PDB-7luy: Crystal Structure of guanylate kinase from Bartonella henselae st...

ID or keywords:

Entry

Database: PDB / ID: 7luy

Title

Crystal Structure of guanylate kinase from Bartonella henselae str. Houston-1

Components

Guanylate kinase

Keywords

TRANSFERASE / SSGCID / Guanylate kinasem / gmk / Bartonella henselae / Rochalimaea henselae / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

guanylate kinase / GMP kinase activity / ATP binding / cytosol
Similarity search - Function

Biological species

Bartonella henselae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of guanylate kinase from Bartonella henselae str. Houston-1
Authors: Abendroth, J. / Dranow, D.M. / Sankaran, B. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Feb 23, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 17, 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	7luy.cif.gz	585.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7luy.ent.gz	401.8 KB	Display	PDB format
PDBx/mmJSON format	7luy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7luy_validation.pdf.gz	517.3 KB	Display	wwPDB validaton report
Full document	7luy_full_validation.pdf.gz	526.1 KB	Display
Data in XML	7luy_validation.xml.gz	45.3 KB	Display
Data in CIF	7luy_validation.cif.gz	62.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lu/7luy ftp://data.pdbj.org/pub/pdb/validation_reports/lu/7luy	HTTPS FTP

-
Related structure data

Related structure data	2f3tS S: Starting model for refinement
Similar structure data	4a63-2 2h2q-3 3owg-2 1exb-d 3v3k-1 2wwh-1 3wfp-7 1ufo-1 3bgh-d 3owg-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2f3tS

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Guanylate kinase

B: Guanylate kinase

C: Guanylate kinase

D: Guanylate kinase

E: Guanylate kinase

F: Guanylate kinase

hetero molecules

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

1

A: Guanylate kinase

F: Guanylate kinase

hetero molecules

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

2

B: Guanylate kinase

E: Guanylate kinase

hetero molecules

defined by author&software
57.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Guanylate kinase

D: Guanylate kinase

hetero molecules

defined by author&software
56.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.820, 101.910, 86.660
Angle α, β, γ (deg.)	90.000, 115.982, 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

#1: Protein	Guanylate kinase / GMP kinase Mass: 28254.342 Da / Num. of mol.: 6 / Fragment: BaheA.00713.a.A1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: ATCC 49882 / DSM 28221 / Houston 1 / Gene: gmk, BH05390 / Plasmid: BaheA.00713.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6G439, guanylate kinase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.01 Å³/Da / Density % sol: 38.9 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: RigakuReagents JCSG+ screen, condition H9: 200mM lithium sulfate, 100mM BisTris pH 5.5, 25% (w/V) PEG 3350: BaheA.00713.a.A1.PS00367 at 20mg/ml: tray 205529 H9: cryoprotectant: 25% ethylene glycol: puck: ekw2-5

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.9774 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2010

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9774 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. obs: 59593 / % possible obs: 99.7 % / Redundancy: 4.574 % / B_iso Wilson estimate: 46.792 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.063 / R_rim(I) all: 0.071 / Χ²: 0.902 / Net I/σ(I): 19.22

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.3-2.36	4.616	0.622	2.59	4389	0.786	0.701	99.8
2.36-2.42	4.62	0.532	3.04	4270	0.832	0.6	99.8
2.42-2.49	4.62	0.463	3.5	4162	0.88	0.522	99.9
2.49-2.57	4.62	0.372	4.27	4062	0.913	0.419	99.8
2.57-2.66	4.628	0.293	5.46	3889	0.944	0.331	99.7
2.66-2.75	4.598	0.239	6.86	3791	0.961	0.269	99.8
2.75-2.85	4.615	0.197	8.24	3705	0.973	0.222	99.8
2.85-2.97	4.622	0.144	10.86	3512	0.985	0.163	99.7
2.97-3.1	4.616	0.109	14.08	3385	0.991	0.123	99.9
3.1-3.25	4.604	0.084	18.06	3249	0.995	0.095	99.8
3.25-3.43	4.599	0.063	23.25	3065	0.997	0.071	99.6
3.43-3.64	4.553	0.049	29	2911	0.998	0.055	99.7
3.64-3.89	4.473	0.037	35.25	2734	0.999	0.042	99.8
3.89-4.2	4.486	0.029	43.19	2547	0.999	0.033	99.3
4.2-4.6	4.506	0.025	49.21	2361	0.999	0.029	99.7
4.6-5.14	4.472	0.025	50.38	2137	0.999	0.028	99.5
5.14-5.94	4.385	0.028	44.8	1875	0.999	0.031	99.8
5.94-7.27	4.529	0.027	44.99	1606	0.999	0.031	99.4
7.27-10.29	4.511	0.016	62.35	1251	1	0.019	99.2
10.29-50	4.223	0.015	67.66	692	1	0.017	97.7

