PDB-5bk5: Crystal structure of the anti-circumsporozoite protein 663 germli...

ID or keywords:

Entry

Database: PDB / ID: 5bk5

Title

Crystal structure of the anti-circumsporozoite protein 663 germline antibody

Components

663 germline antibody, heavy chain
663 germline antibody, light chain

Keywords

IMMUNE SYSTEM / Malaria / Circumsporozoite protein / Fab

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Scally, S.W. / Bosch, A. / Triller, G. / Wardemann, H. / Julien, J.P.

Citation

Journal: Immunity / Year: 2017
Title: Natural Parasite Exposure Induces Protective Human Anti-Malarial Antibodies.
Authors: Triller, G. / Scally, S.W. / Costa, G. / Pissarev, M. / Kreschel, C. / Bosch, A. / Marois, E. / Sack, B.K. / Murugan, R. / Salman, A.M. / Janse, C.J. / Khan, S.M. / Kappe, S.H.I. / Adegnika, ...

History

Deposition	Sep 12, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2018	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name
Revision 1.2	Feb 26, 2020	Group: Data collection / Category: reflns / reflns_shell Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.3	Apr 3, 2024	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	5bk5.cif.gz	653.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5bk5.ent.gz	547.3 KB	Display	PDB format
PDBx/mmJSON format	5bk5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5bk5_validation.pdf.gz	498.2 KB	Display	wwPDB validaton report
Full document	5bk5_full_validation.pdf.gz	512.2 KB	Display
Data in XML	5bk5_validation.xml.gz	58.4 KB	Display
Data in CIF	5bk5_validation.cif.gz	78.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bk/5bk5 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/5bk5	HTTPS FTP

-
Related structure data

Related structure data	5bk0C 5bk3C 6azmC 6azxC C: citing same article (ref.)
Similar structure data	4yhy-2 5ezl-2 1cly-d 5mx3-1 5eoq-d 2orb-2 5v7r-d 6y1n-d 4nrx-3 1vpo-d 5mp5-2 6azx-2 5wuv-d 1hq4-1 4kvc-d 4r7n-6 4odu-1 6x1s-2 3qg7-d 6x1v-d 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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

B: 663 germline antibody, heavy chain

H: 663 germline antibody, heavy chain

A: 663 germline antibody, light chain

G: 663 germline antibody, light chain

D: 663 germline antibody, heavy chain

F: 663 germline antibody, heavy chain

C: 663 germline antibody, light chain

E: 663 germline antibody, light chain

hetero molecules

192 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: 663 germline antibody, heavy chain

A: 663 germline antibody, light chain

hetero molecules

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

2

H: 663 germline antibody, heavy chain

G: 663 germline antibody, light chain

hetero molecules

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

3

D: 663 germline antibody, heavy chain

C: 663 germline antibody, light chain

hetero molecules

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

4

F: 663 germline antibody, heavy chain

E: 663 germline antibody, light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.177, 134.171, 111.796
Angle α, β, γ (deg.)	90.00, 98.24, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	663 germline antibody, heavy chain Mass: 23606.441 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	663 germline antibody, light chain Mass: 23980.699 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₃H₈O₃

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50.85 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM Tris pH 8.5, 200 mM MgCl2, 20% (w/v) PEG 4000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 1, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 3→40 Å / Num. obs: 36998 / % possible obs: 98.4 % / Redundancy: 2.6 % / R_pim(I) all: 0.121 / Net I/σ(I): 6.41
Reflection shell	Resolution: 3→3.1 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3460 / R_pim(I) all: 0.422 / % possible all: 98.6

-
Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
SHELXPREP		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 663 Fab

Resolution: 3→39.038 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.47

	R_factor	Num. reflection	% reflection
R_free	0.3142	1847	5 %
R_work	0.2569	-	-
obs	0.2598	36970	98.43 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 3→39.038 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12886	0	84	0	12970

