PDB-4l6t: GM1 bound form of the ECX AB5 holotoxin

ID or keywords:

Entry

Database: PDB / ID: 4l6t

Title

GM1 bound form of the ECX AB5 holotoxin

Components

ECXA
ECXB

Keywords

HYDROLASE / CHOLERA-LIKE TOXIN / MATRIX METALLOPROTEINASE / BACTERIAL MMP / METZINCIN / AB5 / OB FOLD / TRANSFERASE / TOXIN / PROTEASE / PENTASACHARIDE / GM1 / GANGLIOSIDE / OLIGOSACCHARIDE COMPLEX / TOXILYSIN

Function / homology

Function and homology information

metallopeptidase activity / extracellular region / metal ion binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.859 Å

Authors

Littler, D.R. / Ng, N.M. / Rossjohn, J. / Beddoe, T.

Citation

Journal: Structure / Year: 2013
Title: EcxAB Is a Founding Member of a New Family of Metalloprotease AB5 Toxins with a Hybrid Cholera-like B Subunit.
Authors: Ng, N.M. / Littler, D.R. / Paton, A.W. / Le Nours, J. / Rossjohn, J. / Paton, J.C. / Beddoe, T.

History

Deposition	Jun 12, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2013	Group: Database references
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4l6t.cif.gz	343.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4l6t.ent.gz	281.7 KB	Display	PDB format
PDBx/mmJSON format	4l6t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4l6t_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	4l6t_full_validation.pdf.gz	2.3 MB	Display
Data in XML	4l6t_validation.xml.gz	35.9 KB	Display
Data in CIF	4l6t_validation.cif.gz	52.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l6/4l6t ftp://data.pdbj.org/pub/pdb/validation_reports/l6/4l6t	HTTPS FTP

-
Related structure data

Related structure data	4l63SC 2wv6 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6j0t-d 3nzs-d 3c8d-6 4qfl-d 4eu6-d 4hle-d 3a8e-d 3c87-d 3rcn-1 2ycw-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	#69 - Sep 2005 Cholera Toxin similarity (3) #28 - Apr 2002 Anthrax Toxin similarity (1) #237 - Sep 2019 Nanodiscs and HDL similarity (1) #44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: ECXA

B: ECXB

C: ECXB

D: ECXB

E: ECXB

F: ECXB

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	120.441, 120.441, 273.479
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein

ECXA

Mass: 29492.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: 176 / Gene: ecxA / Plasmid: pBAD / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8GAV4, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

#2: Protein

ECXB

Mass: 12775.468 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: 176 / Gene: ecxB / Plasmid: pBAD / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GAV3

#3: Polysaccharide

beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...

Type: oligosaccharide / Mass: 998.885 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5NCC/3=O][a2112h-1b_1-5_2NCC/3=O]/1-2-3-4-2/a4-b1_b3-c2_b4-d1_d3-e1	WURCS	PDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}}	LINUCS	PDB-CARE

#4: Chemical

ChemComp-ZN / ZINC ION

Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 561 / 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: 59.89 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.8 M NaH2PO4, 0.8 M KH2PO4, 0.1 M Na Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953699 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2011 / Details: MONOCHROMATOR
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.953699 Å / Relative weight: 1
Reflection	Resolution: 1.8→34.3 Å / Num. obs: 107527 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / R_merge(I) obs: 0.043
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.388 / Mean I/σ(I) obs: 2 / Num. unique all: 15448 / % possible all: 99.5

-
Processing

Software

Name	Version	Classification
DNA		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4L63

4l63

Resolution: 1.859→29.818 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1984	4923	4.99 %	RANDOM
R_work	0.1781	-	-	-
obs	0.1791	98562	99.65 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.859→29.818 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6057	0	341	561	6959

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6601
X-RAY DIFFRACTION	f_angle_d	1.103	8982
X-RAY DIFFRACTION	f_dihedral_angle_d	20.898	2581
X-RAY DIFFRACTION	f_chiral_restr	0.049	1094
X-RAY DIFFRACTION	f_plane_restr	0.006	1108