-
Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19	refinement
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2f3t in two domains as per Morda

2f3t

Resolution: 2.3→45.71 Å / SU ML: 0.3185 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9884
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2525	2017	3.39 %	0
R_work	0.1984	57564	-	-
obs	0.2002	59581	99.91 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 51.21 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→45.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9236	0	86	311	9633

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0057	9511
X-RAY DIFFRACTION	f_angle_d	0.739	12854
X-RAY DIFFRACTION	f_chiral_restr	0.0456	1449
X-RAY DIFFRACTION	f_plane_restr	0.0065	1644
X-RAY DIFFRACTION	f_dihedral_angle_d	13.6771	3428

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 (%)
2.3-2.36	0.2957	156	0.2553	4082	X-RAY DIFFRACTION	99.93
2.36-2.42	0.2611	152	0.2414	4091	X-RAY DIFFRACTION	100
2.42-2.49	0.3183	131	0.2391	4106	X-RAY DIFFRACTION	99.98
2.49-2.57	0.3085	132	0.236	4092	X-RAY DIFFRACTION	99.95
2.57-2.66	0.3193	152	0.2472	4094	X-RAY DIFFRACTION	99.93
2.66-2.77	0.301	178	0.2299	4065	X-RAY DIFFRACTION	99.93
2.77-2.9	0.2804	196	0.2171	4038	X-RAY DIFFRACTION	99.95
2.9-3.05	0.2429	178	0.2034	4076	X-RAY DIFFRACTION	99.95
3.05-3.24	0.293	123	0.21	4127	X-RAY DIFFRACTION	100
3.24-3.49	0.2243	85	0.1953	4172	X-RAY DIFFRACTION	99.88
3.49-3.84	0.2536	107	0.1848	4141	X-RAY DIFFRACTION	99.91
3.84-4.4	0.2191	157	0.1664	4110	X-RAY DIFFRACTION	99.86
4.4-5.54	0.2157	147	0.1766	4138	X-RAY DIFFRACTION	99.88
5.54-45.71	0.2421	123	0.1918	4232	X-RAY DIFFRACTION	99.7