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	13256
X-RAY DIFFRACTION	f_angle_d	0.786	18058
X-RAY DIFFRACTION	f_dihedral_angle_d	14.156	7880
X-RAY DIFFRACTION	f_chiral_restr	0.051	2072
X-RAY DIFFRACTION	f_plane_restr	0.006	2294

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 (%)
3-3.0811	0.4394	141	0.3585	2687	X-RAY DIFFRACTION	99
3.0811-3.1717	0.3937	143	0.3193	2709	X-RAY DIFFRACTION	98
3.1717-3.274	0.3911	141	0.3069	2674	X-RAY DIFFRACTION	98
3.274-3.391	0.354	142	0.3047	2704	X-RAY DIFFRACTION	99
3.391-3.5267	0.3578	141	0.2869	2675	X-RAY DIFFRACTION	98
3.5267-3.6871	0.3219	141	0.2685	2683	X-RAY DIFFRACTION	98
3.6871-3.8813	0.3118	143	0.2564	2710	X-RAY DIFFRACTION	98
3.8813-4.1242	0.2937	143	0.2495	2707	X-RAY DIFFRACTION	99
4.1242-4.4423	0.2829	141	0.219	2682	X-RAY DIFFRACTION	98
4.4423-4.8885	0.2908	142	0.2105	2717	X-RAY DIFFRACTION	98
4.8885-5.5942	0.2578	143	0.2167	2703	X-RAY DIFFRACTION	99
5.5942-7.0413	0.3125	142	0.2566	2720	X-RAY DIFFRACTION	98
7.0413-39.0414	0.2757	144	0.242	2752	X-RAY DIFFRACTION	98

