PDB-6obo: Ricin A chain bound to VHH antibody V6A6

ID or keywords:

Entry

Database: PDB / ID: 6obo

Title

Ricin A chain bound to VHH antibody V6A6

Components

Ricin A chain
VHH antibody V6A6

Keywords

TOXIN

Function / homology

Function and homology information

rRNA N-glycosylase /

rRNA N-glycosylase activity / AMP binding / defense response /

toxin activity /

carbohydrate binding / killing of cells of another organism / negative regulation of translation
Similarity search - Function

Biological species

Ricinus communis (castor bean)

Vicugna pacos (alpaca)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

Authors

Rudolph, M.J.

Funding support

United States, 1items

Citation

Journal: J.Mol.Biol. / Year: 2020
Title: Intracellular Neutralization of Ricin Toxin by Single-domain Antibodies Targeting the Active Site.
Authors: Rudolph, M.J. / Czajka, T.F. / Davis, S.A. / Thi Nguyen, C.M. / Li, X.P. / Tumer, N.E. / Vance, D.J. / Mantis, N.J.

History

Deposition	Mar 21, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 1, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 14, 2020	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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6obo.cif.gz	326.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6obo.ent.gz	274.7 KB	Display	PDB format
PDBx/mmJSON format	6obo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ob/6obo ftp://data.pdbj.org/pub/pdb/validation_reports/ob/6obo	HTTPS FTP

-
Related structure data

Related structure data	6obcC 6obeC 6obgC 6obmC 6ocaC 6ocdC C: citing same article (ref.)
Similar structure data	2a99-d 5iby-d 4jp8-d 5icl-2 5icl-1 3hc2-d 2z58-d 6jom-2 5cxw-d 3r19-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) 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	#161 - May 2013 Ricin similarity (15) #69 - Sep 2005 Cholera Toxin similarity (15) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Ricin A chain

B: Ricin A chain

C: VHH antibody V6A6

D: VHH antibody V6A6

hetero molecules

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

1

A: Ricin A chain

C: VHH antibody V6A6

hetero molecules

defined by author
Evidence: surface plasmon resonance
42.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Ricin A chain

D: VHH antibody V6A6

hetero molecules

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

Unit cell

Length a, b, c (Å)	123.242, 112.929, 93.081
Angle α, β, γ (deg.)	90.000, 127.490, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-967- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain C and (resid 2 through 29 or resid 31 through 94 or resid 96 through 120))
2	1	(chain D and (resid 2 through 29 or resid 31 through 94 or resid 96 through 120))
1	2	(chain A and (resid 5 through 71 or resid 73...
2	2	(chain B and (resid 5 through 71 or resid 73...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	(chain C and (resid 2 through 29 or resid 31 through 94 or resid 96 through 120))	C	2 - 29
1	2	1	(chain C and (resid 2 through 29 or resid 31 through 94 or resid 96 through 120))	C	31 - 94
1	3	1	(chain C and (resid 2 through 29 or resid 31 through 94 or resid 96 through 120))	C	96 - 120
2	1	1	(chain D and (resid 2 through 29 or resid 31 through 94 or resid 96 through 120))	D	2 - 29
2	2	1	(chain D and (resid 2 through 29 or resid 31 through 94 or resid 96 through 120))	D	31 - 94
2	3	1	(chain D and (resid 2 through 29 or resid 31 through 94 or resid 96 through 120))	D	96 - 120
1	1	2	(chain A and (resid 5 through 71 or resid 73...	A	5 - 71
1	2	2	(chain A and (resid 5 through 71 or resid 73...	A	73 - 118
1	3	2	(chain A and (resid 5 through 71 or resid 73...	A	5 - 261
1	4	2	(chain A and (resid 5 through 71 or resid 73...	A	5 - 261
1	5	2	(chain A and (resid 5 through 71 or resid 73...	A	139 - 205
1	6	2	(chain A and (resid 5 through 71 or resid 73...	A	207 - 233
1	7	2	(chain A and (resid 5 through 71 or resid 73...	A	235
1	8	2	(chain A and (resid 5 through 71 or resid 73...	A	237 - 261
2	1	2	(chain B and (resid 5 through 71 or resid 73...	B	5 - 71
2	2	2	(chain B and (resid 5 through 71 or resid 73...	B	73 - 118
2	3	2	(chain B and (resid 5 through 71 or resid 73...	B	120 - 36
2	4	2	(chain B and (resid 5 through 71 or resid 73...	B	5 - 261
2	5	2	(chain B and (resid 5 through 71 or resid 73...	B	207 - 233
2	6	2	(chain B and (resid 5 through 71 or resid 73...	B	235
2	7	2	(chain B and (resid 5 through 71 or resid 73...	B	237 - 261

