACTION	99.94
2.66-2.7	0.3316	404	0.3033	8395	X-RAY DIFFRACTION	99.98
2.7-2.75	0.2943	399	0.2906	8329	X-RAY DIFFRACTION	99.93
2.75-2.8	0.3197	409	0.2751	8378	X-RAY DIFFRACTION	99.84
2.8-2.86	0.3283	401	0.2656	8311	X-RAY DIFFRACTION	99.9
2.86-2.92	0.2857	406	0.2591	8379	X-RAY DIFFRACTION	99.8
2.92-2.99	0.3107	405	0.2552	8365	X-RAY DIFFRACTION	99.83
2.99-3.07	0.3165	403	0.2707	8337	X-RAY DIFFRACTION	99.81
3.07-3.15	0.3176	399	0.2723	8299	X-RAY DIFFRACTION	99.44
3.15-3.24	0.3317	400	0.2604	8308	X-RAY DIFFRACTION	99.37
3.24-3.35	0.2636	399	0.2427	8282	X-RAY DIFFRACTION	99.25
3.35-3.47	0.2947	389	0.2373	8303	X-RAY DIFFRACTION	99.03
3.47-3.61	0.2514	402	0.2302	8227	X-RAY DIFFRACTION	98.24
3.61-3.77	0.2425	386	0.1973	8041	X-RAY DIFFRACTION	95.99
3.77-3.97	0.2508	398	0.2017	8251	X-RAY DIFFRACTION	99.11
3.97-4.22	0.238	395	0.181	8306	X-RAY DIFFRACTION	99.04
4.22-4.54	0.1949	392	0.1667	8263	X-RAY DIFFRACTION	98.88
4.54-5	0.1941	393	0.1732	8296	X-RAY DIFFRACTION	98.74
5-5.72	0.2626	390	0.1987	8223	X-RAY DIFFRACTION	98.58
5.72-7.19	0.2224	393	0.2053	8058	X-RAY DIFFRACTION	96.38
7.2-37.86	0.1763	395	0.1665	8134	X-RAY DIFFRACTION	97.15

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	2.39568724647	0.245916404819	0.790712651723	2.84252458563	-0.154627406937	2.62483804433	-0.0569641146616	-0.137093124425	0.230754217533	0.428009852757	0.0336134149348	-0.0772571135253	-0.213545055743	0.129832420222	0.00589859163122	0.465334768798	-0.0146830496809	-0.0548073226944	0.398797725471	-0.019150780288	0.386601005601	83.7417935776	112.648866685	70.9511794616
2	4.88033056766	-6.10144638279	-0.0382666629858	9.99261262615	1.12331422835	6.50070262521	-0.00925841423652	0.119323543994	-0.146677444241	0.471652462721	0.271146258607	-2.58159624318	0.0860012412127	0.599198491363	-0.349077784039	0.658480420871	-0.0468647441465	-0.135051313282	0.932560896223	-0.0353693866412	0.976150652609	94.8720812182	107.419287106	57.7590593119
3	0.618254711602	-1.27722726017	1.45402106449	2.87373576455	-4.40678003756	8.52430217912	-0.0554118790771	0.219443337106	0.307661873976	-0.36068640141	0.0507407846487	-0.117317561975	0.241579370966	0.505894257808	-0.000611405680624	0.639527825008	-0.0728142512831	-0.0850410488866	0.733754270395	-0.0453374686104	0.584547418646	93.7611082035	112.327319012	70.2941597073
4	1.42821237519	0.063656852634	0.711021984428	1.92740184639	0.458032616594	2.61427442765	0.113623347649	-0.122046611871	-0.0850172301112	0.409362290559	-0.0645606660942	-0.288053922315	0.323677435164	0.292985556606	-0.0918596026173	0.512202520712	0.0083462123505	-0.0263682241943	0.505317145409	-0.00779509267595	0.503871126758	90.7122263734	97.5855364378	71.8099243959
5	2.39397548861	-0.61883019429	0.181268543425	3.67971994815	0.103720337646	2.05574688848	-0.00202248124592	-0.209658396973	-0.0339329183604	0.274552984493	0.10295224255	0.113872248662	-0.0556108825159	0.12618728737	-0.0814219421971	0.667580918785	0.0378182100208	0.0960721643774	0.506742652131	-0.0403629784086	0.468292986677	69.0717337569	102.581396754	91.5468353893
6	0.756583080305	0.119846681457	1.10901589343	1.74853182579	-1.93723770494	4.63670976383	0.0326038899735	-0.272682300441	0.119322437211	0.601482690583	0.189565872627	0.515796606021	-0.0816199532992	-0.0909955554436	-0.278382494537	0.724453721017	0.0832415864211	0.227697197667	0.623027677295	0.0320510654062	0.761931819777	59.1835556665	105.013370006	94.5619152754
7	2.59629639027	-0.75978464917	0.315931632717	3.35149243191	-0.0126381479239	1.85577926062	0.191531596533	0.179830403171	0.0355502087429	-0.370221764629	-0.145856467591	0.212696402612	0.0946812051774	-0.0553254256444	-0.0458878290259	0.514574130515	-0.00743368027939	0.0235452527278	0.469051436158	-0.0253623542761	0.447397499302	51.9340675539	77.6235955075	27.0321243607
