PDB-5vxj: 2.50 A resolution structure of IpaD from Shigella flexneri in com...

ID or keywords:

Entry

Database: PDB / ID: 5vxj

Title

2.50 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody JMK-E3

Components

Invasin IpaD
single-domain antibody JMK-E3

Keywords

IMMUNE SYSTEM / tip protein / VHH / T3SS

Function / homology

Function and homology information

effector-mediated activation of programmed cell death in host / extracellular region
Similarity search - Function

Biological species

Shigella flexneri (bacteria)

Vicugna pacos (alpaca)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Barta, M.L. / Lovell, S. / Battaile, K.P. / Picking, W.D. / Picking, W.L.

Citation

Journal: To Be Published
Title: 2.50 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody JMK-E3
Authors: Barta, M.L. / Lovell, S. / Battaile, K.P. / Picking, W.D. / Picking, W.L.

History

Deposition	May 23, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 30, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5vxj.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb5vxj.ent.gz	909.2 KB	Display	PDB format
PDBx/mmJSON format	5vxj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5vxj_validation.pdf.gz	491.6 KB	Display	wwPDB validaton report
Full document	5vxj_full_validation.pdf.gz	496.1 KB	Display
Data in XML	5vxj_validation.xml.gz	62.5 KB	Display
Data in CIF	5vxj_validation.cif.gz	86 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vx/5vxj ftp://data.pdbj.org/pub/pdb/validation_reports/vx/5vxj	HTTPS FTP

-
Related structure data

Related structure data	2j0oS S: Starting model for refinement
Similar structure data	4r5o-3 4k34-3 4bq6-1 4r5o-2 3egg-1 6hue-1 4bq7-2 1hpl-1 2x1l-2 4k95-8 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) 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

2j0oS

S: Starting model for refinement

Similar structure data

-
Links

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

Deposited unit

A: Invasin IpaD

B: single-domain antibody JMK-E3

C: Invasin IpaD

D: single-domain antibody JMK-E3

E: Invasin IpaD

F: single-domain antibody JMK-E3

G: Invasin IpaD

H: single-domain antibody JMK-E3

I: Invasin IpaD

J: single-domain antibody JMK-E3

238 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Invasin IpaD

B: single-domain antibody JMK-E3

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

2

C: Invasin IpaD

D: single-domain antibody JMK-E3

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

3

E: Invasin IpaD

F: single-domain antibody JMK-E3

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

4

G: Invasin IpaD

H: single-domain antibody JMK-E3

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

5

I: Invasin IpaD

J: single-domain antibody JMK-E3

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

Unit cell

Length a, b, c (Å)	79.014, 163.350, 216.021
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Invasin IpaD / 36 kDa membrane antigen Mass: 31904.623 Da / Num. of mol.: 5 / Mutation: C322S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaD, CP0126 / Production host: Escherichia coli (E. coli) / References: UniProt: P18013
#2: Antibody	single-domain antibody JMK-E3 Mass: 15662.462 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.86 Å³/Da / Density % sol: 56.93 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Trimethylamine N-oxide dehydrate, 0.1 M Tris-HCl (pH 8.5), 20% (w/v) PEG 2000

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 17-ID / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2016

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.5→48.62 Å / Num. obs: 96196 / % possible obs: 98.6 % / Redundancy: 6.8 % / B_iso Wilson estimate: 38.83 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.145 / R_pim(I) all: 0.06 / R_rim(I) all: 0.157 / Net I/σ(I): 10.8 / Num. measured all: 651001 / Scaling rejects: 123

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
2.5-2.54	7	1.213	33653	4787	0.683	0.495	1.312	2	100
13.69-48.62	6.3	0.039	4297	685	0.991	0.018	0.043	33.8	97.8

-
Processing

Software

Name	Version	Classification
PHENIX	1.12rc1_2803	refinement
Aimless	0.5.27	data scaling
PDB_EXTRACT	3.22	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2J0O

2j0o

Resolution: 2.5→45.048 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.259	9228	5.02 %	RANDOM SELECTION
R_work	0.1964	174630	-	-
obs	0.1995	183858	98.39 %	-