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	1.49059858016	-1.33601908642	2.42319080638	4.05402319866	0.745587956977	6.69245831881	-0.0798965124816	-0.226894390274	0.406371444458	-0.0822522683893	-0.185538574667	0.347306515555	-0.812698379925	-0.322279752217	0.206462846051	0.284010762314	0.0143469800326	0.0697859835216	0.324060522231	0.00049851721939	0.420981340285	-1.2357566152	63.9593016837	53.7586969007
2	2.47618483727	0.082100434644	0.545764313127	2.32923123442	0.556747348126	3.59487927579	0.0259888474067	-0.181248050169	0.00604080582254	0.161916972613	0.17422257819	0.016830577705	-0.127494284874	0.230770862363	-0.201976225537	0.196051906099	-0.0118304469357	0.0796416425503	0.302868366502	-0.000958904952364	0.315574140339	7.89585343169	57.9457443083	57.7884315098
3	3.31753455154	-2.4171427491	4.63825902661	8.69359401573	-1.70435564541	6.89285868942	-0.307987538675	-0.89036912573	0.336537586529	0.782276549291	0.807397997329	0.134420787229	-1.91982680607	0.322753003198	-0.388683955626	0.645865743043	-0.0163671896942	0.184176461446	0.801039793734	-0.101987542861	0.589530715344	12.8051630102	81.857702712	51.2277987577
4	8.01053087628	2.32318218177	1.23806324427	2.56425358002	-0.0457835320501	3.1228728994	0.0323926275573	0.119463347546	0.107878209119	0.117742359795	0.100466932222	0.281313292114	-0.33156467302	-0.0307284777807	-0.0591500961644	0.30135493007	0.0412640143224	0.0338660383089	0.282840442611	0.0798009238526	0.226699249549	-1.79752435871	62.5222303617	43.7312157995
5	4.19616807911	-1.35972471698	2.26731185456	2.84085802639	-0.923904260774	6.79576729015	0.213214752727	0.840452664432	0.268889776174	-0.672024318566	-0.24994149988	-0.139997291928	-0.160428459836	0.470508342076	0.00913058017973	0.439723634687	0.0351456373524	0.0642042501362	0.345378850014	0.00525463368446	0.345200167497	-44.174352477	43.6676645195	53.2901725627
6	1.58089381335	-0.765751658161	1.30715535962	1.99063334708	-0.628355734335	2.01476956731	-0.0309133307655	0.146848054006	0.0946953563048	-0.179982087627	-0.0572348056612	-0.116258919995	-0.194560375475	0.0508763866256	0.0838370318837	0.279559805344	-0.00627528551976	0.0147855656728	0.246253487105	-0.00285473935544	0.303710139884	-40.7315030388	46.0909755835	64.993782388
7	3.83054129096	0.84052863344	1.31924451628	2.58630140918	0.305958996779	0.911791747411	0.548578872313	-1.14186549748	-0.400377505848	1.00148002309	-0.411578504878	-0.168472340588	0.0374930664086	-0.23207424335	-0.138214848958	0.647855262164	-0.208586800536	-0.0273641811892	0.624340873196	0.0992911285409	0.340792538411	25.3334328134	28.3488133297	84.6315028804
8	6.57519179593	1.53935947032	2.32537473402	4.17249362795	-0.914468014534	1.84242775553	0.0631393118032	-0.939115441405	0.21703762935	0.675913030369	-0.0286200206858	-0.0715378375946	-0.274881879047	-0.183359757704	0.00018877240754	0.429268686741	-0.0329587087174	-0.00339654297065	0.409287461097	-0.0330531515051	0.330071319521	28.483466348	33.9661851354	79.4326741104
9	2.39421790135	-0.149062020648	-1.21895437663	1.95987649104	1.17371710965	4.40414766695	0.295164583032	-0.296935060797	0.112311176693	0.324271847053	-0.172095845006	0.116569699446	-0.46497591127	-0.02727440336	-0.113965556633	0.333878506367	-0.0254768260266	0.0193649784062	0.295909860413	0.02971553864	0.276308541644	13.4761694943	31.2103605242	74.3268595219
10	2.41770676793	0.260301893185	2.9369224378	5.84808438954	1.61607673664	5.40103362991	0.0631871209693	0.135693752809	-0.251465306228	0.184573725876	-0.0155952674374	0.088585957148	0.43304334937	-0.546087534457	0.0955933493118	0.197916367746	-0.0902087073987	0.00968630450301	0.298256296597	0.0453354372288	0.333682700724	4.87281659037	29.156574696	55.130321572
11	3.49014428217	1.26523728409	2.85144897764	3.13233336023	0.0466970656123	4.21257905323	-0.307493504168	0.3611089213	-0.34264363303	-0.340137140677	0.219015158106	-0.0213656779606	-0.0919354298028	0.0261931045999	0.121763798905	0.27348808314	-0.0431828708648	0.0820572507844	0.372287440343	-0.0065538634276	0.395568308762	-1.04414826159	31.1903392925	43.8985797999
12	2.95955150648	-1.53492648321	-0.309900021421	3.89512090227	0.89921389166	3.00005352254	0.023585642951	0.508171509628	-0.617557844402	-0.0669875338194	0.0445802556965	0.450645371922	0.644407591099	0.142186177345	-0.108039568524	0.280989311357	-0.006926621807	-0.0356731075215	0.379415101946	-0.0662020294572	0.317326212447	12.383020014	17.7843641899	46.6248743243
