PDB-4lin: Exploring the atomic structure and conformational flexibility of ...

ID or keywords:

Entry

Database: PDB / ID: 4lin

Title

Exploring the atomic structure and conformational flexibility of a 320 angstrom long engineered viral fiber using X-ray crystallography

Components

Tail needle protein gp26

Keywords

VIRAL PROTEIN / helical / trimeric coiled-coil / viral fiber / in-frame extension / elongated coiled coil protein / protein engineering / bacteriophage P22 / tail needle gp26 / α / -helical coiled coil / engineered protein fiber / engineered viral protein

Function / homology

Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / symbiont genome entry into host cell via pore formation in plasma membrane / Up-down Bundle / Mainly Alpha / Tail needle protein gp26

Function and homology information

Biological species

Bacteriophage P22 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Bhardwaj, A. / Cingolani, G.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Exploring the atomic structure and conformational flexibility of a 320 angstrom long engineered viral fiber using X-ray crystallography.
Authors: Bhardwaj, A. / Casjens, S.R. / Cingolani, G.

History

Deposition	Jul 2, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 12, 2014	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4lin.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb4lin.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	4lin.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/li/4lin ftp://data.pdbj.org/pub/pdb/validation_reports/li/4lin	HTTPS FTP

-
Related structure data

Related structure data	3c9i
Similar structure data	6rib-1 6rib-2 6l5j-2 6l5j-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) 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

3c9i

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Tail needle protein gp26

B: Tail needle protein gp26

C: Tail needle protein gp26

D: Tail needle protein gp26

E: Tail needle protein gp26

F: Tail needle protein gp26

G: Tail needle protein gp26

H: Tail needle protein gp26

I: Tail needle protein gp26

J: Tail needle protein gp26

K: Tail needle protein gp26

L: Tail needle protein gp26

hetero molecules

381 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tail needle protein gp26

B: Tail needle protein gp26

C: Tail needle protein gp26

hetero molecules

defined by author&software
95.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Tail needle protein gp26

E: Tail needle protein gp26

F: Tail needle protein gp26

hetero molecules

defined by author&software
95.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Tail needle protein gp26

H: Tail needle protein gp26

I: Tail needle protein gp26

hetero molecules

defined by author&software
95.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: Tail needle protein gp26

K: Tail needle protein gp26

L: Tail needle protein gp26

hetero molecules

defined by author&software
95.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	38.689, 147.929, 151.011
Angle α, β, γ (deg.)	87.94, 90.05, 89.95
Int Tables number	1
Space group name H-M	P1

#1: Protein	Tail needle protein gp26 Mass: 31744.014 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: gp26-2M, engineered in-frame extension of gp26 / Source: (gene. exp.) Bacteriophage P22 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P35837*PLUS
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 764 / 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: 2.27 Å³/Da / Density % sol: 45.75 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% (w/v) Polyethylene glycol 8000, 0.1M dibasic potassium phosphate, 0.1M sodium citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	CHESS	F1	1	0.92
SYNCHROTRON	NSLS	X6A	2	0.92

Detector

Type	ID	Detector	Date
ADSC QUANTUM 270	1	CCD	Dec 3, 2008
DSC Quantum 270	2	CCD

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Rh coated Si	SINGLE WAVELENGTH	M	x-ray	1
2				x-ray	1

Radiation wavelength

Wavelength: 0.92 Å / Relative weight: 1

Reflection twin

Type: merohedral / Operator: h,-k,-l / Fraction: 0.48

Reflection

Resolution: 2.7→30 Å / Num. obs: 84119 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

-
Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASES		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→14.99 Å / σ(F): 0.6 / Phase error: 34.66 / Stereochemistry target values: TWIN_LSQ_F
Details: TWINNING INFORMATION. FRACTION: 0.480 OPERATOR: h,-k,-l

	R_factor	Num. reflection	% reflection
R_free	0.2682	2136	2.55 %
R_work	0.2288	-	-
obs	0.2318	83626	91.53 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.7→14.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25776	0	12	764	26552

