PDB-4y7m: T6SS protein TssM C-terminal domain (835-1129) from EAEC

ID or keywords:

Entry

Database: PDB / ID: 4y7m

Title

T6SS protein TssM C-terminal domain (835-1129) from EAEC

Components

Hi113 protein
Type VI secretion protein IcmF

Keywords

MEMBRANE PROTEIN / Type 6 secretion system / Alpha-beta fold / periplasmic protein

Function / homology

Function and homology information

: / : / Type VI secretion protein IcmF helical domain / Type VI secretion system IcmF, C-terminal / Type VI secretion protein IcmF C2-like domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology

Biological species

Lama glama (llama)

Escherichia coli 2-156-04_S3_C3 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.92 Å

Authors

Nguyen, V.S. / Spinelli, S. / Durand, E. / Roussel, A. / Cambillau, C.

Citation

Journal: Nature / Year: 2015
Title: Biogenesis and structure of a type VI secretion membrane core complex.
Authors: Eric Durand / Van Son Nguyen / Abdelrahim Zoued / Laureen Logger / Gérard Péhau-Arnaudet / Marie-Stéphanie Aschtgen / Silvia Spinelli / Aline Desmyter / Benjamin Bardiaux / Annick ...
Abstract: Bacteria share their ecological niches with other microbes. The bacterial type VI secretion system is one of the key players in microbial competition, as well as being an important virulence ...

History

Deposition	Feb 15, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Aug 5, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2018	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2	Jan 10, 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
Revision 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4y7m.cif.gz	300 KB	Display	PDBx/mmCIF format
PDB format	pdb4y7m.ent.gz	241.7 KB	Display	PDB format
PDBx/mmJSON format	4y7m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4y7m_validation.pdf.gz	462.5 KB	Display	wwPDB validaton report
Full document	4y7m_full_validation.pdf.gz	469.1 KB	Display
Data in XML	4y7m_validation.xml.gz	36.2 KB	Display
Data in CIF	4y7m_validation.cif.gz	54.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y7/4y7m ftp://data.pdbj.org/pub/pdb/validation_reports/y7/4y7m	HTTPS FTP

-
Related structure data

Related structure data	2927C 2928C 4y7lC 4y7oC 4qgyS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4p2m-d 6nmg-2 4b93-d 4ll6-d 1c81-1 1yal-1 3oqi-d 4o4u-3 3eed-d 6len-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
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

A: Hi113 protein

B: Hi113 protein

C: Type VI secretion protein IcmF

D: Type VI secretion protein IcmF

hetero molecules

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

1

A: Hi113 protein

C: Type VI secretion protein IcmF

hetero molecules

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

2

B: Hi113 protein

D: Type VI secretion protein IcmF

hetero molecules

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

Unit cell

Length a, b, c (Å)	95.230, 95.230, 172.950
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	172
Space group name H-M	P6₄

#1: Antibody	Hi113 protein Mass: 13897.462 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Gene: hi113 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein	Type VI secretion protein IcmF Mass: 32425.207 Da / Num. of mol.: 2 / Fragment: residues 835-1129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli 2-156-04_S3_C3 (bacteria) Gene: AC43_2230 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A070IVV8, UniProt: A0A0M3KL16*PLUS
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 804 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.66 Å³/Da / Density % sol: 53.72 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 18-20 % PEG4000, 0.25 M Ammonium sulfate. / PH range: 8

-
Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: 1 crystal
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.93 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.93 Å / Relative weight: 1
Reflection	Resolution: 1.92→50 Å / Num. all: 67557 / Num. obs: 67557 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / B_iso Wilson estimate: 37.1 Å² / R_merge(I) obs: 0.079 / Net I/σ(I): 18
Reflection shell	Resolution: 1.91→1.97 Å / Redundancy: 11.3 % / R_merge(I) obs: 1 / Mean I/σ(I) obs: 2 / % possible all: 100

-
Processing

Software

Name	Version	Classification
BUSTER	2.11.5	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4QGY