Solvent computation

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

Displacement parameters

B_iso max: 202.16 Å² / B_iso mean: 54.3366 Å² / B_iso min: 14.41 Å²

Refinement step

Cycle: final / Resolution: 2.5→45.048 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14944	0	0	186	15130
B_iso mean	-	-	-	37.96	-
Num. residues	-	-	-	-	1955

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	15181
X-RAY DIFFRACTION	f_angle_d	0.477	20552
X-RAY DIFFRACTION	f_chiral_restr	0.037	2329
X-RAY DIFFRACTION	f_plane_restr	0.002	2671
X-RAY DIFFRACTION	f_dihedral_angle_d	12.056	9182

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.5-2.5284	0.3672	264	0.3037	6019	6283	100
2.5284-2.5582	0.3422	309	0.3059	5899	6208	100
2.5582-2.5893	0.3143	335	0.2889	5872	6207	100
2.5893-2.6221	0.3424	322	0.2878	5889	6211	100
2.6221-2.6566	0.3698	335	0.2846	5861	6196	100
2.6566-2.693	0.3596	245	0.2802	4404	4649	75
2.693-2.7315	0.3668	292	0.2778	5985	6277	100
2.7315-2.7722	0.3097	310	0.2756	5900	6210	100
2.7722-2.8156	0.3486	311	0.2656	5958	6269	100
2.8156-2.8617	0.2935	306	0.2504	5804	6110	100
2.8617-2.911	0.3065	355	0.2497	5965	6320	100
2.911-2.964	0.3053	282	0.2447	5850	6132	100
2.964-3.021	0.3337	306	0.2405	5962	6268	100
3.021-3.0826	0.293	327	0.2382	5898	6225	100
3.0826-3.1496	0.3042	336	0.2348	5909	6245	100
3.1496-3.2229	0.3196	345	0.2313	5838	6183	100
3.2229-3.3034	0.3361	298	0.2324	6007	6305	100
3.3034-3.3927	0.2726	334	0.2082	5856	6190	100
3.3927-3.4925	0.2477	276	0.1887	5946	6222	100
3.4925-3.6052	0.2595	310	0.1808	5933	6243	100
3.6052-3.734	0.2452	345	0.1794	5855	6200	100
3.734-3.8834	0.2606	285	0.1743	5645	5930	97
3.8834-4.0601	0.2116	253	0.1581	4961	5214	97
4.0601-4.274	0.1816	307	0.1427	5912	6219	100
4.274-4.5415	0.2123	312	0.1306	5939	6251	100
4.5415-4.8918	0.1826	277	0.1335	5948	6225	100
4.8918-5.3833	0.1868	284	0.1448	5918	6202	100
5.3833-6.1606	0.2661	323	0.1792	5927	6250	100
6.1606-7.7553	0.2305	331	0.1864	5881	6212	100
7.7553-45.0553	0.1886	313	0.1721	5889	6202	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	0.0036	-0.0019	-0.0019	0.0174	0.0036	0.0057	-0.1237	0.1065	0.02	0.0318	-0.1409	0.1237	-0.0128	-0.1089	-0	0.3109	0.0215	-0.0112	0.5684	-0.0483	0.4402	-56.2912	110.3376	163.103
2	0.0243	0.0075	-0.0028	0.0105	-0.024	-0.0098	0.0749	-0.1569	-0.134	0.0102	-0.0298	0.0204	0.0511	-0.0304	-0	0.3197	-0.01	0.0566	0.2799	0.0018	0.2739	-42.3266	101.9458	166.064