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	25992
X-RAY DIFFRACTION	f_angle_d	0.991	35400
X-RAY DIFFRACTION	f_dihedral_angle_d	18.041	9324
X-RAY DIFFRACTION	f_chiral_restr	0.07	4428
X-RAY DIFFRACTION	f_plane_restr	0.003	4668

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 (%)
2.7042-2.7711	0.4205	115	0.3307	4828	X-RAY DIFFRACTION	73
2.7711-2.8452	0.3096	132	0.2983	5276	X-RAY DIFFRACTION	83
2.8452-2.928	0.327	132	0.2857	5765	X-RAY DIFFRACTION	88
2.928-3.0212	0.3403	157	0.2775	5909	X-RAY DIFFRACTION	91
3.0212-3.1276	0.3104	151	0.271	6000	X-RAY DIFFRACTION	94
3.1276-3.2508	0.3129	144	0.2748	6153	X-RAY DIFFRACTION	94
3.2508-3.3961	0.2908	157	0.2539	6066	X-RAY DIFFRACTION	94
3.3961-3.5713	0.3177	145	0.2426	6012	X-RAY DIFFRACTION	93
3.5713-3.7894	0.3125	131	0.2612	5255	X-RAY DIFFRACTION	81
3.7894-4.0729	0.2338	142	0.2063	5938	X-RAY DIFFRACTION	92
4.0729-4.4664	0.1942	148	0.1822	6084	X-RAY DIFFRACTION	94
4.4664-5.0758	0.2232	138	0.1778	6065	X-RAY DIFFRACTION	94
5.0758-6.2633	0.2481	151	0.2312	6075	X-RAY DIFFRACTION	94
6.2633-12.6584	0.233	159	0.1986	5799	X-RAY DIFFRACTION	89