4qgy

Resolution: 1.92→47.61 Å / Cor.coef. F_o:F_c: 0.9498 / Cor.coef. F_o:F_c free: 0.9352 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.143 / SU R_free Blow DPI: 0.127 / SU R_free Cruickshank DPI: 0.124

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2105	3356	4.97 %	RANDOM
R_work	0.1827	-	-	-
obs	0.184	67543	100 %	-

Displacement parameters

B_iso mean: 43.42 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.2521 Å²	0 Å²	0 Å²
2-	-	-4.2521 Å²	0 Å²
3-	-	-	8.5043 Å²

Refine analyze

Luzzati coordinate error obs: 0.23 Å

Refinement step

Cycle: LAST / Resolution: 1.92→47.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5522	0	15	804	6341

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.009	5671	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.05	7729	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		1846	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		118	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		840	HARMONIC	5
X-RAY DIFFRACTION	t_it		5671	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.65
X-RAY DIFFRACTION	t_other_torsion	17.18
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		731	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		6907	SEMIHARMONIC	4

LS refinement shell

Resolution: 1.92→1.97 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2504	223	4.51 %
R_work	0.2338	4721	-
all	0.2346	4944	-
obs	-	-	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	0.0628	-0.0173	-0.1157	-0.0406	-0.0443	0.01	-0.0017	-0.0004	-0.0017	0.0016	-0.0015	0.0011	0.0005	-0.0018	0.0033	0.0007	-0.0036	0.0218	-0.0031	0.0179	-0.001	-22.6581	32.4739	3.7163
2	0.0081	0.0527	-0.0197	0.0818	-0.1052	0	0.0002	-0.0007	-0.0002	0.0006	0.0007	0.0005	0.0024	0.0012	-0.0009	0.0123	-0.0011	0.0012	-0.0153	0.0171	0.0058	-9.4921	15.0354	9.0524
3	0.0194	0.0143	-0.0698	0.0162	-0.1888	0.0129	0.0017	-0.0019	-0.0006	0.0032	-0.0025	0.0009	0.0049	-0.0057	0.0008	0.0114	0.0018	0.004	-0.0238	0.0013	0.003	-16.8217	23.1972	0.3444
4	0.3735	-0.117	-0.6725	0.2739	0.3988	0.4606	-0.0067	0.0047	-0.0023	0.009	0.0031	0.0065	0.0068	-0.0085	0.0036	-0.0068	0.0195	-0.0255	0.0209	0.0067	-0.0262	-13.1185	31.8983	-0.2104
5	-0.0074	0.0257	-0.039	0.0322	-0.02	0.0277	0.0006	-0.002	0.0002	0.001	-0.0004	-0.0014	-0.0003	0	-0.0002	-0.0012	-0.0016	-0.0109	0.0077	0.0082	-0.0079	-3.5922	32.1673	6.1756