3	0.069	-0.0585	-0.1013	0.1552	-0.0184	0.0675	-0.2998	-0.0237	-0.0349	-0.2989	0.1472	-0.0446	-0.1703	-0.1061	-0	0.2749	0.0033	-0.0244	0.2183	-0.0015	0.2927	-45.848	108.974	157.9833
4	0.0142	0.013	-0.0139	-0.001	0.0002	0.013	0.1161	-0.0911	-0.0779	-0.0869	-0.0883	0.0643	-0.0652	0.1189	-0	0.3248	0.061	-0.0134	0.2553	0.0116	0.2697	-31.0211	116.8218	162.1494
5	0.0061	-0.0274	0.0076	0.0884	0.0126	-0.0139	0.1564	0.0918	0.1499	-0.3993	0.0805	-0.3035	0.1059	0.1675	-0.0033	0.3558	0.0291	-0.1193	0.488	-0.0548	0.301	-44.8654	104.7799	150.1937
6	0.701	0.1785	0.5586	0.3816	0.3027	0.2909	-0.067	-0.0684	0.0649	0.0466	0.0451	0.043	-0.0216	0.0048	-0.0523	0.177	-0.0191	-0.0264	0.19	-0.0171	0.1982	-42.3671	123.9898	118.217
7	0.2519	0.0602	0.4842	0.1529	0.0544	0.2012	-0.0826	0.074	0.1017	0.0098	-0.0656	-0.0505	-0.0972	0.0877	-0.0001	0.182	0.0059	-0.0159	0.1991	0.0093	0.1782	-54.5812	115.251	87.4724
8	0.3332	-0.1587	0.0898	0.0109	-0.0901	0.1585	-0.0083	0.001	0.0762	-0.0022	0.0124	0.0228	0.065	-0.0681	0.0124	0.1956	0.0033	-0.0169	0.2045	-0.0093	0.2265	-58.9333	118.1479	93.2768
9	0.194	-0.1228	0.1069	0.1143	0.0247	0.0378	0.1348	-0.0159	0.0294	-0.085	-0.1018	0.0425	0.072	0.0957	-0	0.3235	-0.0241	0.0135	0.1736	0.0315	0.2256	-38.0494	104.2741	114.986
10	0.364	0.3865	0.2273	0.5053	0.336	0.2787	0.3525	0.1526	0.1389	0.0259	-0.4158	-0.2511	0.1704	-0.0897	-0.0195	0.304	0.1958	0.1063	0.2451	0.0255	0.2873	-27.2474	99.6977	112.0512
11	0.0092	0.0069	0.0087	0.0761	0.0365	0.016	0.0776	-0.3148	-0.0147	0.3044	0.0256	-0.1859	0.1515	0.2099	0.0018	0.1932	0.0538	0.0167	0.2297	-0.038	0.1761	-28.0264	105.1177	123.9707
12	0.026	0.0838	0.0647	0.0619	0.0601	0.0304	-0.0964	0.1139	0.0934	-0.0299	0.0746	-0.1233	0.0465	-0.0305	0	0.2794	0.0153	-0.0035	0.2482	-0.0214	0.2839	-33.7665	109.2793	118.0733
13	0.0549	-0.014	-0.0016	0.02	0.0305	0.0243	0.2148	0.0214	-0.1172	0.0678	-0.2025	0.062	0.1203	0.0328	0	0.3368	0.0461	-0.0237	0.2098	-0.0345	0.3087	-36.5503	96.9851	115.5807
14	0.0014	0.0159	-0.0023	0.0173	0.0076	0.0133	0.1365	0.0207	-0.0367	-0.1756	-0.0709	-0.0804	0.0365	-0.1527	0	0.5068	0.0358	-0.0384	0.2344	0.06	0.3221	-39.3165	88.8769	117.026
15	0.0047	0.0059	-0.0268	0.0203	-0.0031	0.0203	0.1405	0.0144	-0.014	-0.0205	0.0819	-0.0891	0.0108	0.1982	0	0.3247	-0.0383	-0.0316	0.4405	0.0393	0.3141	-32.92	109.3478	105.0872