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	0.3458	1.0402	-0.4894	3.3575	-2.0735	1.376	-0.2057	0.1199	0.0952	1.0456	0.7491	0.4283	-0.6073	-0.8547	-0.503	0.6301	0.1829	0.1719	0.568	-0.0227	0.4835	-4.7804	225.1011	-133.8769
2	4.0865	-0.6412	1.6693	3.7976	-1.2373	3.8505	-0.4336	0.4171	0.1227	0.0605	0.2116	-0.2186	0.5926	0.8709	0.1952	0.6477	0.0868	0.1369	0.4618	0.0238	0.251	4.3526	168.1591	-104.0026
3	1.5007	-1.9201	0.1546	3.6574	-2.4498	4.7741	0.5885	0.3441	-0.4484	-0.1434	0.6461	0.864	0.1781	-0.2967	-0.8088	0.6348	0.0817	-0.0824	0.3553	0.0957	0.5269	-2.7066	129.968	-86.0728
4	1.3922	0.1631	0.628	3.2165	-0.419	1.9795	0.2069	-0.1806	0.4294	0.2956	-0.1477	0.1938	-0.1162	-0.3067	-0.0888	0.6856	0.0798	0.272	0.3135	-0.0499	0.4531	-1.587	92.9228	-56.1027
5	2.5617	-0.8282	1.6593	5.0185	-1.6053	1.3232	0.0262	0.0957	0.1428	-0.6759	0.7766	-0.076	-0.2196	0.6377	-0.2202	0.7249	0.0284	0.3347	0.2907	0.2091	0.4441	5.5448	55.8906	-42.9095
6	1.9019	0.4236	-0.3278	2.8191	-1.3888	2.6919	0.0256	0.1362	0.2267	-0.431	0.0983	-0.1618	-0.0451	-0.0049	-0.088	0.309	0.041	0.0422	0.267	0.0292	0.2037	2.4389	12.937	-24.9135
7	3.4251	-3.4858	0.7128	9.5777	-4.1512	2.848	-0.3102	-0.1218	0.6784	0.3107	0.186	-0.953	0.0059	-0.3694	0.1395	0.3327	0.0836	0.0107	0.3538	-0.0258	0.2602	7.1101	0.2848	-15.6619
8	0.5598	0.8336	-0.4374	4.5645	-3.1528	2.0631	-0.2805	0.24	0.0803	0.436	0.6748	0.2782	-0.2306	-0.5268	-0.3983	0.6069	0.1053	0.0302	0.4336	0.0111	0.3364	-2.7117	214.746	-134.8312
9	-0.0031	0.1918	-0.3538	8.0211	-3.2758	1.5163	-0.0774	-0.1251	-0.0083	-0.4861	-0.062	-0.1613	0.2559	0.0816	0.1412	0.4809	0.0388	0.0549	0.3261	0.079	0.5177	0.0223	104.6169	-67.6371
10	1.1109	0.8984	-0.334	4.2189	-2.3578	3.1971	-0.0101	0.1372	0.2758	0.1473	0.1287	0.1564	-0.0338	-0.2152	-0.0416	0.2147	-0.0099	-0.0128	0.2376	0.0109	0.3687	-0.1708	8.533	-19.3302
11	0.9854	-0.346	-0.4718	2.387	-2.0101	2.2891	0.052	-0.2021	0.1289	-0.15	-0.5092	-1.6114	-0.1612	0.3189	0.267	0.4575	0.0908	0.0306	0.4951	0.0764	0.7131	2.9871	235.4608	-139.7995
12	-0.1793	-0.489	0.0045	7.2286	-4.3725	2.8259	0.033	0.0754	-0.0725	0.5717	-0.0696	0.1482	-0.3621	0.0813	0.109	0.4408	-0.0836	0.078	0.427	0.1781	0.8914	0.0304	130.9992	-84.1074
13	0.9637	-0.3405	0.3907	5.9683	-1.5102	0.5041	0.0289	0.114	0.2774	0.1087	0.1193	0.1274	-0.1435	-0.1206	-0.1812	0.3725	0.0423	0.0729	0.2269	-0.0395	0.3426	-0.1876	8.7292	-24.3472
14	0.0563	0.015	-0.035	-0.0183	-0.0296	0.0445	0.0333	-0.0317	0.1901	-0.688	0.6485	1.0975	0.5101	-0.3929	-0.6628	1.0693	-0.1521	0.0647	0.3721	0.2099	0.99	16.0615	-47.4751	-49.0122
15	1.3936	2.3944	-0.879	7.0582	-1.5169	1.2681	-0.1325	-0.1312	-0.0749	-1.0381	0.6287	0.5391	0.6772	-0.129	-0.3289	0.7018	0.0082	-0.1119	0.3236	0.1671	0.658	22.4777	66.2743	-115.2102