8	9.76094236291	2.10692607646	8.98213104619	6.39390113478	1.03231173123	8.84413960085	-0.653370743054	1.32217531243	2.05684939969	-1.092939622	-0.097719854481	0.544858198395	-0.735796635258	1.29915724048	0.655849084304	0.724063969188	0.0436552707885	0.173901664281	0.889651429203	0.163734582132	0.959570538113	70.59948978	87.6875714002	26.6160173494
9	3.02772046123	-1.67436921628	-1.22984090902	4.41624592803	3.18885775531	4.40156124316	-0.00984843558696	0.508438970523	0.10906802725	-0.792664098554	0.0106258036323	-0.266109447343	0.172611964544	0.515900077829	-0.0477770514785	0.682152531167	0.0410754035221	0.0269980937803	0.56523945368	0.074317999167	0.576130905756	54.0927207345	86.2974361825	22.3206852346
10	2.44758158855	-1.25203878183	0.347123132351	3.24938937106	-0.186385431839	0.616031999713	-0.0906386112711	0.0112560980928	0.270194468868	-0.0297170372139	0.113050358875	-0.155529185983	-0.0539824052109	-0.00802961713608	-0.0134580716884	0.475844453806	-0.0488662816923	-0.000329218263947	0.49023339998	0.016114611199	0.475800630272	57.1611923644	89.1056847262	36.5275675382
11	1.26799691948	0.18289629991	0.804804107777	2.84848351627	0.549705486736	2.78633892995	-0.0423991483982	-0.0488400059354	0.0720396987088	-0.0603437731462	-0.00647902313353	0.529781010369	0.148810741418	-0.223937438288	0.0455158343604	0.477955865691	-0.0286876014069	0.0845696419156	0.526571151175	0.0267271105146	0.679355717536	33.0710168727	74.6059459864	46.7175563425
12	9.1898218827	1.47153935313	5.36675682095	7.0963661647	-0.341720669815	3.3993611127	0.703846432734	-1.74350535968	-0.28823874346	0.33686564586	-0.187333329039	0.771857884976	1.52421560445	0.150068750871	-0.578397156053	0.909445757851	-0.0174623827684	0.158248135234	0.929728513439	0.118914752306	0.852982559466	32.085595298	64.5417240108	64.5999811504
13	1.84284079621	-0.438245702335	0.0337204752708	4.82553779896	-0.602002212417	1.76463084668	-0.184773946483	-0.0490094523737	-0.0366780658939	-0.351721835192	0.0428021113441	-0.838626838167	0.201995464113	0.307709804475	0.162819359443	0.446562443973	-0.0180937645487	0.123048168946	0.55958509708	-0.00387746991036	0.837488321698	99.7264966755	49.2512246086	61.8962161924
14	1.56555604708	-1.49190283803	-1.17007202704	5.96584071826	-2.87267432136	4.38574001187	-0.0789724531264	-0.660782003618	-0.328962582988	-0.895542189891	-0.793346063887	-1.10797016587	0.855410962049	0.533037609678	0.770003150781	0.562156034666	-0.138007015884	0.325509298741	0.661694560597	-0.0553371718408	1.21808556872	102.625038491	58.2468434091	49.1591915589
15	4.75628366059	3.83488975427	1.75414078933	4.35690242722	0.0394362255342	1.88874124785	-0.181676932302	0.0802914156072	0.295559299079	-0.768781397155	0.0204189011302	-0.871036011033	0.172837624464	0.40308624405	0.138898340794	0.820386636747	-0.0558993586239	0.300668741968	0.650542285413	0.00117919293571	0.882710141978	100.911742884	46.491164401	53.2060178691
16	2.51930578408	-0.492768818042	0.220121780539	3.85977643808	-0.366771021143	2.41644357054	-0.0237549430501	-0.05754569722	-0.227537412605	0.1651385788	0.0791137642186	-0.0898800673006	0.162602847674	0.140996334663	-0.0332009562211	0.424181769041	-0.0178421607815	-0.0132229014299	0.485902625082	0.00225372666116	0.546454351457	79.1814551993	39.411831767	76.8949102672
17	9.37132451637	-7.38366661531	-2.61426378524	5.87814830107	1.65878666589	6.16216876976	-0.834716934786	-0.824539561508	-0.547193605245	0.947251373088	0.479664422226	0.98313342832	0.368477595489	-0.252207616123	0.370801869677	0.690094657783	0.0151686105042	0.0776740267799	0.751066683391	0.0513887138844	0.868821690025	63.8956748894	49.420513724	91.5181595738
18	4.76046015646	1.07583308443	0.596820819316	2.61438128499	1.48318268419	0.605362694689	-0.311884143813	-0.298439597639	0.117591708146	0.539021779165	0.350959308504	0.413135921177	0.264486859506	-0.0209515297954	-0.0530421586831	0.797175253725	0.044690486896	-0.056760951148	0.809812311668	0.0616530176832	0.696112221548	78.9844093532	39.3805835477	87.5175276065