16	0.1262	-0.4185	-0.0765	0.228	0.0696	0.2325	0.1021	-0.0331	0.0083	0.0525	-0.1059	0.1531	-0.0282	-0.5368	-0	0.3245	-0.0307	0.0105	0.4413	-0.0773	0.2787	-17.7774	51.9031	97.0947
17	0.0171	-0.0104	0.0124	0.0038	-0.0196	0.0222	0.0063	-0.1956	0.0685	0.2666	-0.2403	-0.1336	0.0091	0.1459	0	0.5179	-0.0302	0.0042	0.2726	-0.004	0.4423	-5.1449	47.9877	109.3546
18	-0.0044	0.1211	0.1486	0.1049	-0.0492	0.1156	0.0425	-0.0024	-0.0394	0.0157	-0.0762	0.0383	0.0661	0.0393	-0	0.2482	0.0204	0.0058	0.228	-0.0311	0.2282	-6.1934	44.2086	75.455
19	0.3516	0.0827	0.0568	0.0535	0.238	0.143	0.0792	0.0027	0.0747	0.0339	0.0444	-0.0384	0.0604	0.1732	0	0.3411	0.0457	-0.0413	0.24	-0.0592	0.3059	4.52	43.6716	78.2203
20	0.0828	0.1604	0.0404	0.0915	0.1795	0.0569	0.1548	-0.0534	-0.0234	0.0439	0.0142	0.006	0.2418	-0.0033	0.011	0.4616	-0.0071	-0.0115	0.277	-0.0178	0.3317	-7.9641	34.5944	76.4043
21	0.0072	0.0014	0.0004	0.0214	0.0175	0.0043	-0.0026	0.0841	-0.0114	-0.1128	-0.0023	-0.19	0.1353	-0.0019	0	0.4051	0.0312	0.0778	0.3052	-0.0662	0.3452	8.5282	57.5335	93.2919
22	0.0053	-0.0019	0.0114	0.0009	0.0063	0.0055	-0.0709	-0.0196	0.1375	-0.0916	0.0428	0.1189	-0.1133	0.0376	-0	0.6711	0.049	0.0948	0.5127	0.0134	0.4713	-13.3022	65.6495	88.8177
23	0.0184	0.0342	0.0336	0.0155	0.004	-0.0237	0.2084	0.0684	0.0395	-0.2521	0.0348	0.0048	-0.0295	-0.0837	0	0.4295	0.0222	0.0504	0.2984	0.0161	0.3734	3.4716	59.4979	98.1878
24	0.0775	-0.0336	-0.1012	0.0022	0.0287	0.0765	0.0526	0.1088	0.1468	-0.2231	-0.2272	-0.167	-0.1267	0.2479	0.0001	0.439	-0.0097	0.0919	0.2362	0.0394	0.3644	6.629	67.1123	98.7193
25	0.0032	-0.019	-0.0097	0.305	0.1151	0.0443	-0.4281	0.0935	0.3259	-0.0561	-0.0512	0.0725	0.0044	0.1582	-0.1773	0.6183	-0.0726	0.0373	-0.1115	0.5271	-0.1042	2.6827	74.9294	91.8885
26	0.2792	0.1126	-0.1706	0.0284	0.0109	0.1045	0.0468	0.0077	-0.0031	-0.0438	-0.1205	-0.0167	-0.0386	-0.0722	0	0.323	0.0424	0.0571	0.1984	0.0172	0.2614	-3.5197	68.2739	100.4656
27	0.0412	-0.0063	-0.0637	0.0936	0.0251	0.0539	0.0408	0.0743	0.1034	-0.1725	-0.0576	-0.253	-0.1661	-0.0312	-0	0.3665	0.0222	0.0996	0.1836	-0.0009	0.3601	6.8389	67.2046	94.8396
28	0.0016	0.0054	0.0069	0.0131	0.0316	0.0388	0.0699	-0.042	0.1184	-0.2591	0.257	-0.2205	0.1419	0.017	0.0009	0.3281	-0.0143	0.1577	0.2857	-0.0001	0.5342	17.2876	66.2805	98.0766