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8586-1.8797	0.3694	177	0.3072	2991	X-RAY DIFFRACTION	97
1.8797-1.9018	0.301	165	0.2738	3030	X-RAY DIFFRACTION	99
1.9018-1.925	0.2615	144	0.2212	3067	X-RAY DIFFRACTION	100
1.925-1.9494	0.2399	179	0.2111	3075	X-RAY DIFFRACTION	100
1.9494-1.975	0.2357	146	0.1849	3112	X-RAY DIFFRACTION	100
1.975-2.0021	0.1871	161	0.1765	3062	X-RAY DIFFRACTION	100
2.0021-2.0307	0.2063	168	0.1814	3061	X-RAY DIFFRACTION	100
2.0307-2.061	0.2075	156	0.1794	3115	X-RAY DIFFRACTION	100
2.061-2.0932	0.2188	159	0.1758	3073	X-RAY DIFFRACTION	100
2.0932-2.1275	0.2094	178	0.1751	3071	X-RAY DIFFRACTION	100
2.1275-2.1641	0.1943	164	0.1758	3095	X-RAY DIFFRACTION	100
2.1641-2.2035	0.2271	155	0.1755	3088	X-RAY DIFFRACTION	100
2.2035-2.2458	0.2011	154	0.1799	3111	X-RAY DIFFRACTION	100
2.2458-2.2917	0.1963	146	0.1796	3111	X-RAY DIFFRACTION	100
2.2917-2.3415	0.22	154	0.1835	3070	X-RAY DIFFRACTION	99
2.3415-2.3959	0.2231	166	0.1784	3105	X-RAY DIFFRACTION	100
2.3959-2.4558	0.201	181	0.1753	3092	X-RAY DIFFRACTION	99
2.4558-2.5222	0.1926	156	0.1877	3077	X-RAY DIFFRACTION	99
2.5222-2.5964	0.2107	168	0.187	3091	X-RAY DIFFRACTION	99
2.5964-2.6801	0.2274	168	0.1869	3124	X-RAY DIFFRACTION	100
2.6801-2.7758	0.2205	161	0.1856	3121	X-RAY DIFFRACTION	100
2.7758-2.8869	0.2049	164	0.1872	3118	X-RAY DIFFRACTION	100
2.8869-3.0182	0.2275	160	0.1862	3174	X-RAY DIFFRACTION	100
3.0182-3.1771	0.2041	172	0.1881	3139	X-RAY DIFFRACTION	100
3.1771-3.3759	0.1765	151	0.1723	3168	X-RAY DIFFRACTION	100
3.3759-3.6362	0.1841	165	0.1629	3174	X-RAY DIFFRACTION	100
3.6362-4.0013	0.1598	187	0.1548	3180	X-RAY DIFFRACTION	100
4.0013-4.5785	0.1445	164	0.1449	3204	X-RAY DIFFRACTION	100
4.5785-5.7616	0.1728	159	0.159	3287	X-RAY DIFFRACTION	100
5.7616-29.8213	0.2053	195	0.1988	3453	X-RAY DIFFRACTION	100