NCS ensembles :

ID
1
2

-
Protein / Antibody , 2 types, 4 molecules ABCD

#1: Protein	Ricin A chain Mass: 28806.449 Da / Num. of mol.: 2 / Fragment: Toxin catalytic subunit, residues 40-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody	VHH antibody V6A6 Mass: 12992.228 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 4 types, 844 molecules

#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-ACY / ACETIC ACID / Acetic acid Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₄O₂
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 833 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.07 Å³/Da / Density % sol: 59.99 %
Crystal grow	Method: vapor diffusion / pH: 8 Details: 100 mM imidazole (pH 8.0), 200 mM calcium acetate, and 15% PEG 8,000

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 23, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 79441 / % possible obs: 99.9 % / Redundancy: 5.5 % / R_merge(I) obs: 0.308 / R_pim(I) all: 0.142 / R_rim(I) all: 0.34 / Χ²: 1.068 / Net I/σ(I): 3.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.9-1.93	3.9	1.353	3899	0.46	0.712	1.536	0.451	99.4
1.93-1.97	5.1	1.632	3928	0.524	0.769	1.808	0.47	99.9
1.97-2.01	5.4	1.569	3995	0.48	0.727	1.733	0.486	99.9
2.01-2.05	5.3	1.541	3950	0.419	0.73	1.709	0.486	100
2.05-2.09	5.5	1.263	3990	0.558	0.58	1.394	0.51	100
2.09-2.14	5.7	1.062	3935	0.753	0.47	1.164	0.543	99.9
2.14-2.19	5.7	0.897	3948	0.808	0.399	0.983	0.568	100
2.19-2.25	5.6	0.748	3985	0.823	0.34	0.823	0.61	99.9
2.25-2.32	5.5	0.622	3984	0.888	0.286	0.686	0.657	99.9
2.32-2.39	5.7	0.591	3975	0.902	0.265	0.649	0.659	99.9
2.39-2.48	5.4	0.513	3931	0.876	0.24	0.568	0.704	99.8
2.48-2.58	5.7	0.395	3993	0.94	0.179	0.435	0.775	100
2.58-2.7	5.8	0.345	3971	0.964	0.154	0.378	0.843	99.9
2.7-2.84	5.6	0.278	3964	0.97	0.126	0.306	0.997	99.9
2.84-3.02	5.9	0.247	3982	0.969	0.11	0.27	1.224	99.9
3.02-3.25	5.5	0.201	3971	0.978	0.094	0.222	1.457	99.9
3.25-3.58	5.7	0.153	3998	0.986	0.069	0.169	1.931	100
3.58-4.09	5.7	0.129	3967	0.99	0.059	0.142	2.406	99.8
4.09-5.16	5.3	0.107	4021	0.99	0.051	0.119	2.621	99.9
5.16-50	5.4	0.107	4054	0.991	0.051	0.119	2.642	99.9

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3 Å	48.89 Å
Translation	3 Å	48.89 Å

-
Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHASER	2.7.17	phasing
PHENIX	(1.11.1_2575)	refinement
PDB_EXTRACT	3.24	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→48.894 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.58

	R_factor	Num. reflection	% reflection
R_free	0.2438	3954	4.98 %
R_work	0.2071	-	-
obs	0.2089	79403	99.02 %

Solvent computation

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

Displacement parameters

B_iso max: 88.33 Å² / B_iso mean: 27.8142 Å² / B_iso min: 2.4 Å²

Refinement step

Cycle: final / Resolution: 1.9→48.894 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5872	0	38	833	6743
B_iso mean	-	-	29.55	40.01	-
Num. residues	-	-	-	-	754

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	6121
X-RAY DIFFRACTION	f_angle_d	1.057	8320
X-RAY DIFFRACTION	f_chiral_restr	0.063	911
X-RAY DIFFRACTION	f_plane_restr	0.007	1105
X-RAY DIFFRACTION	f_dihedral_angle_d	2.923	4917