16	1.8002	0.9682	-0.1699	3.8494	-1.8967	2.1335	-0.0627	0.0363	-0.1749	0.2238	0.2192	-0.1112	-0.0341	-0.0662	-0.0298	0.4507	0.0485	0.1272	0.2871	-0.0704	0.2293	21.8674	119.3167	-134.8325
17	1.8797	0.5908	-0.253	7.1611	-2.451	1.6752	-0.019	-0.0826	0.0991	0.1699	0.3098	-0.7565	-0.0224	-0.1295	-0.2131	0.2142	-0.0044	-0.0173	0.2469	-0.0033	0.2019	25.8972	142.3271	-146.2113
18	7.3787	0.5717	3.0983	6.1479	3.6633	3.215	0.5708	-0.8304	-0.6697	0.8495	0.3322	0.5345	-0.1012	-0.802	-0.9638	0.5716	0.0872	0.0603	0.6486	-0.0036	0.4322	7.8153	-79.6358	-23.2799
19	2.157	-0.6059	2.757	0.7347	-1.2839	5.5599	0.1035	0.0732	0.4079	0.1115	0.7022	0.0891	-0.2239	-0.2698	-0.7769	0.972	-0.3523	-0.0263	0.5784	0.1615	0.874	20.2015	-103.2143	-3.9697
20	0.6773	-0.7169	0.8771	6.7771	-3.8544	2.3968	-0.5119	-0.0896	0.2623	0.486	0.494	-0.1232	-0.0228	-0.6749	0.0021	0.74	0.0313	0.1412	0.4012	0.0459	0.3778	16.4051	-68.7433	-34.3615
21	0.949	-0.5868	0.3269	5.192	-2.268	1.5024	-0.0445	0.0467	0.3225	-0.3617	0.5833	-0.2529	0.2265	-0.6063	-0.4633	0.621	-0.0377	0.1755	0.402	0.1352	0.7918	21.6917	9.5798	-80.4967
22	0.2321	0.0823	0.0338	3.5686	-2.6083	1.8908	-0.1762	-0.0355	-0.3306	-0.7297	0.5296	0.5097	0.5676	-0.3645	-0.356	0.6665	-0.0159	-0.1666	0.2353	0.001	0.7544	17.9094	84.2429	-121.0653
23	2.3931	-1.7373	0.3861	1.496	-1.0759	2.87	-0.1298	-0.6104	0.1705	-0.2794	-0.2536	-0.3056	0.6073	0.0176	0.323	0.4643	-0.108	0.0051	0.2085	-0.0302	0.6648	17.3291	126.3391	-130.9843
24	2.8571	1.6516	-0.674	1.4353	-0.2773	1.0217	-0.0449	-0.1129	-0.6713	-0.4158	-0.1921	-0.0835	0.1859	-0.1505	-0.0132	0.1582	0.0561	-0.0725	0.5866	-0.1357	0.5536	22.769	145.8961	-155.3151
25	0.2606	0.3071	-0.3096	2.0363	-0.4735	0.3759	-0.2869	0.221	-0.2091	0.1195	0.3314	0.0919	0.3013	-0.3522	-0.0644	0.3681	-0.0126	-0.0814	0.2775	-0.0687	0.3475	15.8222	134.2636	-145.2026
26	0.943	0.0853	0.8368	3.8431	-0.439	0.816	0.0704	0.2464	-0.3906	-0.3973	-0.1434	-0.8623	0.1859	0.0845	0.0522	1.0715	0.1904	0.3147	0.4161	0.2327	1.2725	22.6509	-102.8754	-18.8253
27	5.0064	1.8164	-2.134	4.0197	1.6301	2.6282	0.505	1.4807	0.3819	-0.505	0.0974	0.6965	-0.6834	-0.5653	-0.4771	0.2799	0.099	0.0429	0.6088	0.2612	0.7455	18.3518	-103.0185	-22.4552
28	-0.0123	0.2068	-0.204	2.7653	-2.5822	2.1048	-0.1124	-0.0065	-0.0485	-0.5605	0.1055	-0.0311	0.412	-0.1077	-0.1846	0.6714	-0.0401	0.0772	0.3545	0.0349	0.4528	19.3244	0.0775	-73.8379
29	1.4864	-0.8051	-0.2203	2.0003	-0.9175	1.2786	-0.0334	-0.3139	0.0229	0.0705	0.0782	0.1344	0.0177	-0.1975	-0.0272	0.3143	-0.0958	-0.0838	0.2441	-0.0946	0.2943	19.7005	131.3668	-138.2533
30	0.1011	0.3705	-0.3863	1.644	-1.3588	1.8285	-0.5648	0.1838	-0.2402	-0.2302	0.0503	-0.7609	0.6538	0.1705	0.073	0.6344	-0.0458	0.0609	0.2477	-0.0093	1.5345	25.5027	-171.0754	56.0823
31	9.4297	-1.785	1.2895	3.0175	4.1165	7.2707	0.6288	0.7785	-0.4551	-0.6111	0.5183	-0.1697	0.8314	-0.1022	-0.9274	0.8593	-0.0787	0.2604	0.2566	0.0105	0.9647	15.7859	-179.7943	56.872