29	0.0141	-0.0149	0.0113	-0.0038	0.004	0.0005	0.0597	0.0856	-0.0022	-0.0227	0.0627	-0.0478	0.073	0.0298	-0	0.4895	0.0364	0.0162	0.3661	0.0143	0.3563	-3.4412	65.5976	85.835
30	0.1967	-0.2427	0.0644	0.2016	-0.0752	0.0366	-0.1234	-0.1457	-0.1598	-0.1797	-0.0469	-0.1168	0.2435	0.2539	0	0.2996	-0.0161	0.0617	0.3951	0.0819	0.4278	20.9979	57.6671	135.2242
31	0.0747	-0.0599	-0.0896	0.0096	0.0314	0.0375	-0.1295	-0.3956	0.146	0.1474	0.1964	-0.0533	-0.0967	0.2745	0	0.3459	-0.0605	0.0026	0.505	0.071	0.4274	14.8135	65.3545	154.8187
32	0.3842	0.0762	-0.0107	0.1639	-0.158	0.0747	-0.0188	-0.1228	0.0243	-0.2181	0.062	-0.1288	0.1346	0.0535	-0.1623	0.2792	-0.034	0.1046	0.2747	0.0613	0.3975	17.6002	71.9652	116.3363
33	0.0987	-0.0281	0.0394	0.081	-0.0612	0.0829	-0.0102	0.0362	-0.0668	-0.0212	0.1035	-0.0917	-0.0962	-0.0727	0.0056	0.194	-0.0744	0.0827	0.17	-0.0277	0.3343	7.4026	77.7648	124.2277
34	-0.0067	0.0133	-0.0005	0.0163	0.0035	0.0058	-0.1101	-0.0076	-0.0229	-0.132	0.1498	0.0975	-0.0531	-0.0243	-0	0.4401	-0.0208	0.0953	0.178	0.0401	0.4087	16.2216	85.3292	105.7288
35	0.2682	-0.1305	-0.3991	-0.046	-0.0665	0.2794	0.1291	-0.5814	0.4537	0.0807	0.6108	-0.1808	-0.1261	0.3627	0.6087	0.0741	-0.3758	0.1693	0.0082	0.1657	0.4582	24.1647	76.6591	119.963
36	0.0095	0.0153	0.0019	0.0173	0.0067	0.0015	-0.1202	0.0429	0.0209	-0.1356	0.0021	-0.1279	-0.1784	-0.0448	-0	0.2966	-0.023	-0.0171	0.3193	0.1385	0.3549	-3.1396	72.0559	135.2251
37	0.007	0.0036	0.0068	0.0028	-0.0061	-0.0017	-0.1648	0.0602	-0.4568	0.1896	-0.0699	0.0161	0.3264	0.2106	0	0.3029	0.0164	0.078	0.3949	0.0298	0.3502	7.8408	51.8128	131.2621
38	0.1716	-0.0411	0.0986	0.0094	-0.0336	0.1239	-0.0672	0.2337	0.0516	-0.1304	0.0585	-0.1221	-0.1781	-0.0317	-0.0002	0.1875	-0.0597	0.0137	0.286	0.017	0.2555	-5.0579	65.3457	140.5303
39	0.0401	-0.0452	0.0826	0.0442	0.017	0.4353	-0.1606	0.2363	-0.0173	-0.0933	-0.1208	-0.2263	-0.3613	0.049	-0.0148	0.23	-0.0676	0.0256	0.3661	-0.0422	0.2002	-10.3313	55.8779	133.3259
40	0.015	-0.0097	-0.0124	0.0124	-0.0265	0.0308	-0.1963	-0.2325	0.1148	-0.0969	0.0888	0.0249	0.0224	-0.1685	-0	0.207	-0.0312	0.0013	0.2164	0.009	0.2185	-6.342	58.1118	149.5804
41	0.02	-0.0043	-0.0026	0.0027	0.0023	0.0009	-0.1286	0.0724	-0.1616	-0.1508	-0.0646	-0.1069	0.1418	-0.0383	-0	0.4536	-0.0135	-0.0426	0.4459	-0.0245	0.4236	-5.0474	47.1108	140.3561
42	-0.0138	0.0204	-0.024	0.0013	0.0065	-0.0091	0.0944	-0.0131	-0.008	0.1613	-0.1508	-0.1722	0.044	-0.0606	0	0.1841	-0.0541	-0.0129	0.1879	0.047	0.3254	0.613	62.1535	144.4566