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	C	1030	X-RAY DIFFRACTION	7.527	TORSIONAL
1	2	D	1030	X-RAY DIFFRACTION	7.527	TORSIONAL
2	1	A	2354	X-RAY DIFFRACTION	7.527	TORSIONAL
2	2	B	2354	X-RAY DIFFRACTION	7.527	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 28

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8944-1.9175	0.3069	108	0.2873	2033	2141	76
1.9175-1.9417	0.3541	167	0.2721	2741	2908	100
1.9417-1.9673	0.2928	147	0.2541	2599	2746	100
1.9673-1.9942	0.2895	155	0.2509	2765	2920	100
1.9942-2.0227	0.2952	148	0.2477	2710	2858	100
2.0227-2.0529	0.3037	143	0.2526	2682	2825	100
2.0529-2.085	0.2903	156	0.2412	2722	2878	100
2.085-2.1192	0.2701	130	0.2284	2731	2861	100
2.1192-2.1557	0.2537	140	0.2344	2692	2832	100
2.1557-2.1949	0.2445	142	0.2168	2704	2846	100
2.1949-2.2371	0.2528	144	0.2102	2686	2830	100
2.2371-2.2828	0.254	150	0.2167	2759	2909	100
2.2828-2.3324	0.265	146	0.2169	2681	2827	100
2.3324-2.3867	0.2574	121	0.2197	2765	2886	100
2.3867-2.4464	0.229	127	0.212	2713	2840	100
2.4464-2.5125	0.2669	147	0.2177	2733	2880	100
2.5125-2.5865	0.2549	141	0.2099	2683	2824	100
2.5865-2.6699	0.2498	142	0.2117	2707	2849	100
2.6699-2.7654	0.2672	149	0.2031	2709	2858	100
2.7654-2.8761	0.2233	150	0.2033	2715	2865	100
2.8761-3.0069	0.2367	144	0.203	2743	2887	100
3.0069-3.1654	0.2567	143	0.2003	2691	2834	100
3.1654-3.3637	0.229	142	0.1907	2725	2867	100
3.3637-3.6234	0.2064	134	0.1803	2756	2890	100
3.6234-3.9878	0.2007	124	0.1793	2748	2872	100
3.9878-4.5645	0.2015	118	0.1666	2741	2859	100
4.5645-5.7494	0.2274	139	0.1913	2750	2889	100
5.7494-48.9107	0.2331	157	0.2272	2765	2922	99