13	2.87800322621	-2.00130749848	-0.87932404411	4.3312143767	2.89805858905	8.33000980027	0.158577273042	0.228744891425	0.0675517863287	0.0573722096119	-0.0887476524388	0.128874798305	-0.00592715587738	-0.0896121951596	0.0208583658066	0.145798808608	-0.0180877387689	0.010633556012	0.302069127625	0.0524990356529	0.264860740705	10.473927077	27.5125842316	58.0615158515
14	2.71022668817	0.88278270821	-1.24786211711	6.90035095733	-4.37480274716	4.44449233643	0.244424889936	0.0815421457324	0.535753869925	0.3188718332	-0.354649166067	0.435025458179	-0.553925857948	0.507572651076	0.0438264504419	0.487258262563	-0.0436899877227	-0.234900085734	0.298424289438	-0.0166298810745	0.637268369817	-26.8457098348	49.1629783729	83.6401837535
15	2.16633688712	-2.33359872073	1.90478347155	3.61298359644	-3.34478116932	3.18648764399	0.468523826655	0.901741009025	-0.552802000132	-0.485648830987	-0.707453350083	-0.393448317681	0.817748242578	0.990852914177	0.0939805819714	0.692375690138	0.0114708254458	-0.112858005585	0.564563640328	0.0679703843706	0.641152831955	-16.5247568022	36.4505293657	83.2828924709
16	5.48742593384	-1.4722803429	-4.33314106234	5.23953537478	5.4133860801	8.96774788366	-0.000147697927683	-0.876139487434	0.593690871419	0.680015596449	0.134280413855	-0.402388777152	-0.139772936991	2.48473988272	-0.112039923048	0.66628066502	-0.0673041142384	-0.350876442652	0.896108038347	0.0945956757263	0.803443188231	-17.1010897645	50.2089818502	87.7332614
17	6.71300913821	3.0899866137	1.80980854265	6.83493302405	3.39895708819	6.10446860321	0.502986594204	-1.33669521798	-0.0758510743451	0.460417291859	-0.705923787031	-0.0621126050519	-1.31600855927	1.03440263202	0.134089475471	1.16698162606	-0.244206157955	-0.290298494585	1.0550582673	-0.212156856551	0.762254137017	-13.1573144744	49.1544462276	102.96675844
18	4.09530799164	3.55557236492	0.869769836811	7.43152705479	0.992133846463	5.5656043537	0.0932974045157	-0.815831403953	-0.0763041529708	2.02344116329	0.0654997542174	-0.0622181645034	-0.236665062131	-0.217689607447	-0.202515164965	1.23135757296	-0.140250768611	-0.0485912650354	0.683838461846	-0.19557457895	0.962266311268	-25.7244860128	47.5825493136	105.391833374
19	5.04451511072	-0.0721944349317	-0.740825517267	3.68383655757	0.976580357375	3.22811563384	-0.0332094013039	-0.74246645185	1.00374020173	0.77917198707	-0.168963883442	-0.963411049697	-0.83366506693	0.738624900127	0.0216994446729	1.00201709275	-0.090660013491	-0.129937009562	0.575396467742	-0.206440883396	0.831774114931	-23.8117174985	53.2733488675	95.0919354777
20	3.91732179769	-1.75016386528	0.609037541759	3.67629826035	1.72678463634	4.41522061762	0.169507918122	-0.424844951649	0.260180764226	1.04822100537	-0.195260556199	-0.345080519062	-0.105559389863	0.469077778731	-0.000821199729686	0.607850059802	-0.0330859672098	-0.20645655162	0.318120049608	-0.0503336377049	0.473393042049	-27.1674562548	44.0780615641	91.2704801148
21	3.60888866028	-1.27335820707	0.652463159978	3.17569447392	-0.991255649553	1.40256288721	0.122009829158	-0.0214109161559	-0.446274340021	-0.284252241216	-0.151753157468	0.138386183378	0.108596843358	0.304104730603	0.0956880380053	0.362209531569	0.0130654864847	-0.0718441426543	0.297685440365	0.0531710732617	0.417144077258	-19.5215629086	29.9260002023	85.8083180587
22	2.49986040742	-2.23148276594	1.1940627482	2.85669470738	-2.14080843862	1.90027304463	0.0439531935647	-0.227774570262	-0.220763349149	0.441100802662	-0.0223664071113	-0.32238636375	0.199111405796	0.163399405756	0.0848128213534	0.562843123637	-0.0561935479395	-0.158072306696	0.304872656301	0.00191009481104	0.481376072419	-25.2710110957	28.1248633986	88.3053357159
23	4.04407230581	-5.37581639599	2.64042954202	8.99335314283	-2.80080275792	2.27533043011	-0.251314496586	-0.0655935786226	0.335152750789	0.184746341527	-0.0172612113392	-0.835107683862	-0.292659212496	0.135682029514	0.351454764145	0.280786725059	-0.0470114318879	-0.0686505913037	0.274841615106	0.0396821861827	0.420573852425	-31.4714147189	54.2536021676	72.6918712047
24	0.932575834414	0.271967257198	1.28949057507	6.15380602527	0.30016619792	9.43852444101	-0.189036586639	0.365542136915	-0.134375655926	-1.50507150859	-0.0842737073581	-0.109712904467	-0.0261185774027	-0.382046284937	0.288658438277	0.641485355943	-0.0117535734092	0.0142035294962	0.627985731642	0.0190546885218	0.431280089856	-14.5225165957	61.6577578464	18.9686087638
25	5.47389012944	1.92216634343	1.75300506635	1.64418382614	0.912738842385	1.6278387226	-0.0019618270332	0.378191671356	-0.142554594892	-0.169188382533	0.0376710323362	0.277260457106	-0.0604939550185	-0.0827902697313	-0.00935254372636	0.315813987316	0.0519624602352	-0.0285561099552	0.362822516384	0.0639602657704	0.365199590284	-14.472565147	58.5731266421	31.9882924181