43	0.0085	-0.003	-0.0143	-0.0058	0.0074	0.0062	0.0542	0.1894	-0.0673	-0.025	0.0448	-0.0729	-0.0555	-0.2298	0	0.4916	-0.0065	0.0399	0.3968	-0.0903	0.4756	1.0069	47.7455	132.5943
44	0.0784	0.0014	0.0725	0.1615	-0.0566	0.0986	-0.2659	0.0311	0.1919	-0.0667	0.2751	0.1661	-0.0138	-0.1418	-0.0572	-0.0038	-0.1226	0.074	0.483	-0.0166	0.3083	-9.1118	65.0538	137.6939
45	0.011	0.0114	0.0021	0.0095	-0.0094	0.0111	-0.2027	-0.0124	0.3071	0.0633	-0.0858	0.1661	-0.1185	-0.0319	-0	0.2112	0.0206	0.0458	0.3076	0.0008	0.3736	-15.4512	70.9794	139.0069
46	0.4753	-0.136	0.4385	0.5693	0.2962	0.7377	0.1496	0.3026	0.1554	0.0063	0.2913	0.0505	0.0198	0.2953	0.2275	0.3062	-0.1952	0.2189	0.4156	0.0484	0.2793	0.6807	58.3414	128.0078
47	0.1991	-0.1285	0.1737	0.3395	0.1425	0.1749	-0.1078	-0.2733	0.1957	0.0543	-0.0386	0.0211	-0.2506	-0.161	-0.0473	0.327	0.0979	-0.0924	0.4381	-0.1082	0.2675	-14.1321	72.8806	186.3398
48	0.127	-0.0728	0.1993	0.4151	0.2402	0.2103	-0.0383	-0.0503	0.111	0.0311	0.0166	-0.0642	-0.1555	-0.1527	-0	0.1359	0.0018	-0.0285	0.2502	-0.0062	0.2135	-21.0877	62.9448	153.4594
49	-0.0028	-0.0707	0.0068	0.0427	0.0947	0.0733	0.149	-0.0614	-0.1127	0.0079	0.072	0.076	0.2868	-0.0069	0	0.1745	-0.0162	-0.0226	0.2314	-0.0109	0.2132	-21.8557	54.2989	152.8781
50	0.3257	-0.3743	0.1302	-0.0091	0.1221	0.0038	-0.1406	-0.1211	0.1117	-0.1529	0.2292	0.0897	0.1364	-0.4119	0.1381	-0.013	0.1166	-0.0109	0.4622	-0.1052	0.2557	-29.1094	66.7801	162.0452
51	0.0199	-0.0057	0.0089	0.0113	0.0033	0.0032	-0.0865	0.0214	-0.0955	-0.1335	-0.1514	0.0418	-0.2459	0.0606	-0	0.2197	0.045	-0.0091	0.358	-0.0701	0.3076	-4.2168	52.3912	176.9641
52	0.0646	0.0074	0.1158	0.0098	0.0283	0.082	0.0324	0.1021	-0.0395	0.1498	-0.2427	0.0711	-0.0942	0.0052	-0.0054	0.2642	-0.0213	-0.0833	0.3035	-0.014	0.3218	-2.6005	64.9194	178.7564
53	0.0653	-0.0685	-0.043	0.0463	0.0507	0.0357	-0.0212	0.2796	-0.0827	0.2228	-0.0133	-0.1188	0.0841	0.2973	-0	0.2659	-0.0016	-0.0041	0.4253	0.0372	0.2051	4.4521	55.8303	182.7496
54	0.0353	0.0152	0.0294	0.0476	0.0101	0.0265	-0.0347	0.1448	0.2502	0.0958	-0.2734	-0.08	0.334	0.0377	0.0003	0.2344	0.0257	0.0369	0.4048	0.0734	0.2451	10.8688	61.0126	176.3795
55	0.212	-0.2136	-0.2726	0.2082	0.2935	0.3706	-0.3509	-0.0223	0.2053	0.2148	0.1416	-0.0711	0.0764	0.0695	-0.0536	0.2324	-0.0663	-0.0757	0.2808	-0.0124	0.2615	8.1915	65.4005	188.4324