32	1.0608	1.4591	-1.213	3.3367	-2.2078	1.5641	-0.1424	0.0694	-0.1287	-0.0512	0.0755	-0.9699	-0.2489	-0.1593	0.1155	0.7679	0.0453	0.0985	0.3037	-0.012	0.3715	22.0891	-137.6357	39.8627
33	-0.047	-0.2223	0.1829	5.4642	-3.5693	2.3274	-0.0638	-0.0108	-0.0647	-0.8342	0.3156	0.1687	0.5884	-0.2716	0.0733	0.5862	0.1068	0.1552	0.3404	0.0045	0.4408	17.3137	-55.617	-10.2314
34	1.4205	-1.0131	0.5486	2.7562	0.4183	1.7512	-0.0244	0.1342	0.2784	0.1257	0.1626	0.2212	-0.3048	-0.3927	-0.1575	0.4817	0.0058	-0.0454	0.3145	0.1018	0.4824	17.1425	25.5941	-46.2045
35	0.6103	0.8102	0.2351	4.9194	0.8978	1.5271	0.0492	-0.1101	0.0126	-0.7272	-0.1773	-0.5146	-0.3043	0.212	0.1089	0.8189	0.1841	0.4524	0.1811	-0.047	0.9595	23.5841	51.8433	-64.2569
36	0.0493	0.4562	-0.3968	5.9201	-5.0809	4.3819	-0.4537	0.0769	-0.0471	-0.502	0.1375	-0.496	0.1073	-0.2487	0.2104	1.1577	0.037	0.4801	0.3763	0.0496	0.8919	10.6922	82.7849	-69.2494
37	0.2599	0.0263	0.0087	0.4738	-0.8022	1.3276	0.0708	-0.2666	0.0958	0.1761	-0.1173	-0.3717	-0.0244	-0.2274	0.0683	0.4985	-0.0916	0.0344	0.277	0.2267	1.1255	21.0402	69.9574	-63.3117
38	2.249	1.3606	-1.7247	2.7194	-1.7045	3.1805	-0.2584	0.2329	-0.5371	-0.3423	0.2345	-0.2643	1.0108	-0.0095	0.3101	0.6076	-0.0655	-0.0061	0.2057	-0.1496	0.7129	12.2985	-171.7647	55.3574
39	5.7968	0.3851	-0.1147	5.47	-4.4695	8.9477	-0.8924	0.1263	-0.8369	0.4953	0.3395	-0.0405	-0.2141	-0.306	0.4914	0.6442	0.0943	0.1299	0.365	-0.0399	0.3261	13.922	-170.3473	66.3615
40	4.2183	-3.6285	1.233	4.1653	-0.033	1.3842	0.0711	-0.707	0.2683	0.015	0.8135	0.4556	1.1593	-0.5424	-0.8769	0.7597	-0.1774	-0.009	0.3185	0.032	0.6969	13.9552	-149.8164	41.0114
41	0.6384	0.208	0.4281	8.191	-4.7638	3.2204	-0.2804	0.2998	0.1372	0.2987	-0.176	-0.49	-0.1693	0.3963	0.3542	0.541	-0.0109	0.0311	0.3675	0.1157	0.3895	21.406	-104.3156	17.5692
42	0.9414	0.9158	0.0402	5.9355	-4.8529	4.9689	-0.0139	0.0645	-0.0831	0.5489	0.0709	0.7199	-0.2554	-0.6507	-0.4558	0.4832	-0.1923	0.2062	0.2629	0.0117	0.7845	12.4043	-49.0406	-9.6343
43	3.2533	-0.3182	-0.3324	1.0782	-2.284	5.1565	0.0912	0.3911	-0.6822	-0.7529	0.1693	0.031	0.4936	-0.4293	-0.0606	0.5553	-0.0389	0.022	0.2515	-0.2697	0.2563	15.5084	-19.1667	-34.7697
44	2.2545	2.7402	-0.5839	3.5878	-1.5534	3.1219	0.4443	0.9062	0.7314	-0.0463	0.0465	-1.3447	-0.1761	0.3292	-0.1992	0.455	0.1781	0.2216	0.453	0.099	0.926	22.9139	9.17	-47.7487
45	1.6793	-0.9524	-0.0141	2.9464	1.3171	1.4072	-0.2343	-0.5249	-0.8511	-0.0977	-0.0111	0.1881	0.0591	-0.0457	0.2676	0.7416	-0.1728	-0.1787	0.3665	0.2579	0.8739	19.0343	38.9171	-53.8124
46	0.9684	0.2014	-0.2315	1.7073	-0.4722	0.1846	0.2803	0.463	0.2308	-0.3903	0.0192	-0.6195	-0.2895	-0.0302	-0.0741	0.8438	-0.0555	0.2608	0.3213	-0.0077	0.9064	21.2578	70.5179	-71.3964