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	1.8272	-0.1078	0.9714	1.517	1.1176	2.5732	0.3009	-0.1043	0.3579	-0.5052	-0.1991	-0.7157	-0.7217	0.3325	-0.135	0.4182	-0.1543	0.0144	0.3466	0.0381	0.4536	74.6853	-10.0299	127.1929
2	5.3494	0.5596	-0.5522	4.3471	-1.7364	4.583	-0.0258	0.2708	0.6071	-0.4136	-0.2933	-0.5035	-0.0811	0.4945	0.4601	0.3257	0.0459	-0.1084	0.3941	0.0822	0.4903	77.5743	-9.0607	135.4874
3	3.1565	0.2563	-0.4798	3.2878	0.9939	4.7869	-0.0167	-0.4036	0.4766	0.0245	-0.1069	-1.0484	0.0268	0.5392	0.0764	0.3791	0.0373	-0.1003	0.3218	0.0076	0.651	80.3776	-12.461	136.605
4	0.0038	0.0416	-0.0071	0.1707	-0.0238	0.006	-0.3013	0.5312	-0.0696	-0.4687	0.0508	-0.001	0.29	-0.0331	0.1613	0.5503	-0.1735	-0.0242	0.3524	0.0126	0.3358	66.6505	-17.5275	119.588
5	2.1439	-0.3854	-1.2955	0.8947	0.3651	2.3678	0.0825	-0.2492	0.7393	0.147	0.1356	-0.0455	0.1381	-0.1215	-0.267	0.3767	-0.1023	-0.1444	0.3295	-0.059	0.5049	50.0286	-9.3222	122.7931
6	6.6374	-0.332	-1.2893	1.3768	1.1793	3.3104	0.1196	0.3042	1.1301	-0.4204	-0.4531	0.1649	-0.527	-0.1787	0.2537	0.586	-0.1366	-0.1305	0.3173	-0.0768	0.3592	43.8432	-2.4928	125.2291
7	3.2546	-1.9091	-0.5206	1.202	0.0032	1.028	0.3134	0.0217	0.8519	-0.1589	0.0764	0.3489	-0.0949	0.2688	-0.3252	0.3445	-0.0654	-0.1296	0.3985	-0.0405	0.8955	53.6246	-3.2306	116.7757
8	2.9299	0.0441	0.9649	0.6624	1.3753	3.141	0.2196	-0.1549	0.1283	0.2547	-0.2064	0.5408	-0.2392	-0.0654	0.0293	0.3271	-0.0681	-0.041	0.2644	-0.1184	0.3241	39.4242	-7.8766	91.2641
9	4.848	0.3696	0.5617	3.2751	0.426	3.9817	-0.0885	0.1667	0.6364	0.4558	-0.4021	0.9063	-0.3807	-0.1953	0.3303	0.3484	-0.0176	-0.0837	0.3305	-0.0602	0.5895	34.1654	-7.5411	80.6016
10	5.4922	0.1796	-0.1996	2.2628	-0.3512	5.308	0.1952	-0.2144	0.2243	0.0317	-0.4056	0.2514	0.3485	-0.9982	0.238	0.3606	-0.1343	-0.2242	0.3432	-0.0981	0.6843	30.2057	-14.1506	82.9875
11	2.1683	0.8587	-1.0449	2.4633	-2.0207	4.0476	-0.1134	0.1214	0.6503	-0.0173	-0.3173	0.4333	-0.3229	-0.0281	0.4133	0.339	-0.0898	-0.2406	0.4	0.0261	0.5325	35.3849	-7.9497	83.9856
12	0.708	-0.0667	-0.0636	1.4222	0.4037	1.5836	-0.0026	0.0802	0.4975	0.0768	-0.1289	0.0692	-0.4272	-0.1405	0.0557	0.4176	-0.0463	-0.0407	0.2881	0.2365	0.707	43.77	-6.8031	86.2514
13	0.3886	-0.7092	-0.1027	1.4074	-0.1488	1.2539	0.1767	0.0075	0.2256	-0.2312	0.077	-0.3118	-0.3218	0.3289	-0.1022	0.3391	0.2024	-0.1048	-0.0084	-0.0461	0.9677	67.4938	-7.8778	98.503
14	0.5125	0.0733	-0.5689	0.7388	0.0109	0.7956	0.2767	-0.0337	1.0898	-0.0703	-0.0226	0.2224	-0.1517	0.1168	-0.3073	0.366	0.0759	-0.0844	0.2671	0.022	0.7796	59.6597	-2.2274	93.5842
15	2.7831	0.5586	-1.4673	7.9108	-2.7533	3.6619	0.4114	0.3387	0.7752	0.0454	0.1954	0.2283	0.4525	0.0639	-0.523	0.4419	0.1261	-0.1044	0.2828	-0.0189	0.5684	62.9258	-11.8999	93.0762