6	-0.1993	0.0893	0.0899	0.3282	-0.0736	0.1479	-0.0139	0.0152	-0.0072	-0.0043	0.0062	-0.0041	0.0139	0.004	0.0077	0.022	-0.0274	-0.0266	-0.0155	-0.0263	-0.0012	-6.6818	27.2203	-6.9066
7	-0.0957	0.0751	0.2785	0.188	0.1436	0	-0.0052	0.0027	0.0008	0.0031	0.0079	0.0049	0.0156	-0.0022	-0.0027	0.0118	-0.0217	0.0005	-0.0326	-0.0081	0.0203	-17.1595	22.0542	-4.5704
8	0.0387	-0.0349	0.0093	0.0048	0.021	0.023	-0.0002	-0.0017	-0.0004	0.0007	0.0014	-0.0007	0.0006	0.0003	-0.0012	-0.0034	0.0159	-0.0038	0.0101	-0.0015	-0.0083	-0.2361	18.7667	5.795
9	0.2219	-0.1313	-0.5924	0.6614	0.6876	0.434	-0.0145	-0.0072	-0.0034	0.0093	0.028	0.0022	-0.0029	0.008	-0.0136	0.0113	0.0155	-0.0108	0.0216	0.0279	-0.0522	-10.6644	36.0827	-1.3086
10	0.0026	-0.0015	-0.0947	-0.0026	-0.1067	0.1066	-0.001	0.0019	-0.0029	-0.0003	0.0036	-0.0024	0.0002	-0.0022	-0.0026	0.0047	0.0089	-0.0091	0.0066	0.0295	-0.0109	-7.1208	18.8739	11.5664
11	0.0243	-0.0223	-0.0616	0.0104	0.0816	0.0206	-0.0008	0.0026	-0.0026	0.0006	-0.0033	0.0005	0.001	-0.0019	0.0041	-0.0093	0.0086	0.0055	0.0066	-0.0224	0.0014	-30.9506	36.1649	-36.3187
12	0	-0.0027	0.1172	0.0199	0.3306	0.0014	0.0002	-0.0005	0.0021	0.0001	0.0006	0.0045	0.0017	-0.0022	-0.0008	-0.0016	0.0037	-0.0269	0.0023	-0.0345	-0.0031	-53.3053	34.2522	-42.1614
13	-0.1507	0.3696	0.4027	0.5601	0.3597	0.1787	-0.0051	0.0009	-0.012	-0.0092	0.0135	-0.0093	0.0058	0.0042	-0.0085	-0.0284	-0.0088	-0.0343	0.0101	-0.0127	0.0057	-38.7851	38.3283	-31.7218
14	-0.053	0.0558	0.0034	0.1368	-0.0216	0.0284	-0.0003	0.0012	0.0007	-0.0039	0.0011	0.0022	-0.0008	-0.0001	-0.0008	0.0129	-0.0019	-0.017	-0.0026	0.0048	-0.0063	-45.0865	49.847	-40.2416
15	0.0899	-0.0633	0.164	0.0088	0.5928	0.1221	0.0022	-0.0063	0.0001	0.0074	-0.0084	0.0134	-0.0041	0.004	0.0063	-0.0072	-0.0135	-0.0019	0.0001	-0.022	0.0105	-43.8595	44.5132	-24.3752
16	0.1473	0.167	-0.1816	0.6064	0.4906	0.2023	0.0011	-0.0133	-0.0103	0.0121	-0.0065	-0.011	0.0087	0.0045	0.0054	0.0039	-0.0016	-0.002	0.002	-0.0085	0.0209	-43.8323	35.2943	-27.0371
17	0.008	0.0984	0.1843	0.1816	0.1955	0.0141	0.0022	0.0003	0.0003	-0.0014	-0.0076	0.0056	-0.0038	-0.008	0.0053	-0.0202	0.003	-0.0188	0.01	-0.0114	0.0101	-52.731	38.7026	-34.8869
18	0.8214	0.2511	-0.1971	0.4076	0.1332	0	0.0128	0.0083	-0.0028	-0.0158	-0.0027	0.0172	-0.0004	0.0143	-0.0101	-0.0092	-0.0134	-0.021	0.033	-0.0171	-0.04	-37.4905	46.585	-31.4534