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	3.4262	2.5837	-0.3145	8.4552	2.0223	1.0005	0.1719	-0.0825	-0.0313	0.6148	-0.2873	0.0701	-0.2007	-0.1501	0.1241	0.2183	0.0124	-0.0372	0.1617	0.0417	0.1378	1.4056	117.0529	31.8821
2	1.3489	0.0815	-0.532	0.2064	-0.5267	1.5774	0.0355	0.0778	0.3658	-0.5026	-0.112	0.1476	-0.4682	-0.152	-0.1052	0.379	0.0522	0.0242	0.1853	0.0618	0.2007	7.9588	127.4211	22.4798
3	1.9818	0.963	0.0674	5.7589	-0.5432	3.6509	-0.118	-0.1022	-0.1057	0.1026	0.0596	0.2538	0.0844	-0.1682	0.0075	0.2051	0.0248	-0.0097	0.1297	0.0267	0.1727	5.8383	115.3711	35.2075
4	2.8282	-0.7635	0.4871	3.7252	-0.9585	3.2803	0.1385	-0.0212	0.2186	0.1506	-0.1681	-0.2218	-0.0735	0.2348	-0.1077	0.1943	0.0315	-0.0106	0.1241	-0.0026	0.1479	16.4994	120.3564	36.4235
5	2.4581	-1.1839	0.2199	2.5937	-0.1183	2.1817	-0.0498	-0.2197	0.4476	0.4061	0.1665	-0.2174	-0.4486	0.0219	-0.0585	0.3988	0.006	-0.0183	0.1315	-0.0183	0.1838	18.5362	122.7856	41.1222
6	1.3229	0.485	-0.4159	1.3589	-0.3742	2.0255	-0.0088	-0.0317	-0.1445	0.0026	0.0342	0.0521	0.1945	0.0505	0.0119	0.1885	0.0115	0.0033	0.1096	0.0231	0.1256	16.6765	106.8151	31.5405
7	1.5828	0.7914	-0.5674	3.0691	-0.4201	2.5064	-0.2316	0.2464	-0.0271	-0.3887	0.1508	0.0734	0.3395	0.0314	-0.0678	0.241	0.0434	-0.0179	0.1568	0.0228	0.143	8.817	112.8699	17.6052
8	1.011	0.3369	-0.7008	1.3532	-0.9914	2.1471	-0.1058	0.1484	-0.0033	-0.1485	0.0923	0.0555	0.133	-0.0227	-0.0052	0.2532	0.0289	-0.009	0.1478	0.0316	0.11	17.2464	114.0515	15.991
9	0.4033	-0.3376	-0.3357	2.552	-0.4281	0.5917	-0.0116	0.169	0.0559	0.0188	0.0136	-0.2323	0.1997	0.0954	0.0133	0.37	0.0157	0.0133	0.2107	0.0523	0.16	21.8122	119.6125	5.8177
10	1.9992	0.4022	-0.0388	2.2951	0.0493	1.3703	0.108	0.2536	0.2893	0.0722	-0.0113	0.0318	-0.3494	0.2865	-0.0289	0.5242	-0.0258	-0.0138	0.2677	0.0664	0.1817	15.4555	128.8382	15.3551
11	1.2582	-0.3783	0.3828	0.1653	-0.3067	1.039	0.1174	0.0899	-0.2089	-0.3165	-0.0927	-0.0138	0.3052	0.1064	-0.0847	0.3256	0.0322	0.0015	0.1656	-0.0477	0.1476	58.3571	76.9414	21.4472
12	2.0105	-0.6295	-0.585	1.6937	0.0755	2.1855	-0.0152	-0.0561	-0.1152	0.3287	0.0208	0.0027	0.2634	0.0557	-0.0098	0.3036	0.0256	-0.0036	0.1008	-0.0072	0.1192	52.3966	81.8529	35.5639
13	1.23	0.106	0.1294	0.996	0.0464	2.7546	0.0424	0.0347	0.1487	-0.0948	0.0031	-0.0884	-0.2384	0.0618	-0.042	0.1909	0.0058	0.0204	0.0985	-0.0175	0.127	51.1164	94.1655	24.1567
14	0.622	-0.153	0.1292	2.5045	1.7223	2.1424	-0.0209	0.168	-0.0308	-0.0713	-0.0252	0.1637	-0.0759	-0.138	0.0529	0.2964	0.0041	0.0063	0.1816	-0.0384	0.1279	41.3066	81.2658	8.0717
15	2.5895	-0.1822	0.0467	2.3683	1.7879	2.797	-0.0139	0.2468	-0.2936	-0.205	0.2069	-0.1018	0.9649	-0.4595	-0.1769	0.513	-0.0569	0.0019	0.2912	-0.05	0.1747	47.8946	73.1206	13.3951
16	3.1268	1.2191	0.386	1.538	-0.6697	2.6692	0.2953	0.4102	0.3338	-0.5244	0.0805	-0.7896	-0.5322	0.2267	-0.4103	0.2075	-0.007	0.0361	0.2501	0.0778	0.2649	48.3364	116.6357	12.4395
17	9.0793	-4.9105	-0.0462	2.8432	0.8445	4.1293	-0.1555	0.0664	-0.0305	-0.1325	0.2034	-0.1417	0.5291	0.2065	-0.0298	0.2864	-0.0355	0.0569	0.1863	0.0308	0.169	45.2804	115.4963	18.541
18	7.4739	5.0267	-1.6998	8.0063	-2.9078	2.5374	0.3162	-0.9414	1.0939	0.9146	-0.1323	0.1356	-0.0628	1.0593	-0.1801	0.209	0.029	-0.0366	0.3164	-0.0983	0.295	32.4217	119.6916	28.5193
19	2.6415	-0.5798	0.3222	6.3028	-3.6079	5.2234	-0.1528	0.758	0.626	-0.6807	0.081	-0.1764	-0.4309	-0.1045	-0.0732	0.353	-0.0081	0.007	0.3178	0.1069	0.2457	37.1721	119.932	6.9438
20	2.004	0.1454	-0.3614	1.2191	0.4316	2.7411	-0.0324	0.12	-0.0449	-0.3457	0.0654	-0.0897	-0.1857	0.0162	-0.0191	0.2705	0.0334	0.0136	0.1301	-0.0063	0.1152	37.4993	109.5733	15.5621
21	3.8995	-0.796	-2.0943	1.8392	-0.5564	2.8294	-0.0245	0.1072	0.0656	-0.0805	0.0121	-0.105	-0.1334	0.2177	0.0297	0.2646	-0.0157	-0.0187	0.165	0.0065	0.1066	36.044	117.6468	13.5237
22	7.4078	-2.0785	-5.7249	5.5085	2.3142	6.8336	0.2599	0.2783	0.4814	-0.4754	0.162	-0.1393	-0.2408	0.1049	-0.3143	0.2481	-0.0127	-0.0435	0.2008	0.0661	0.207	41.9975	121.3633	11.3326
23	4.1884	-0.6698	2.001	3.1662	-2.7525	6.0647	0.3826	0.3729	-0.3593	-0.4162	0.0136	0.6769	0.6363	-0.2139	-0.4919	0.2194	-0.0291	-0.0037	0.2367	-0.0716	0.2074	15.134	85.1427	14.5555
24	8.3152	2.9904	1.1907	1.5855	1.5031	2.7791	-0.0502	-0.4552	-0.5715	0.0117	-0.0442	0.0333	-0.0053	-0.1013	0.135	0.2013	0.0215	0.0495	0.1632	-0.0065	0.1554	26.5727	84.1051	24.529
25	4.4541	-0.4843	-0.6283	6.8786	3.6851	6.7582	-0.1695	0.8794	-0.6064	-0.5294	0.1917	0.1433	0.144	-0.1414	-0.0685	0.3325	-0.0177	-0.0009	0.3079	-0.0804	0.216	25.4754	81.9424	7.7189
26	2.0876	-0.0176	1.051	1.8959	-0.3425	2.6332	0.0287	0.1196	0.0449	-0.287	0.0566	0.0812	-0.0003	-0.0204	-0.1194	0.2922	0.0383	0.0048	0.1234	-0.0059	0.1278	26.2846	92.2661	16.2716
27	4.702	-1.005	1.7582	1.3917	0.1098	1.2452	0.0293	0.1714	-0.0513	-0.024	-0.0239	0.1103	0.0741	-0.115	0.06	0.3349	-0.0153	0.0004	0.1687	-0.0108	0.1186	27.5236	84.2094	14.1438
28	7.2688	-2.163	5.8252	3.367	-1.8478	4.6805	0.5639	-0.0811	-0.9532	-0.2153	0.0155	-0.0283	0.6365	-0.0927	-0.5094	0.2124	-0.0085	0.0154	0.2164	-0.0582	0.3407	28.0262	76.5425	18.312
29	6.3268	1.7132	-0.2405	3.5922	2.8714	2.7609	0.4277	0.9508	0.2451	-1.5566	0.1578	1.1483	0.4422	-0.2541	-0.4595	0.4718	-0.015	-0.1012	0.4377	0.0187	0.3643	11.7482	87.4573	3.4634