16	2.5634	1.3697	0.169	2.4068	-0.3962	1.1408	0.3975	-0.3113	1.0244	-0.2834	-0.2328	-0.7521	-0.3274	-0.0282	-0.1381	0.5879	0.1351	0.0158	0.4002	-0.0806	1.3581	64.6804	0.8202	99.3861
17	3.6981	3.3878	1.1807	7.4122	0.7932	2.3124	0.3693	-0.1793	-0.0368	0.4509	-0.0878	-0.2089	0.2478	0.0345	-0.2845	0.5363	0.0287	-0.106	0.2952	-0.2255	1.1478	62.4986	-2.2422	104.6012
18	2.0071	-3.6527	-0.0731	3.6982	0.7645	3.8464	-0.5845	-0.5427	-0.7179	0.3107	0.3609	-0.4344	0.5452	-0.2207	0.2071	0.6183	-0.0661	-0.0643	0.3395	0.0996	0.7127	62.125	-18.712	153.7783
19	1.854	0.2231	-1.5002	4.493	0.4736	1.268	0.2043	-0.2964	-0.2132	0.1206	-0.3895	-0.2679	0.1555	0.0436	0.0598	0.3721	-0.0202	-0.1555	0.4649	-0.0347	0.3562	73.2393	-12.1786	151.7918
20	6.5384	0.9556	1.0705	1.9062	0.4591	4.8807	0.0168	-0.7769	0.2228	0.1898	-0.2194	-0.0319	0.2305	0.1744	0.2944	0.3527	-0.0544	-0.0422	0.3778	0.0785	0.3972	66.0354	-9.6878	155.1369
21	2.905	0.3194	0.0954	1.0756	-0.391	1.0805	-0.4092	-0.6672	-0.2689	0.318	-0.0997	-0.3618	0.4544	-0.131	0.3017	0.5819	0.1718	-0.0625	0.519	-0.3265	0.2997	61.6573	-15.9699	147.1093
22	2.0978	-0.8021	-0.1473	2.6337	0.9433	5.6004	-0.0143	-0.2068	0.218	0.1382	-0.002	0.2813	-0.3273	-0.0052	0.0362	0.2027	-0.0039	0.0061	0.2049	-0.0723	0.3056	40.7975	-18.1139	125.2514
23	0.8607	0.7213	0.8128	0.5001	0.6887	3.9566	-0.035	-0.1332	-0.1198	-0.1291	0.2052	0.0901	-0.1	-0.3828	-0.12	0.2966	0.0935	-0.1061	0.3499	0.0184	0.3763	41.5762	-17.6247	126.7129
24	2.8504	0.4794	-2.6576	2.9193	0.5918	4.2113	-0.4276	-0.2435	0.041	-0.3765	-0.2869	0.0636	-0.3383	0.5706	0.6256	0.2851	0.0056	-0.0854	0.124	-0.0121	0.4886	31.803	-16.1203	128.0367
25	9.3039	6.7767	-1.6618	7.2623	-0.8996	2.3388	-0.5236	1.1845	0.3786	-0.5228	0.2049	-0.1309	0.3557	1.024	0.2908	0.4937	-0.0236	-0.1132	0.9278	0.1927	0.4208	52.5366	-11.6223	63.1743
26	2.0103	-8.2605	-0.5542	8.0705	3.6777	8.4007	-0.1899	0.6635	0.3101	-0.0972	-0.408	0.7933	-0.5106	0.2043	0.5798	0.2582	-0.1193	-0.1129	0.529	0.0959	0.6136	33.1573	-8.5945	58.7433
27	1.0257	-0.9683	-1.3356	1.2741	0.3716	3.8812	-0.0705	-0.2911	0.1636	-0.0326	0.3522	-0.3554	-0.5105	0.4687	-0.152	0.4083	-0.2005	-0.1292	0.5355	0.2149	0.5327	47.6518	-3.1051	71.9353
28	0.8303	0.132	2.2995	2.5221	0.4988	6.3856	-0.1692	0.2142	0.4876	-0.5809	-0.4251	-0.2381	-0.2426	0.3584	0.5188	0.6689	-0.0985	-0.2179	0.8946	0.3833	0.5952	45.6633	3.8998	63.3353
29	3.0284	1.1946	-0.1804	1.6872	-0.1804	0.6465	-0.2852	0.3075	0.3732	-0.1614	0.0341	-0.2374	-0.1361	0.6982	0.23	0.5871	-0.0139	-0.2413	0.8221	0.2111	0.568	50.3795	-4.8736	63.9276