56	0.0568	-0.0208	0.082	0.0393	0.0163	0.0368	0.0489	-0.2543	0.0092	0.3481	-0.1543	0.0161	-0.1141	-0.1878	0	0.2535	-0.0012	-0.0541	0.2865	-0.0322	0.2145	-1.9416	62.2874	186.5638
57	0.0038	-0.0041	0.0041	-0.0004	-0.0016	0.0034	-0.0627	0.1098	0.1839	-0.0807	0.0071	-0.1414	-0.1014	0.1202	0	0.4226	-0.1083	-0.08	0.3878	0.0348	0.4003	6.6597	74.6485	175.5372
58	0.0252	-0.0176	0.0189	0.0032	-0.0159	0.0011	-0.0257	0.1275	-0.0211	0.0343	-0.0522	-0.1493	-0.0253	-0.1635	-0	0.3246	0.044	-0.0206	0.4631	0.0063	0.3009	4.5755	55.9104	178.8556
59	0.0142	0.0045	0.012	0.0039	0.0023	0.0069	0.2374	0.1306	-0.1156	-0.0255	-0.0671	0.0109	0.0281	-0.095	0	0.281	0.0579	-0.06	0.2662	-0.0068	0.3103	6.0376	45.4322	181.5814
60	0.0005	0.0271	0.0047	0.0259	-0.0232	0.006	0.0552	0.1912	-0.0773	-0.0581	0.0981	-0.0796	-0.2077	0.1761	-0.0001	0.3523	-0.0621	-0.0827	0.4764	0.0462	0.3169	1.0509	67.5177	170.1121
61	0.034	0.0079	-0.1211	0.2655	0.0196	0.1282	-0.022	0.0286	0.0147	0.262	-0.063	0.2406	0.4203	-0.2206	0.0046	0.5904	-0.1186	0.0849	0.3225	-0.0799	0.3952	-47.035	86.933	163.6445
62	0.0672	0.1443	0.0166	0.229	-0.0765	0.0373	0.0038	0.0188	-0.0267	-0.0109	-0.1716	0.0565	0.0884	0.1148	-0.0063	0.2857	0.0696	-0.0227	0.1888	-0.0164	0.2265	-32.1551	84.7501	126.6976
63	0.147	0.0987	0.0265	0.1829	0.0924	0.0127	0.0546	-0.0139	0.1309	0.0009	-0.0725	-0.0525	-0.1621	0.2239	-0	0.3403	0.0441	-0.009	0.2982	0.0003	0.3055	-25.5058	91.8671	137.846
64	-0.2176	0.0108	-0.1883	0.9336	-0.0765	0.0502	0.1701	0.0289	-0.153	0.228	-0.2299	0.004	-0.0572	0.231	0.0473	0.328	0.013	-0.0204	0.2604	0.0073	0.2799	-31.7961	77.8368	141.5415
65	0.0192	0.0001	0.0045	0.0084	0.0012	-0.0009	-0.0895	0.1514	0.1031	-0.0404	-0.2589	-0.0351	-0.2009	-0.0062	-0.0008	0.4154	0.0442	0.0906	0.3064	-0.0388	0.4235	-31.7806	104.7113	157.3024
66	0.0124	-0.0341	-0.029	0.0881	0.025	0.0115	-0.0434	0.2173	-0.0831	-0.136	-0.0088	-0.0182	0.4443	0.1151	-0	0.3783	-0.0089	0.0198	0.3138	-0.0511	0.2937	-43.4992	101.1069	158.2954
67	0.0379	-0.0102	-0.0639	0.0614	-0.0223	0.0522	-0.2357	0.0874	0.0446	0.027	0.1029	0.0765	-0.1019	-0.0624	0.0001	0.3201	-0.0256	-0.0019	0.3042	0.007	0.2184	-39.172	110.7406	163.309
68	0.007	-0.0283	-0.033	0.0494	0.0345	0.0502	-0.1625	0.0474	0.0749	0.0151	-0.1107	0.199	0.0161	0.2287	0	0.366	0.0122	-0.0232	0.2544	0.0289	0.2896	-46.0281	112.0164	163.788