19	0.0689	-0.0398	-0.0243	-0.0689	0.0064	0.0769	-0.0001	-0.0003	0.0005	0.0008	-0.0007	0.0053	0.0011	0.0006	0.0008	0.0009	0.0099	-0.0345	0.0129	0.0014	-0.0164	-53.0016	38.9829	-44.9906
20	-0.0699	0.0413	-0.0488	0.071	0.1018	0.0005	0.0016	0.0003	0.0024	-0.0022	-0.003	0	0.003	0	0.0014	-0.0064	-0.0195	-0.0053	-0.0116	0.017	0.0012	15.6624	75.7114	-34.4099
21	-0.0665	0.1088	0.021	0.1479	0.015	0.0038	0.0009	0.0037	0.0004	-0.0022	-0.0006	-0.0012	-0.001	0.0015	-0.0003	0.0313	-0.028	-0.0138	-0.0516	0.0172	0.019	8.9793	77.2933	-20.4006
22	0.0033	0.0523	0.0717	0.0593	-0.0238	0.0273	-0.0002	-0.0004	0.0034	0.0017	-0.0006	-0.0011	-0.0005	0.0016	0.0007	0.0308	-0.0392	-0.0185	-0.034	0.0147	0.0029	8.4883	70.7934	-8.4513
23	-0.311	0.1737	0.1392	0.3314	-0.0696	0.0064	0.0022	-0.0047	0.0097	0.0019	0.0009	-0.0009	-0.0031	0.0003	-0.0031	0.0384	-0.0193	-0.0154	-0.0443	0.0052	0.0046	0.5742	74.1394	-11.612
24	-0.0063	0.0116	0.088	0.033	-0.0413	0.1777	0.0003	0.0044	0.0055	0.0003	-0.0017	0.0105	0.0037	-0.0002	0.0014	0.0116	-0.0416	-0.0259	-0.0229	0.0594	0.0053	0.9551	73.2349	-28.8454
25	-0.0392	0.0659	0.1012	0.0892	0.1041	0.0755	-0.001	0.0023	0	0.0001	-0.0026	0.0029	-0.0005	0.0011	0.0036	0.02	-0.0134	0.0138	-0.0058	0.0045	-0.0149	1.8727	62.5604	-35.1142
26	-0.0835	0.1273	-0.0931	0.1804	0.1884	0.0496	0.001	0.005	-0.0012	-0.0047	-0.0023	-0.0006	0.0052	0.0029	0.0013	-0.0075	-0.0098	0.0157	0.0083	0.0087	-0.0043	12.0703	63.6297	-36.7052
27	0.0203	-0.0055	-0.0251	-0.0109	-0.007	0.0022	0.0006	0.0019	0.0001	-0.0024	-0.0015	-0.0025	0.0026	0.0018	0.0009	0.0388	-0.0208	-0.0144	-0.0257	0.0069	-0.0139	5.7741	62.4618	-24.6819
28	-0.1098	0.2186	0.1625	0.4322	0.2478	0.2148	-0.0047	0.0033	0.0249	0.0011	0.0027	0.0031	-0.0001	-0.0006	0.0021	0.0357	-0.0422	-0.0171	-0.0308	0.0346	-0.0112	-8.1154	60.5523	-13.3146
29	-0.047	0.0347	0.0302	0.1801	0.4411	0.5426	0.0019	-0.0135	0.0034	0.0049	-0.004	0.005	0	-0.004	0.0021	0.0292	0.0012	0.0038	-0.0061	0.0026	-0.0288	-7.3999	54.9474	5.0206
30	-0.069	0.0398	-0.0632	0.069	0.0248	0.0819	-0.0005	-0.0013	-0.0005	0.001	-0.0006	0.002	0.0014	-0.003	0.0011	0.0105	-0.007	0.0167	0.0123	0.0031	-0.0211	-12.9203	50.8528	6.4435
31	-0.0217	0.0038	0.0676	0.0518	-0.0713	0.0198	-0.003	0.0021	0.0063	-0.0001	0.001	0.0021	-0.0031	0.0016	0.002	0.0292	-0.0068	-0.0216	-0.0226	0.0211	-0.0104	-12.0895	56.9404	-5.8074
32	0.0064	-0.0188	0.0378	0.0459	0.0063	0.0125	0.001	-0.0021	0.0003	-0.0004	-0.001	0.0016	0.0006	0.0018	0	0.0136	0.0061	-0.0111	-0.0121	-0.0118	0.0005	-10.9359	71.9623	-1.8525