30	1.3015	-0.3308	0.3645	0.1675	-0.0148	0.9603	-0.6398	0.8913	0.0888	-0.1507	-0.6049	0.4345	-0.2495	0.2019	0.438	0.4267	0.0116	-0.3505	0.591	0.9755	-0.0762	53.2743	-9.9158	70.3058
31	3.1043	3.3093	-3.4	3.6306	-3.4167	5.4981	0.5539	-0.023	0.7171	0.8372	0.0192	0.2949	-1.3096	-0.5716	-0.5189	0.3075	0.0825	0.0124	0.2298	-0.0353	0.3471	73.2429	-11.8885	100.9791
32	2.8074	0.0334	-0.5622	3.0363	-0.7918	2.9924	-0.1004	0.8017	0.1056	-0.1896	-0.1606	0.2163	-0.2112	-0.1777	0.0998	0.2238	-0.0271	-0.0583	0.3461	0.0167	0.4586	73.4085	-14.6158	85.8371
33	3.8287	-0.3777	-0.9639	1.8967	-1.0908	1.3041	-0.1803	0.3255	0.0704	0.0399	0.4476	0.0725	-0.046	-0.541	-0.1077	0.3555	-0.0239	-0.1158	0.3503	0.0079	0.3887	70.5906	-15.9071	89.6266
34	2.3639	-0.5316	0.3643	1.3679	-0.7668	3.3163	-0.4434	0.0738	-0.2119	0.08	0.2463	0.0972	-0.0079	0.1398	-0.0326	0.4083	-0.0218	-0.1353	0.3106	-0.1004	0.3447	81.7365	-16.3991	90.0161
35	0.3883	0.2294	-0.6709	0.1317	-0.3222	1.2676	0.0124	0.0767	-0.0512	-0.5479	-0.0157	0.1743	0.3248	0.0162	0.0456	0.5119	-0.0183	-0.1039	0.4077	0.0013	0.2102	39.5135	16.2872	129.8755
36	9.3133	1.5725	-4.0376	4.094	-0.5613	6.6887	-0.3193	0.0058	-1.1818	-0.116	0.2608	0.3326	0.653	-0.0254	0.0631	0.591	0.1374	-0.0509	0.441	-0.0191	0.2792	32.1718	8.373	136.7011
37	3.0191	-1.2633	0.2361	4.5674	-0.1667	4.0139	-0.0341	-0.1552	0.2801	-0.298	0.0437	0.7141	-0.328	0.0595	0.064	0.3229	0.1003	-0.0164	0.2983	-0.0322	0.3561	33.4514	20.546	141.0814
38	8.3051	1.5231	-1.4378	9.5636	-1.5849	7.3496	0.3175	0.2588	-0.1669	0.4771	-0.3302	0.4649	-0.2457	0.4889	-0.0195	0.2569	0.0475	0.1258	0.3789	-0.0364	0.2028	33.5836	20.6251	132.9896
39	6.2094	-2.2155	-0.2164	4.6909	-0.8643	6.6428	-0.3714	0.185	-0.3388	0.0317	0.0036	0.2971	0.3647	0.2807	0.344	0.2253	0.1723	0.0087	0.5127	0.0705	0.2848	38.3631	11.8213	143.4997
40	2.2261	0.053	1.9265	7.748	-0.8561	1.7713	-0.0663	-0.2894	-0.2444	0.0383	0.229	0.3864	0.2295	-0.4117	-0.1672	0.4617	-0.1176	-0.0857	0.4522	0.3226	0.711	40.0273	5.6844	146.0315
41	0.8768	-0.4709	-1.1997	4.4369	0.0561	1.5372	-0.0788	0.2143	0.5701	-0.4238	0.046	-1.0144	-0.3483	-0.1426	-0.081	0.4276	-0.0317	-0.1103	0.2108	0.0338	0.2964	59.2449	20.4553	122.7609
42	0.4615	-1.0865	0.4191	2.2699	-0.9144	2.2192	0.2586	0.039	-0.8653	0.084	0.1233	0.4499	0.4218	-0.3432	-0.3209	0.4194	-0.0817	0.0486	0.2472	0.0095	0.6484	59.8373	11.3153	127.2689
43	1.9246	-0.8689	1.2501	2.3433	-1.5263	3.7685	0.4586	0.0224	-0.8153	-0.2969	-0.3917	-0.8047	-0.0777	0.3768	-0.0048	0.3865	-0.0557	0.0094	0.2992	-0.0133	0.792	66.4029	16.0259	126.6354
44	8.2742	-5.3089	1.0599	7.2954	-0.6263	3.3694	0.9234	0.3148	-1.3368	-0.351	-0.3849	-0.0741	0.4304	-0.0831	-0.5484	0.3783	-0.0444	-0.0992	0.3245	-0.0222	0.7213	60.2698	11.9046	118.3805