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 52 )	A	A	15 - 52	1 - 38
2	2	chain 'A' and (resid 53 through 140 )	A	A	53 - 140	39 - 126
3	3	chain 'A' and (resid 141 through 155 )	A	A	141 - 155	127 - 141
4	4	chain 'A' and (resid 156 through 221 )	A	A	156 - 221	142 - 207
5	5	chain 'B' and (resid 15 through 79 )	B	F	15 - 79	1 - 65
6	6	chain 'B' and (resid 80 through 221 )	B	F	80 - 221	66 - 202
7	7	chain 'C' and (resid 16 through 79 )	C	J	16 - 79	1 - 64
8	8	chain 'C' and (resid 80 through 126 )	C	J	80 - 126	65 - 111
9	9	chain 'C' and (resid 127 through 221 )	C	J	127 - 221	112 - 204
10	10	chain 'D' and (resid 15 through 31 )	D	L	15 - 31	1 - 17
11	11	chain 'D' and (resid 32 through 126 )	D	L	32 - 126	18 - 112
12	12	chain 'D' and (resid 127 through 155 )	D	L	127 - 155	113 - 141
13	13	chain 'D' and (resid 156 through 219 )	D	L	156 - 219	142 - 205
14	14	chain 'E' and (resid 16 through 26 )	E	Q	16 - 26	1 - 11
15	15	chain 'E' and (resid 27 through 39 )	E	Q	27 - 39	12 - 24
16	16	chain 'E' and (resid 40 through 52 )	E	Q	40 - 52	25 - 37
17	17	chain 'E' and (resid 53 through 70 )	E	Q	53 - 70	38 - 49
18	18	chain 'E' and (resid 71 through 91 )	E	Q	71 - 91	50 - 70
19	19	chain 'E' and (resid 92 through 107 )	E	Q	92 - 107	71 - 86
20	20	chain 'E' and (resid 108 through 126 )	E	Q	108 - 126	87 - 105
21	21	chain 'E' and (resid 127 through 155 )	E	Q	127 - 155	106 - 134
22	22	chain 'E' and (resid 156 through 184 )	E	Q	156 - 184	135 - 163
23	23	chain 'E' and (resid 185 through 221 )	E	Q	185 - 221	164 - 200
24	24	chain 'F' and (resid 16 through 107 )	F	X	16 - 107	1 - 76
25	25	chain 'F' and (resid 108 through 221 )	F	X	108 - 221	77 - 190

-
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