33	0.0902	0.019	0.0065	0.0418	0.1657	0.1185	-0.003	0.0009	-0.0007	0.0009	0.0008	0.0042	-0.002	0	0.0022	0.0086	0.004	0.0016	0.0028	0.024	-0.0165	-3.1197	55.5371	9.2077
34	0.0642	0.0279	0.09	0.0135	0.0343	0.0329	-0.0013	-0.0009	-0.0012	0.001	0.0023	-0.0007	-0.0007	0.0004	-0.001	0.0077	-0.0038	-0.0164	0.0038	0.0101	-0.0118	-0.5991	55.4526	13.6885
35	-0.0882	0.0388	0.2352	0.2049	0.0058	0.0738	-0.0038	0.0014	0.0005	0.0011	0.0036	-0.005	-0.0064	-0.003	0.0003	0.0677	-0.0394	-0.0369	-0.0472	0.0138	-0.021	0.8759	63.9534	-2.4764
36	-0.0038	0.0039	0.0068	0.0058	-0.0055	0.003	-0.0009	0.0005	0.0014	0.0001	0.0009	-0.002	0.001	-0.0016	0	0.0035	-0.0053	-0.001	-0.0071	-0.0135	0.0005	2.9181	49.1059	-7.8356
37	-0.0617	0.3466	-0.0309	0.8272	-0.2537	0.0606	-0.0019	-0.0039	-0.0073	-0.0024	0.0011	-0.011	0.0099	0.0105	0.0009	0.0512	-0.0256	-0.0307	-0.0271	-0.0048	-0.0291	-0.4554	49.5667	-1.0039
38	-0.1832	0.1373	0.517	0.3602	-0.5647	0.4933	-0.0041	0.0026	0.0072	0.0078	-0.0037	-0.0143	0.008	-0.0021	0.0078	0.0351	-0.033	-0.0245	-0.0317	0.0314	-0.0065	1.9459	60.2032	-14.4276
39	-0.0039	0.0237	-0.0229	0.0286	-0.0258	0.0061	0.001	0.0008	0.0003	-0.0001	-0.0017	-0.002	-0.0006	0.0028	0.0007	-0.0068	-0.0008	0.0029	0.0054	-0.0001	-0.0018	17.0874	69.2588	-30.5734
40	0.0105	-0.0056	0.0074	-0.0016	-0.0003	0	0.0001	-0.0002	-0.0003	0.0001	-0.0001	0.0002	0.0001	-0.0001	0	0.0006	0.0011	-0.0014	-0.0014	-0.0039	0.0018	-25.2921	92.4428	1.1828
41	-0.0432	0.0134	0.0318	0.0833	0.0115	0	0.0022	-0.0039	0.002	-0.0005	-0.001	0.002	-0.0009	0.0006	-0.0012	0.0048	0.0005	-0.019	-0.0215	0.0021	0.0179	-21.4177	89.547	-12.2104
42	0.0044	-0.0059	0.0279	0.0073	-0.0615	0	-0.0004	0.0012	0.0024	0.0003	-0.0007	-0.0017	-0.0016	0	0.0011	-0.0053	0.0037	-0.0234	-0.0116	0.0286	0.0149	-25.7957	84.0819	-24.0586
43	-0.1203	0.0695	0.0651	0.1203	-0.065	0	-0.0033	0.0027	0.0124	0.0018	0.0022	-0.0027	-0.0019	-0.0005	0.0011	-0.001	-0.004	-0.0582	-0.0424	-0.0036	0.0384	-17.1689	80.007	-13.8102
44	0.0146	-0.0099	0.0874	-0.0096	0.0286	0.0139	0.0019	-0.003	-0.0017	0.0006	-0.0009	0.0004	0.0007	0.0003	-0.0011	0.0009	0.0127	-0.0135	-0.0114	-0.0403	0.005	-18.1967	81.641	-0.4225
45	0.0184	-0.0106	-0.0039	-0.0184	0.054	0	0.0002	-0.0021	0.0021	0.002	-0.0006	0.0002	-0.0022	-0.0003	0.0003	-0.0025	0.0019	0.0055	-0.0012	-0.0116	-0.0071	-27.1064	74.6894	3.7582