47	1.2618	0.2795	0.9756	8.7011	-1.6281	1.1601	0.4763	0.0305	0.4272	-0.3661	0.6084	-0.3241	0.2394	0.0849	-0.1095	1.2802	0.0062	0.4201	0.3502	0.0724	0.7461	21.7096	67.1425	-73.0126
48	2.4755	-3.6283	3.3069	6.5154	-5.7666	5.1148	0.0483	-0.4819	-0.3294	-0.179	0.7331	0.7682	0.1227	-0.1084	-0.6611	0.986	0.0181	0.1462	0.4097	0.0569	0.6352	21.0559	-168.4649	65.3185
49	-0.3822	0.0491	0.0048	0.2807	-0.3524	0.163	0.0348	-0.1097	-0.0549	0.3427	0.1394	0.2504	-0.1663	-0.0489	-0.3715	0.6475	-0.0007	0.2043	0.4585	0.1462	0.721	17.3199	-88.2725	10.9527
50	0.6351	-0.7958	0.2025	1.3755	0.2159	0.6808	-0.2261	-0.1296	-0.1434	-1.1731	0.0246	-0.0075	0.0473	-0.0951	0.1813	0.6974	-0.0424	-0.0229	0.2631	-0.0062	0.6689	17.7839	24.5527	-51.7852
51	1.6218	-1.867	0.846	3.8809	0.0846	1.662	0.1637	-0.0809	0.73	0.2494	-0.6881	0.5894	-0.2339	-0.2503	0.0747	0.6601	-0.1331	0.1967	0.4153	0.0686	1.2322	15.0867	61.1149	-53.4753
52	4.9378	1.7275	-1.9312	4.3882	-1.2704	2.1101	0.2943	0.6462	0.6456	-1.0195	-0.0843	0.0011	0.3216	0.4308	-0.4981	0.7684	-0.0731	0.0771	1.0935	0.1894	0.6143	15.0084	75.2875	-79.7516
53	8.4362	-0.5446	2.3853	5.7976	-6.2622	7.1455	0.3804	1.09	-0.9453	-1.0091	0.0457	-0.3063	1.6202	-0.0885	-0.3472	0.7876	-0.0234	0.1701	0.4607	-0.1944	0.5914	13.1268	76.1388	-74.2458
54	1.6964	-1.2803	1.1008	1.4343	-1.4201	1.5231	-0.534	-0.0441	-0.0818	0.4886	0.3428	0.0932	-0.0682	-0.0856	0.249	0.5577	-0.0025	0.2265	0.3021	-0.0562	0.7626	12.0461	60.3007	-62.814
55	0.0564	-0.1295	0.0997	6.3422	-3.8171	2.3199	-0.0903	0.0033	0.0147	-0.1136	-0.201	-0.6532	-0.0341	0.1095	0.3231	0.4787	-0.0167	0.1015	0.3439	-0.0285	0.4774	0.6701	235.4636	-176.6737
56	0.7005	-0.0626	0.4921	5.1353	-1.1557	2.0284	-0.0679	-0.0206	0.1511	0.4663	-0.0899	-0.4758	0.1613	0.2667	0.1532	0.7205	0.0725	0.1867	0.272	0.0161	0.7911	-0.9413	78.5235	-99.6223
57	-0.0389	0.0812	-0.0362	5.4725	-3.0593	1.7277	-0.186	-0.0052	0.0171	0.3828	0.2552	-0.2012	-0.2274	-0.2742	-0.0359	0.4661	-0.0385	0.0822	0.3373	0.0122	0.5404	-2.3552	233.7583	-175.0039
58	1.2277	0.6651	0.141	0.5539	0.373	0.5315	0.122	-0.7073	0.1667	-0.3248	0.4643	-0.2691	0.326	0.409	0.2219	0.9535	-0.0859	0.2583	0.1977	0.088	0.9322	1.3246	79.0152	-95.2145
59	0.3863	-0.5023	0.7504	2.0003	-1.7142	2.9412	-0.2204	0.1609	0.2168	-0.813	0.2091	-0.2827	0.5091	-0.2302	-0.0066	0.4726	0.0395	0.1099	0.3302	0.0401	0.4913	-1.4768	287.4928	-212.7156
60	-0.0152	-0.7532	0.1781	4.9115	-2.1553	1.3116	-0.2415	0.083	-0.0185	-0.2313	-0.1754	-1.3761	0.2197	0.0152	0.4656	0.264	-0.0058	0.0176	0.3411	0.073	0.7428	-1.2738	167.4851	-137.8067
61	2.3022	3.3856	-0.3487	4.9778	-0.6202	0.7489	0.1067	0.5358	0.3662	-1.2743	0.6428	0.0621	-0.1406	0.225	-0.3681	0.8862	-0.0823	0.0634	0.334	-0.0877	0.8844	1.5794	84.9055	-106.161
62	2.2511	-0.8558	0.463	2.1605	-0.0604	0.114	-0.2775	-0.4558	-0.6081	0.7913	0.5453	0.4669	0.1266	-0.2683	-0.071	1.1886	-0.0914	0.2773	0.2337	0.0439	0.6642	-5.9828	67.514	-88.3438