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 17 )	A	5 - 17
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 56 )	A	18 - 56
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 57 through 75 )	A	57 - 75
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 76 through 97 )	A	76 - 97
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 98 through 122 )	A	98 - 122
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 123 through 174 )	A	123 - 174
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 175 through 193 )	A	175 - 193
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 194 through 219 )	A	194 - 219
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 220 through 248 )	A	220 - 248
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 249 through 261 )	A	249 - 261
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 5 through 56 )	B	5 - 56
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 57 through 122 )	B	57 - 122
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 123 through 201 )	B	123 - 201
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 202 through 248 )	B	202 - 248
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 249 through 261 )	B	249 - 261
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 2 through 17 )	C	2 - 17
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 18 through 25 )	C	18 - 25
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 26 through 33 )	C	26 - 33
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 34 through 45 )	C	34 - 45
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 46 through 82 )	C	46 - 82
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 83 through 106 )	C	83 - 106
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 107 through 120 )	C	107 - 120
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 2 through 17 )	D	2 - 17
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 18 through 33 )	D	18 - 33
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 34 through 45 )	D	34 - 45
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 46 through 82 )	D	46 - 82
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 83 through 106 )	D	83 - 106
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 107 through 113 )	D	107 - 113
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 114 through 122 )	D	114 - 122

-
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 / Antibody , 2 types, 4 molecules ABCD

-
Non-polymers , 4 types, 844 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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 / Antibody , 2 types, 4 molecules ABCD

-Non-polymers , 4 types, 844 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-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 / Antibody , 2 types, 4 molecules ABCD

-
Non-polymers , 4 types, 844 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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