46	0.0324	-0.0201	0.0337	-0.0277	0.0167	0.0116	0.0003	-0.0002	0.0002	0.0003	0	0.0011	0.0007	-0.0001	-0.0003	-0.0046	0.0078	-0.004	0.0048	-0.0134	-0.0018	-32.721	82.3397	-2.0295
47	0.0888	0.2885	-0.4622	0.4439	0.0576	0.1558	-0.0157	0.0053	0.0215	0.0119	0.0081	-0.0241	-0.0048	-0.019	0.0076	0.0024	-0.0221	-0.0196	-0.0287	0.0191	0.0159	-22.5993	67.5952	-15.99
48	-0.0168	0.1873	-0.1913	0.234	-0.9244	0.6435	0.0047	0.0117	0.0022	-0.0123	-0.0122	-0.0077	-0.0015	-0.0003	0.0075	-0.0401	-0.0215	-0.0127	0.0515	0.0551	-0.024	-25.7792	62.6094	-36.4428
49	-0.0421	0.0244	-0.037	0.0422	-0.03	0.0854	0.0008	0.002	-0.0004	-0.0017	-0.0035	-0.0039	0.0029	0.0036	0.0026	0.0064	0.0005	0.0022	0.011	-0.0062	-0.0146	-24.701	55.8838	-37.9928
50	0.029	0.0272	0.0685	0.0217	-0.0331	0.1014	-0.0041	0.0083	0.0083	0.0029	-0.004	-0.0104	-0.0015	-0.0012	0.0081	-0.0122	-0.0083	-0.0053	0.0151	0.0318	-0.007	-20.6196	60.9746	-25.6417
51	-0.0175	0.1484	0.0141	0.1772	-0.8039	0.1766	0.0013	0.0059	0.0015	-0.0003	-0.0096	-0.0208	-0.0055	-0.0058	0.0083	-0.0458	-0.0088	-0.0048	0.0357	0.058	0.0001	-21.1577	69.0078	-35.8761
52	-0.0241	0.0058	0.0363	0.0524	-0.072	0.0501	-0.0005	0.0017	-0.0013	0	-0.001	0.0001	0.0009	-0.0001	0.0016	0.0024	0.0006	-0.0056	0.0035	0.0108	0.0017	-31.5677	65.3076	-47.1155
53	0.0081	-0.0085	0.2876	0.0491	-0.3705	0	-0.0023	0.0047	0.0059	0.0029	-0.0016	-0.0023	-0.0014	0.0005	0.0039	-0.0187	-0.0063	-0.0231	-0.0171	0.1261	0.0321	-25.6255	74.5043	-29.5946
54	0.0304	-0.024	-0.0203	-0.0011	-0.0101	0	-0.0002	0.0007	0.0012	0.0002	-0.0009	-0.0003	0.0009	-0.0007	0.0011	-0.0131	0.0026	0.0097	-0.0007	0.0044	0.0124	-37.7862	67.2167	-25.2457
55	0.2256	-0.0063	0.0345	-0.0725	-0.2054	0	-0.0001	0.0005	0.002	0.0022	-0.0026	0.0019	-0.0037	-0.0027	0.0026	-0.0109	-0.0276	0.0115	-0.0151	0.0001	0.0222	-34.6026	59.7957	-22.0699
56	0.0626	-0.0033	-0.0044	-0.0247	-0.0774	0.0035	0.0003	0.0009	-0.0014	-0.0022	-0.0014	0.005	-0.0011	-0.001	0.0011	-0.0258	0.0104	0.0012	0.0215	0.0345	0.0069	-37.0584	67.5939	-38.7099
57	-0.1306	0.2633	0.2772	0.3476	0.0377	0.0139	-0.0145	0.0085	0.0215	0.0085	0.0121	-0.0058	0.0055	-0.0131	0.0024	0.0282	-0.038	-0.0105	-0.0479	0.0497	0.0136	-29.0603	67.0372	-21.216
58	0.0517	-0.0429	0.0497	-0.0066	0.0169	0	0.001	-0.0015	-0.0006	0.0004	-0.0004	0.0017	-0.0001	0.0005	-0.0006	-0.003	0.0078	-0.01	-0.0051	-0.0063	0.0086	-30.3148	86.897	-8.885