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	1.0137	-0.5504	0.0825	4.8696	0.6985	2.322	0.4038	0.5402	-0.5785	-0.1214	0.0289	0.2802	1.1689	0.3454	-0.151	0.6967	0.2758	-0.2646	0.4685	-0.1762	0.4829	19.8911	22.6924	5.1001
2	2.614	2.0222	-1.6984	3.7126	-2.8398	2.238	-0.2936	-0.1435	-0.768	-0.0439	0.3586	1.0342	1.1551	-0.2634	-0.0636	1.1508	-0.013	-0.2077	0.8058	0.3673	1.2151	7.7041	4.7082	24.5551
3	2.8891	-0.0106	2.2863	2.7306	-0.7684	2.3815	0.5045	-0.6265	-1.1946	0.0692	0.3367	0.8842	1.4065	-0.3835	-0.6408	1.0586	0.0235	-0.2067	0.542	0.1596	1.0561	13.9851	12.015	16.7269
4	4.3658	1.4753	1.4784	3.5943	0.0426	2.6174	0.5289	-1.2549	-1.5918	0.5191	0.2116	1.5862	0.8247	-0.8239	-0.458	0.8186	-0.0556	0.0076	0.7723	0.4376	1.22	6.2833	17.2656	20.9418
5	3.0687	-1.8326	3.098	5.531	-2.8425	3.5738	0.2709	-0.3025	-0.4554	0.4394	0.2334	0.4779	0.4551	-0.0897	-0.4011	0.437	0.1248	-0.0556	0.3511	-0.0275	0.3617	16.8986	28.4023	12.911
6	6.177	-1.8432	-0.3689	6.6507	0.3035	6.1729	0.3004	-0.2254	-0.967	0.065	0.2647	1.5087	0.8491	-0.6246	-0.2059	0.4358	-0.0074	-0.1323	0.3867	0.1033	0.7506	8.5123	24.6417	7.9482
7	3.5483	-2.3938	-0.6092	7.6002	-0.2563	5.0646	-0.135	0.3301	0.0134	0.1486	0.1969	-0.7496	0.3622	0.5113	0.0024	0.2031	0.0243	-0.064	0.3939	-0.0913	0.3005	18.0623	36.4391	-3.6962
8	1.9547	0.0895	0.2221	1.0465	-0.1668	1.4202	-0.0751	0.4065	-0.1255	-0.1474	0.1092	0.1613	0.1294	-0.1664	-0.0377	0.1833	-0.0815	-0.0463	0.3587	-0.0527	0.1728	-1.6	45.0166	-21.0805
9	6.4496	-4.677	2.2208	5.0063	-2.8187	2.4161	-0.0739	0.3455	0.2056	-0.1059	0.0277	0.0329	-0.0326	0.0957	0.0918	0.092	-0.0554	-0.0213	0.2983	-0.0592	0.1063	5.3093	49.4584	-14.7189
10	3.8158	-1.2885	2.0323	2.6407	0.8299	3.2144	-0.2197	0.3241	-0.4704	-0.0844	0.295	0.2551	0.1959	-0.4667	-0.2501	0.0856	-0.1039	-0.0289	0.3174	-0.0596	0.1887	-3.8384	41.6874	-17.4686
11	3.0549	-3.9307	1.5066	6.4993	0.5396	5.4797	-0.0017	-0.0663	0.5163	-0.0549	0.2899	-0.5781	-0.3778	0.6893	-0.0858	0.1103	-0.0348	-0.0254	0.2796	-0.0822	0.2383	30.7786	63.6581	11.4059
12	3.5531	-0.0304	-0.6403	7.7539	-5.5906	8.0448	-0.0469	-0.1808	0.3252	0.5764	0.1747	-0.0247	-0.2352	0.1305	-0.1168	0.1086	0.0178	-0.0494	0.1739	-0.076	0.1243	21.132	65.3108	17.293
13	5.8093	2.6821	5.9829	7.7161	2.6748	6.4868	0.3375	-0.4042	-0.5338	0.4366	-0.0428	-0.2527	0.315	0.0764	-0.2518	0.1588	0.0296	-0.0253	0.1963	-0.0124	0.0953	14.6811	48.6551	16.5148
14	0.9291	0.543	0.0496	0.8387	0.1301	0.5991	-0.0744	0.055	0.148	0.0287	0.0353	0.1422	-0.0789	-0.071	0.0221	0.0793	0.0351	-0.0244	0.1528	-0.034	0.1357	6.9858	61.1596	9.6863
15	4.2256	4.7606	-0.7996	8.631	-1.1526	0.7775	-0.1335	0.2026	0.1586	-0.1414	0.0942	0.0022	-0.041	0.0008	0.0216	0.0646	0.029	-0.0273	0.2261	-0.0567	0.1227	13.4012	57.773	1.927
16	1.6856	1.9432	0.5901	2.2517	0.713	3.0832	0.0503	-0.0453	-0.0061	0.2031	-0.0004	-0.2844	0.0983	0.0548	-0.0037	0.0663	0.0055	-0.0409	0.165	-0.0336	0.1166	18.0795	57.6831	13.3509
17	3.2198	-0.9526	-4.1875	2.4873	-0.0528	6.2062	0.0896	0.9815	-0.2155	-0.3034	-0.1441	0.1792	0.035	-0.2257	0.1034	0.3423	-0.1297	-0.0012	0.7379	-0.2112	0.1811	10.9799	41.7718	-32.9035
18	0.5426	-0.3918	0.1375	0.6751	0.2426	3.0585	-0.0375	0.4673	-0.0773	-0.1941	-0.0419	-0.0558	0.1265	0.2242	-0.1958	0.3383	-0.1125	0.0379	0.8002	-0.2338	0.0656	21.8224	42.2396	-32.9064