19	9.41458904391	6.10939203965	3.96099416249	5.13658044526	4.85205083877	6.02817924952	0.508676094918	0.124940392424	1.14941356223	0.953004205773	-0.53565061097	1.97643249494	0.350052064816	-0.430838856542	0.263834582263	0.91028687816	0.0338587856035	0.21437904619	0.709080726616	0.153287350974	1.19672898548	51.1045890905	88.4800758989	92.8696750005
20	0.95873956964	-0.23180025368	0.544645582939	1.89923236745	-0.739047704918	1.40690636273	0.0381783311744	-0.179576394364	-0.0524696686212	0.133346569548	0.17431242145	0.57839277887	-0.00143477119818	-0.207152526873	-0.22285320269	0.475643123257	0.00752665542222	0.100203124787	0.425054219888	0.0171041912994	0.581596695083	58.6091727189	99.5745222307	80.9405592528
21	2.58143374994	-4.41847772816	-2.2881634508	7.95781641464	3.68038077583	3.46347805551	0.117228763725	-0.630793123158	0.40240235252	0.37965850071	0.203067929291	-0.0822823499774	0.282457276615	0.104816063558	-0.322029849779	0.655154131545	-0.10315225183	0.0712319075859	0.575428317799	-0.0341312401417	0.836138972071	29.0448955723	65.2299293809	49.8625851091
22	1.26350524396	0.846826558117	0.894118781621	4.4723314228	1.57508479359	2.14033752751	0.0204370346213	0.135599567248	-0.199970050286	0.215166663108	0.227151109667	-0.110540132766	0.187519122454	0.117089077603	-0.278574362916	0.374386435823	-0.061244220105	0.0708468626948	0.413074196365	0.0339844490959	0.484941773763	43.3702859843	62.6885806462	51.9736584787
23	1.16665920172	0.464516557031	0.0526634218772	3.54164344858	-0.116797411251	1.24028679876	-0.261751006359	0.230624200964	-0.100821814666	-0.702167017536	0.169563922507	-0.252960379353	0.221363410424	0.134181554331	0.0751001513949	0.662268350236	-0.039697000608	0.075302671003	0.491519355123	-0.0101757186489	0.509591495495	87.8394515468	52.3050162724	51.3225179412
24	2.56079306291	-0.81457691428	0.969180733632	2.51982338512	-0.124760790238	1.66233907707	-0.215418303336	-0.385600699288	0.310056406917	0.488088897492	0.0840085427793	-0.218652365281	-0.0611512393815	0.0760383334509	0.153863416555	0.548384231045	0.0299995918224	0.0152803728796	0.539688479607	-0.0486575785894	0.544662133547	80.2001953541	54.0420831994	84.0629298165

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 'B' and (resid 5 through 167)	B	A	5 - 167	1 - 151
2	2	chain 'B' and (resid 168 through 198)	B	A	168 - 198	152 - 161
3	3	chain 'B' and (resid 199 through 264)	B	A	199 - 264	162 - 213
4	4	chain 'B' and (resid 265 through 436)	B	A	265 - 436	214 - 385
5	5	chain 'A' and (resid 6 through 167)	A	B	6 - 167	1 - 150
6	6	chain 'A' and (resid 199 through 264)	A	B	199 - 264	173 - 229
7	7	chain 'D' and (resid 5 through 167)	D	C	5 - 167	1 - 150
8	8	chain 'D' and (resid 168 through 198)	D	C	168 - 198	151 - 167
9	9	chain 'D' and (resid 199 through 264)	D	C	199 - 264	168 - 221
10	10	chain 'D' and (resid 265 through 435)	D	C	265 - 435	222 - 392
11	11	chain 'C' and (resid 6 through 167)	C	D	6 - 167	1 - 147
12	12	chain 'C' and (resid 168 through 198)	C	D	168 - 198	148 - 162
13	13	chain 'F' and (resid 6 through 167)	F	E	6 - 167	1 - 146
14	14	chain 'F' and (resid 193 through 198)	F	E	193 - 198	147 - 152
15	15	chain 'F' and (resid 199 through 264)	F	E	199 - 264	153 - 201
16	16	chain 'E' and (resid 8 through 167)	E	F	8 - 167	1 - 149
17	17	chain 'E' and (resid 168 through 198)	E	F	168 - 198	150 - 174
18	18	chain 'E' and (resid 199 through 264)	E	F	199 - 264	175 - 229
19	19	chain 'A' and (resid 168 through 198)	A	B	168 - 198	151 - 172
20	20	chain 'A' and (resid 265 through 435)	A	B	265 - 435	230 - 400
21	21	chain 'C' and (resid 199 through 264)	C	D	199 - 264	163 - 218
22	22	chain 'C' and (resid 265 through 436)	C	D	265 - 436	219 - 390
23	23	chain 'F' and (resid 265 through 436)	F	E	265 - 436	202 - 373
24	24	chain 'E' and (resid 265 through 435)	E	F	265 - 435	230 - 400

-
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