45	0.8523	0.4527	-1.2727	0.7054	-0.913	1.9431	-0.0578	0.0141	-0.6277	-0.0417	-0.2583	-1.2988	0.3535	0.0676	0.3555	0.5283	0.1076	-0.043	0.4789	-0.0323	0.8383	78.2453	16.5585	90.5496
46	4.401	3.2009	-0.8622	4.9186	-0.5832	3.7899	-0.6659	0.4704	-1.1917	-0.4678	0.246	-1.0239	0.3469	-0.0141	0.3838	0.4746	-0.0867	0.0024	0.3379	-0.1009	0.7491	79.0379	24.7433	82.1844
47	3.0101	-1	-1.2593	2.5171	1.8628	6.1052	0.0088	-0.0438	-0.1137	-0.0448	-0.1048	-1.1613	0.1358	0.0322	0.1058	0.4021	-0.156	0.0332	0.2162	0.0544	0.6324	80.0928	22.9858	87.4212
48	2.3756	-0.4294	-0.6298	2.7191	1.6689	1.8797	-0.0819	0.3445	-0.0183	-0.4163	0.0398	0.2586	0.7903	0.2158	0.0083	0.9056	0.0069	0.1878	0.4357	-0.5756	0.9259	74.1936	11.5758	76.1654
49	2.3329	0.5692	-1.248	2.4192	0.6789	1.1511	0.1062	0.1975	-0.7398	0.1954	-0.2667	0.1609	0.2196	-0.0844	0.192	0.434	0.0689	-0.0228	0.244	-0.0029	0.4359	54.0926	18.3363	99.1478
50	1.5331	1.1285	0.9353	1.3861	1.7884	2.7961	0.1943	0.0873	-1.0779	0.08	-0.0604	0.1877	0.1753	-0.228	-0.0416	0.3415	0.0831	-0.0488	0.3558	-0.0771	0.785	50.3887	15.3385	100.0871
51	9.4464	-0.2068	-2.279	0.8952	1.3775	2.3849	-0.1772	-0.963	-0.5491	0.0629	0.1006	0.0977	-0.032	0.3911	0.0929	0.4029	0.0409	-0.0954	0.4064	0.1207	0.2785	45.8167	19.1626	159.2899
52	3.6079	-0.0235	-0.7441	0.3724	0.2789	0.3287	0.0134	-0.2828	-0.3544	0.3489	-0.1771	-0.0878	0.0882	0.1727	0.1609	0.4529	0.0277	-0.004	0.5317	0.1524	0.3149	49.8867	13.2474	153.6082
53	2.5619	-0.7773	0.1001	1.9076	-0.6641	5.6443	-0.0834	-0.1185	0.1749	-0.1151	0.2356	0.1009	0.0005	0.0477	-0.1325	0.2573	-0.0047	-0.0357	0.2422	0.0244	0.3201	74.3307	24.2104	130.5802
54	0.6407	0.3231	1.503	1.9225	2.3695	4.9478	-0.1951	-0.2866	0.001	-0.0294	0.0316	-0.3239	-0.3856	-0.4741	0.1203	0.781	-0.1415	-0.0066	0.6403	0.1162	0.4872	61.5439	28.1029	67.5382
55	6.3692	-0.0775	-1.4784	4.0786	-0.8341	0.7054	0.2702	0.2674	-0.2282	-0.5866	-0.287	-0.0553	-0.6645	0.9372	0.0433	0.5926	-0.2259	0.1317	0.7466	-0.1527	0.4806	71.1615	18.7167	68.1751
56	0.4181	0.1582	0.601	0.4463	0.5404	1.0135	-0.0004	0.414	-0.1656	-0.5378	-0.1652	-0.3762	-0.3339	0.1375	-0.0092	0.7328	-0.3718	0.0626	1.1846	-0.1583	0.4681	62.5886	23.0908	69.7809
57	3.8582	0.9494	-0.4109	2.6678	1.4454	4.8243	-0.1326	0.4403	0.2236	0.1469	-0.0569	0.2048	0.0989	0.1781	0.1283	0.3443	-0.0191	-0.0477	0.2679	0.0742	0.381	40.6818	27.3078	95.831
58	5.5284	0.0529	0.8218	2.3496	1.0701	5.5494	-0.2101	0.3846	0.051	-0.3244	0.2102	0.204	-0.4268	0.2137	0.1655	0.251	-0.0381	-0.008	0.2904	0.0749	0.3326	41.2435	26.4519	94.5419
59	1.7682	0.1432	-0.6992	1.5287	0.5653	2.7763	-0.3253	0.1856	0.1412	-0.0411	0.2302	0.1404	0.3111	0.0973	0.1414	0.4194	-0.2591	0.0384	0.4801	0.2765	0.4539	31.4528	25.2415	93.2296