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{A\|1 - A\|6}
2	X-RAY DIFFRACTION	2	{A\|7 - A\|14}
3	X-RAY DIFFRACTION	3	{A\|15 - A\|27}
4	X-RAY DIFFRACTION	4	{A\|28 - A\|42}
5	X-RAY DIFFRACTION	5	{A\|43 - A\|48}
6	X-RAY DIFFRACTION	6	{A\|49 - A\|71}
7	X-RAY DIFFRACTION	7	{A\|72 - A\|84}
8	X-RAY DIFFRACTION	8	{A\|85 - A\|90}
9	X-RAY DIFFRACTION	9	{A\|91 - A\|122}
10	X-RAY DIFFRACTION	10	{A\|123 - A\|129}
11	X-RAY DIFFRACTION	11	{B\|1 - B\|6}
12	X-RAY DIFFRACTION	12	{B\|7 - B\|15}
13	X-RAY DIFFRACTION	13	{B\|16 - B\|40}
14	X-RAY DIFFRACTION	14	{B\|41 - B\|48}
15	X-RAY DIFFRACTION	15	{B\|49 - B\|64}
16	X-RAY DIFFRACTION	16	{B\|65 - B\|79}
17	X-RAY DIFFRACTION	17	{B\|80 - B\|89}
18	X-RAY DIFFRACTION	18	{B\|90 - B\|123}
19	X-RAY DIFFRACTION	19	{B\|124 - B\|129}
20	X-RAY DIFFRACTION	20	{C\|31 - C\|43}
21	X-RAY DIFFRACTION	21	{C\|44 - C\|54}
22	X-RAY DIFFRACTION	22	{C\|55 - C\|63}
23	X-RAY DIFFRACTION	23	{C\|64 - C\|73}
24	X-RAY DIFFRACTION	24	{C\|74 - C\|91}
25	X-RAY DIFFRACTION	25	{C\|92 - C\|101}
26	X-RAY DIFFRACTION	26	{C\|102 - C\|118}
27	X-RAY DIFFRACTION	27	{C\|119 - C\|127}
28	X-RAY DIFFRACTION	28	{C\|128 - C\|147}
29	X-RAY DIFFRACTION	29	{C\|148 - C\|162}
30	X-RAY DIFFRACTION	30	{C\|163 - C\|170}
31	X-RAY DIFFRACTION	31	{C\|171 - C\|179}
32	X-RAY DIFFRACTION	32	{C\|180 - C\|185}
33	X-RAY DIFFRACTION	33	{C\|186 - C\|194}
34	X-RAY DIFFRACTION	34	{C\|195 - C\|201}
35	X-RAY DIFFRACTION	35	{C\|202 - C\|217}
36	X-RAY DIFFRACTION	36	{C\|218 - C\|222}
37	X-RAY DIFFRACTION	37	{C\|223 - C\|245}
38	X-RAY DIFFRACTION	38	{C\|246 - C\|264}
39	X-RAY DIFFRACTION	39	{C\|265 - C\|271}
40	X-RAY DIFFRACTION	40	{D\|35 - D\|43}
41	X-RAY DIFFRACTION	41	{D\|44 - D\|56}
42	X-RAY DIFFRACTION	42	{D\|57 - D\|65}
43	X-RAY DIFFRACTION	43	{D\|66 - D\|78}
44	X-RAY DIFFRACTION	44	{D\|79 - D\|90}
45	X-RAY DIFFRACTION	45	{D\|91 - D\|113}
46	X-RAY DIFFRACTION	46	{D\|114 - D\|122}
47	X-RAY DIFFRACTION	47	{D\|123 - D\|147}
48	X-RAY DIFFRACTION	48	{D\|148 - D\|162}
49	X-RAY DIFFRACTION	49	{D\|163 - D\|170}
50	X-RAY DIFFRACTION	50	{D\|171 - D\|180}
51	X-RAY DIFFRACTION	51	{D\|181 - D\|193}
52	X-RAY DIFFRACTION	52	{D\|194 - D\|200}
53	X-RAY DIFFRACTION	53	{D\|201 - D\|216}
54	X-RAY DIFFRACTION	54	{D\|217 - D\|221}
55	X-RAY DIFFRACTION	55	{D\|222 - D\|232}
56	X-RAY DIFFRACTION	56	{D\|233 - D\|240}
57	X-RAY DIFFRACTION	57	{D\|241 - D\|260}
58	X-RAY DIFFRACTION	58	{D\|261 - D\|268}

-
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