19	6.1792	5.5872	3.1472	5.1133	3.354	5.683	0.3667	0.3465	-0.7319	0.0718	-0.0176	-0.6609	0.8973	0.1835	-0.4272	0.2716	0.0152	0.0205	0.3757	-0.2024	0.3388	23.73	33.1171	-17.8586
20	2.3406	0.5819	0.608	0.7554	-0.2995	1.3014	-0.1344	0.6125	-0.1537	-0.263	0.1148	-0.2843	0.0005	0.2231	0.0131	0.1089	-0.039	0.0643	0.4381	-0.0811	0.1774	27.9807	49.6693	-19.4598
21	2.65	-1.3655	2.7868	4.6148	-4.9054	7.8115	-0.1422	0.3446	0.0435	-0.155	0.0722	-0.0854	-0.133	0.0462	0.0612	0.0883	-0.0394	0.0002	0.3478	-0.0918	0.1699	17.8955	49.7236	-16.1075
22	4.7755	-1.2663	4.758	0.5283	-1.3353	4.7691	0.0224	0.2633	-0.5744	-0.1001	0.0302	0.1815	0.4982	-0.0765	-0.0378	0.2749	-0.0278	-0.0075	0.3992	-0.1674	0.2972	19.1334	34.2989	-16.1828
23	3.7563	-1.4281	-1.6614	0.615	0.347	7.1689	-0.1076	0.7156	-0.3233	-0.3259	0.2154	-0.2101	0.3291	0.1298	0.1401	0.1615	-0.0333	0.0209	0.5055	-0.182	0.1363	21.2066	42.0369	-25.6403
24	4.6112	-2.9549	0.0932	3.9022	-2.8658	4.0618	-0.1553	-0.3967	0.5084	0.2309	0.0706	0.166	-0.3407	-0.1251	0.088	0.0975	0.0433	0.0047	0.2462	-0.0679	0.1839	-6.2684	60.5839	11.9047
25	7.6582	0.6875	-1.1188	5.551	3.9457	4.1309	0.1458	-0.595	-0.4827	0.4322	-0.2549	0.1815	0.3437	-0.3557	0.1208	0.1088	-0.036	0.0297	0.1999	0.0101	0.2607	-5.1371	41.792	5.4852
26	1.1254	0.1856	0.1934	0.5549	0.2652	0.5102	-0.0997	0.1073	0.0928	-0.085	0.0798	0.1533	-0.047	-0.0783	0.0228	0.0772	-0.0088	-0.0334	0.2497	0.0133	0.1805	-7.3736	52.8329	-6.6476
27	1.4561	-1.5396	0.6084	5.5908	0.8051	1.0085	-0.0235	0.1803	0.0842	-0.1137	0.0144	-0.0867	-0.0545	0.0749	0.0413	0.0511	-0.0154	-0.0177	0.2434	-0.0234	0.1204	2.5477	54.454	-3.4986
28	9.7471	-5.2277	-5.354	2.8422	2.8524	2.9521	-0.1276	-0.3913	-0.4587	0.2244	0.227	0.1897	0.761	0.3144	-0.1316	0.1633	0.0392	-0.0236	0.2282	-0.0193	0.1822	-0.7187	43.9599	7.5607
29	4.8904	-1.6655	0.6004	6.4349	0.2581	1.8166	-0.2452	-0.1598	0.0673	0.2717	0.1377	0.0335	-0.0098	-0.2363	-0.0299	0.0495	-0.0108	0.0118	0.1998	-0.0262	0.1007	-6.6447	54.2005	5.3638
30	6.8264	3.6285	2.3279	3.3129	2.137	2.3126	-0.3402	0.7868	-0.1846	-0.4155	0.2525	-0.3291	-0.1873	0.2897	0.0594	0.1863	-0.0338	0.0467	0.4916	-0.0626	0.2669	38.5759	50.7826	-17.6896
31	2.769	-1.7571	1.9771	3.4559	-1.0233	2.2192	-0.1656	0.2999	0.1087	0.0634	0.1263	-0.2778	-0.1617	0.1402	0.046	0.0708	-0.027	0.0098	0.3081	-0.0382	0.1652	41.6479	55.0807	-7.9292
32	4.7255	-4.9868	-4.3266	5.3718	4.6725	4.0626	-0.23	-0.1428	-0.6736	0.1205	0.1266	-0.1452	0.5159	0.5816	0.1319	0.1318	0.0458	-0.0094	0.2724	-0.0505	0.2741	32.8754	43.5437	2.4217
33	1.6434	0.9463	-0.3339	1.0557	0.389	1.0948	-0.0136	0.2075	-0.024	0.0813	0.0973	-0.3045	-0.0292	0.1469	-0.0235	0.0511	0.0102	-0.0495	0.2268	-0.0525	0.1835	28.7274	59.4197	1.6032
34	2.9313	2.7022	-2.5215	3.3492	-2.333	3.0215	-0.0961	0.3901	0.1412	-0.113	0.1036	0.0487	0.0161	-0.1054	-0.0855	0.057	-0.0047	-0.019	0.2818	-0.0522	0.1563	22.8764	54.8971	-5.8901
35	5.0301	4.6466	-0.7948	8.8992	-4.2802	4.0212	-0.4094	0.3487	-1.0747	0.0493	0.0596	-0.1955	0.4234	-0.0356	0.3353	0.137	-0.0345	0.0547	0.3117	-0.0875	0.2229	29.9265	41.8424	-1.7871