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1001 through 1083 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1084 through 1108 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1109 through 1140 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1141 through 1174 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1175 through 1193 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1194 through 1257 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1258 through 1289 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1001 through 1096 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1097 through 1195 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1196 through 1289 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1001 through 1062 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1063 through 1189 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1190 through 1289 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 1001 through 1154 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 1155 through 1191 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1192 through 1250 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1251 through 1289 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 1001 through 1010 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 1011 through 1028 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 1029 through 1098 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 1099 through 1155 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 1156 through 1219 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 1220 through 1235 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 1236 through 1262 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 1263 through 1289 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 1001 through 1035 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 1036 through 1044 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 1045 through 1195 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 1196 through 1289 )
30	X-RAY DIFFRACTION	30	chain 'G' and (resid 1001 through 1028 )
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 1029 through 1041 )
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 1042 through 1087 )
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 1088 through 1177 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 1178 through 1212 )
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 1213 through 1240 )
36	X-RAY DIFFRACTION	36	chain 'G' and (resid 1241 through 1258 )
37	X-RAY DIFFRACTION	37	chain 'G' and (resid 1259 through 1289 )
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 1001 through 1028 )
39	X-RAY DIFFRACTION	39	chain 'H' and (resid 1029 through 1045 )
40	X-RAY DIFFRACTION	40	chain 'H' and (resid 1046 through 1069 )
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 1070 through 1119 )
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 1120 through 1151 )
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 1152 through 1172 )
44	X-RAY DIFFRACTION	44	chain 'H' and (resid 1173 through 1194 )
45	X-RAY DIFFRACTION	45	chain 'H' and (resid 1195 through 1225 )
46	X-RAY DIFFRACTION	46	chain 'H' and (resid 1226 through 1257 )
47	X-RAY DIFFRACTION	47	chain 'H' and (resid 1258 through 1289 )
48	X-RAY DIFFRACTION	48	chain 'I' and (resid 1001 through 1041 )
49	X-RAY DIFFRACTION	49	chain 'I' and (resid 1042 through 1169 )
50	X-RAY DIFFRACTION	50	chain 'I' and (resid 1170 through 1225 )
51	X-RAY DIFFRACTION	51	chain 'I' and (resid 1226 through 1235 )
52	X-RAY DIFFRACTION	52	chain 'I' and (resid 1236 through 1260 )
53	X-RAY DIFFRACTION	53	chain 'I' and (resid 1261 through 1272 )
54	X-RAY DIFFRACTION	54	chain 'I' and (resid 1273 through 1289 )
55	X-RAY DIFFRACTION	55	chain 'J' and (resid 1001 through 1190 )
56	X-RAY DIFFRACTION	56	chain 'J' and (resid 1191 through 1289 )
57	X-RAY DIFFRACTION	57	chain 'K' and (resid 1001 through 1193 )
58	X-RAY DIFFRACTION	58	chain 'K' and (resid 1194 through 1289 )
59	X-RAY DIFFRACTION	59	chain 'L' and (resid 1001 through 1091 )
60	X-RAY DIFFRACTION	60	chain 'L' and (resid 1092 through 1214 )
61	X-RAY DIFFRACTION	61	chain 'L' and (resid 1215 through 1235 )
62	X-RAY DIFFRACTION	62	chain 'L' and (resid 1236 through 1289 )

-
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