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 18 through 44 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 45 through 106 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 107 through 119 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 120 through 175 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 176 through 193 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 194 through 213 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 1 through 17 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 18 through 59 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 60 through 72 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 73 through 99 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 100 through 119 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 120 through 145 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 146 through 165 )
15	X-RAY DIFFRACTION	15	chain 'H' and (resid 166 through 185 )
16	X-RAY DIFFRACTION	16	chain 'H' and (resid 186 through 203 )
17	X-RAY DIFFRACTION	17	chain 'H' and (resid 204 through 213 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 1 through 25 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 26 through 48 )
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 49 through 90 )
21	X-RAY DIFFRACTION	21	chain 'A' and (resid 91 through 113 )
22	X-RAY DIFFRACTION	22	chain 'A' and (resid 114 through 163 )
23	X-RAY DIFFRACTION	23	chain 'A' and (resid 164 through 197 )
24	X-RAY DIFFRACTION	24	chain 'A' and (resid 198 through 214 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 1 through 25 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 26 through 32 )
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 33 through 48 )
28	X-RAY DIFFRACTION	28	chain 'G' and (resid 49 through 61 )
29	X-RAY DIFFRACTION	29	chain 'G' and (resid 62 through 90 )
30	X-RAY DIFFRACTION	30	chain 'G' and (resid 91 through 113 )
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 114 through 128 )
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 129 through 150 )
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 151 through 187 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 188 through 212 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 1 through 17 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 18 through 33 )
37	X-RAY DIFFRACTION	37	chain 'D' and (resid 34 through 72 )
38	X-RAY DIFFRACTION	38	chain 'D' and (resid 73 through 87 )
39	X-RAY DIFFRACTION	39	chain 'D' and (resid 88 through 99 )
40	X-RAY DIFFRACTION	40	chain 'D' and (resid 100 through 106 )
41	X-RAY DIFFRACTION	41	chain 'D' and (resid 107 through 145 )
42	X-RAY DIFFRACTION	42	chain 'D' and (resid 146 through 165 )
43	X-RAY DIFFRACTION	43	chain 'D' and (resid 166 through 193 )
44	X-RAY DIFFRACTION	44	chain 'D' and (resid 194 through 213 )
45	X-RAY DIFFRACTION	45	chain 'F' and (resid 1 through 33 )
46	X-RAY DIFFRACTION	46	chain 'F' and (resid 34 through 60 )
47	X-RAY DIFFRACTION	47	chain 'F' and (resid 61 through 99 )
48	X-RAY DIFFRACTION	48	chain 'F' and (resid 100 through 106 )
49	X-RAY DIFFRACTION	49	chain 'F' and (resid 107 through 165 )
50	X-RAY DIFFRACTION	50	chain 'F' and (resid 166 through 213 )
51	X-RAY DIFFRACTION	51	chain 'C' and (resid 1 through 32 )
52	X-RAY DIFFRACTION	52	chain 'C' and (resid 33 through 113 )
53	X-RAY DIFFRACTION	53	chain 'C' and (resid 114 through 212 )
54	X-RAY DIFFRACTION	54	chain 'E' and (resid 1 through 25 )
55	X-RAY DIFFRACTION	55	chain 'E' and (resid 26 through 61 )
56	X-RAY DIFFRACTION	56	chain 'E' and (resid 62 through 113 )
57	X-RAY DIFFRACTION	57	chain 'E' and (resid 114 through 163 )
58	X-RAY DIFFRACTION	58	chain 'E' and (resid 164 through 197 )
59	X-RAY DIFFRACTION	59	chain 'E' and (resid 198 through 214 )

-
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