36	1.0541	-0.0425	0.0226	8.9763	-1.1181	0.7697	0.1324	0.5109	-0.0202	-0.1301	-0.2496	-0.0902	0.017	0.035	0.121	0.0716	-0.0089	0.0123	0.305	-0.0307	0.1872	37.0322	53.4525	-6.6902
37	5.6744	1.7176	-3.3075	2.4587	-1.7192	6.2652	-0.0365	-0.5943	-0.2017	0.0898	-0.2673	-0.0252	-0.2155	0.4464	0.3094	0.0593	-0.0074	-0.0386	0.2834	-0.0494	0.1973	38.6952	61.3082	-0.5932
38	4.9871	4.6842	-0.3305	4.416	-0.1371	3.5151	-0.1678	0.2538	-0.7613	-0.2419	0.1086	-0.6046	0.3214	0.0882	-0.0602	0.0911	-0.0134	0.025	0.2908	-0.0696	0.2815	32.2378	46.1944	-7.8153

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 21 through 54 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 55 through 78 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 79 through 156 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 157 through 184 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 185 through 234 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 235 through 258 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 259 through 278 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 22 through 80 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 81 through 100 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 101 through 126 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 22 through 33 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 34 through 41 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 42 through 47 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 48 through 80 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 81 through 100 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 101 through 126 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 22 through 33 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 34 through 41 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 42 through 47 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 48 through 80 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 81 through 100 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 101 through 105 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 106 through 126 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 22 through 41 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 42 through 47 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 48 through 80 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 81 through 100 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 101 through 105 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 106 through 126 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 22 through 33 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 34 through 41 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 42 through 47 )
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 48 through 80 )
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 81 through 100 )
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 101 through 105 )
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 106 through 110 )
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 111 through 116 )
38	X-RAY DIFFRACTION	38	chain 'E' and (resid 117 through 126 )

-
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