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'J' and (resid 62 through 67 )	J	62 - 67
2	X-RAY DIFFRACTION	2	chain 'J' and (resid 68 through 83 )	J	68 - 83
3	X-RAY DIFFRACTION	3	chain 'J' and (resid 84 through 102 )	J	84 - 102
4	X-RAY DIFFRACTION	4	chain 'J' and (resid 103 through 109 )	J	103 - 109
5	X-RAY DIFFRACTION	5	chain 'J' and (resid 110 through 117 )	J	110 - 117
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 39 through 149 )	A	39 - 149
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 150 through 230 )	A	150 - 230
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 231 through 322 )	A	231 - 322
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 39 )	B	1 - 39
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 40 through 51 )	B	40 - 51
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 52 through 67 )	B	52 - 67
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 68 through 91 )	B	68 - 91
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 92 through 102 )	B	92 - 102
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 103 through 109 )	B	103 - 109
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 110 through 119 )	B	110 - 119
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 43 through 116 )	C	43 - 116
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 117 through 130 )	C	117 - 130
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 131 through 206 )	C	131 - 206
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 207 through 261 )	C	207 - 261
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 262 through 320 )	C	262 - 320
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 1 through 7 )	D	1 - 7
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 8 through 17 )	D	8 - 17
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 18 through 28 )	D	18 - 28
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 29 through 39 )	D	29 - 39
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 40 through 51 )	D	40 - 51
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 52 through 91 )	D	52 - 91
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 92 through 101 )	D	92 - 101
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 102 through 109 )	D	102 - 109
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 110 through 118 )	D	110 - 118
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 42 through 101 )	E	42 - 101
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 102 through 130 )	E	102 - 130
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 131 through 206 )	E	131 - 206
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 207 through 250 )	E	207 - 250
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 251 through 261 )	E	251 - 261
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 262 through 322 )	E	262 - 322
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 1 through 7 )	F	1 - 7
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 8 through 17 )	F	8 - 17
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 18 through 39 )	F	18 - 39
39	X-RAY DIFFRACTION	39	chain 'F' and (resid 40 through 51 )	F	40 - 51
40	X-RAY DIFFRACTION	40	chain 'F' and (resid 52 through 61 )	F	52 - 61
41	X-RAY DIFFRACTION	41	chain 'F' and (resid 62 through 67 )	F	62 - 67
42	X-RAY DIFFRACTION	42	chain 'F' and (resid 68 through 83 )	F	68 - 83
43	X-RAY DIFFRACTION	43	chain 'F' and (resid 84 through 91 )	F	84 - 91
44	X-RAY DIFFRACTION	44	chain 'F' and (resid 92 through 102 )	F	92 - 102
45	X-RAY DIFFRACTION	45	chain 'F' and (resid 103 through 109 )	F	103 - 109
46	X-RAY DIFFRACTION	46	chain 'F' and (resid 110 through 118 )	F	110 - 118
47	X-RAY DIFFRACTION	47	chain 'G' and (resid 42 through 149 )	G	42 - 149
48	X-RAY DIFFRACTION	48	chain 'G' and (resid 150 through 230 )	G	150 - 230
49	X-RAY DIFFRACTION	49	chain 'G' and (resid 231 through 267 )	G	231 - 267
50	X-RAY DIFFRACTION	50	chain 'G' and (resid 268 through 320 )	G	268 - 320
51	X-RAY DIFFRACTION	51	chain 'H' and (resid 1 through 7 )	H	1 - 7
52	X-RAY DIFFRACTION	52	chain 'H' and (resid 8 through 28 )	H	8 - 28
53	X-RAY DIFFRACTION	53	chain 'H' and (resid 29 through 39 )	H	29 - 39
54	X-RAY DIFFRACTION	54	chain 'H' and (resid 40 through 51 )	H	40 - 51
55	X-RAY DIFFRACTION	55	chain 'H' and (resid 52 through 67 )	H	52 - 67
56	X-RAY DIFFRACTION	56	chain 'H' and (resid 68 through 83 )	H	68 - 83
57	X-RAY DIFFRACTION	57	chain 'H' and (resid 84 through 91 )	H	84 - 91
58	X-RAY DIFFRACTION	58	chain 'H' and (resid 92 through 101 )	H	92 - 101
59	X-RAY DIFFRACTION	59	chain 'H' and (resid 102 through 109 )	H	102 - 109
60	X-RAY DIFFRACTION	60	chain 'H' and (resid 110 through 119 )	H	110 - 119
61	X-RAY DIFFRACTION	61	chain 'I' and (resid 42 through 149 )	I	42 - 149
62	X-RAY DIFFRACTION	62	chain 'I' and (resid 150 through 206 )	I	150 - 206
63	X-RAY DIFFRACTION	63	chain 'I' and (resid 207 through 268 )	I	207 - 268
64	X-RAY DIFFRACTION	64	chain 'I' and (resid 269 through 321 )	I	269 - 321
65	X-RAY DIFFRACTION	65	chain 'J' and (resid 1 through 7 )	J	1 - 7
66	X-RAY DIFFRACTION	66	chain 'J' and (resid 8 through 28 )	J	8 - 28
67	X-RAY DIFFRACTION	67	chain 'J' and (resid 29 through 39 )	J	29 - 39
68	X-RAY DIFFRACTION	68	chain 'J' and (resid 40 through 61 )	J	40 - 61

-
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