PDB-7ek9: Crystal structure of apo streptavidin at cryogenic temperature

ID or keywords:

Entry

Database: PDB / ID: 7ek9

Title

Crystal structure of apo streptavidin at cryogenic temperature

Components

Streptavidin

Keywords

STRUCTURAL PROTEIN / Streptavidin / cooperative allostery / ambient temperature / cryogenic temperature

Function / homology

Function and homology information

biotin binding / extracellular region
Similarity search - Function

Biological species

Streptomyces avidinii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.1 Å

Authors

DeMirci, H. / Ayan, E. / Destan, E. / Ertem, F.B.

Funding support

United States,

Turkey, 2items

Citation

Journal: To Be Published
Title: Crystal structure of apo streptavidin at cryogenic temperature
Authors: DeMirci, H.

History

Deposition	Apr 4, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 29, 2021	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ek9.cif.gz	231.9 KB	Display	PDBx/mmCIF format
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Others	Other downloads

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Validation report

Summary document	7ek9_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	7ek9_full_validation.pdf.gz	1.5 MB	Display
Data in XML	7ek9_validation.xml.gz	27.8 KB	Display
Data in CIF	7ek9_validation.cif.gz	41.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ek/7ek9 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/7ek9	HTTPS FTP

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Related structure data

Similar structure data	1kl5-d 4cpi-2 4bx5-d 4cph-d 4y59-d 1lcv-1 6avk-1 5b5g-d 6lng-1 4y5d-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Streptavidin

B: Streptavidin

C: Streptavidin

D: Streptavidin

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: native gel electrophoresis

Unit cell

Length a, b, c (Å)	46.373, 85.946, 58.188
Angle α, β, γ (deg.)	90.000, 98.730, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Streptavidin Mass: 12981.024 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Chemical	ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.28 %
Crystal grow	Temperature: 294 K / Method: microbatch / pH: 6 / Details: Pact PremierTM 100 mM MMT buffer, PEG 1500

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.1→18 Å / Num. obs: 147496 / % possible obs: 80.7 % / Redundancy: 2.1 % / R_merge(I) obs: 0.058 / R_pim(I) all: 0.045 / R_rim(I) all: 0.074 / Χ²: 1.119 / Net I/σ(I): 12.9 / Num. measured all: 316645

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.1-1.14	1.7	0.354	8700	0.769	0.296	0.464	0.754	47.8
1.14-1.18	1.9	0.274	12508	0.855	0.219	0.352	0.897	68.6
1.18-1.24	2.2	0.253	15787	0.892	0.195	0.321	0.856	86.7
1.24-1.3	2.2	0.193	15710	0.934	0.15	0.245	0.99	86.3
1.3-1.39	2.2	0.142	15850	0.96	0.109	0.181	1.075	87
1.39-1.49	2.2	0.106	16081	0.975	0.082	0.135	1.225	87.9
1.49-1.64	2.2	0.081	15902	0.984	0.062	0.102	1.341	87.3
1.64-1.88	2.2	0.064	16208	0.988	0.05	0.082	1.35	88.6
1.88-2.37	2.2	0.053	16172	0.991	0.041	0.067	1.302	88.3
2.37-18	2.1	0.045	14578	0.993	0.036	0.058	1.026	78.9

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX	1.19	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.1→17.896 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1871	7384	5.02 %
R_work	0.1587	139839	-
obs	0.1602	147223	80.89 %

Solvent computation

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

Displacement parameters

B_iso max: 100.85 Å² / B_iso mean: 20.9826 Å² / B_iso min: 6.3 Å²

Refinement step

Cycle: final / Resolution: 1.1→17.896 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3580	0	32	624	4236
B_iso mean	-	-	29.03	34.26	-
Num. residues	-	-	-	-	482

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.1-1.1125	0.2419	141	0.2158	2405	42
1.1125-1.1256	0.2485	147	0.2171	2815	49
1.1256-1.1393	0.2336	163	0.2061	3119	54
1.1393-1.1537	0.2341	180	0.1979	3433	60
1.1537-1.1689	0.2237	215	0.1918	3981	69
1.1689-1.1849	0.2022	233	0.1884	4529	79
1.1849-1.2018	0.1967	290	0.1846	4897	86
1.2018-1.2198	0.2123	271	0.1886	5074	87
1.2198-1.2388	0.2183	261	0.1882	4965	87
1.2388-1.2591	0.1969	243	0.1882	5044	87
1.2591-1.2808	0.2023	244	0.1822	5037	87
1.2808-1.3041	0.2056	279	0.1785	4785	84
1.3041-1.3292	0.1971	252	0.1744	4891	84
1.3292-1.3563	0.183	267	0.1727	5075	88
1.3563-1.3858	0.1968	278	0.1687	5059	89
1.3858-1.418	0.1802	257	0.1637	5123	88
1.418-1.4535	0.1776	267	0.1623	5081	88
1.4535-1.4928	0.1693	248	0.1585	5022	87
1.4928-1.5367	0.1712	276	0.152	4747	83
1.5367-1.5862	0.1724	270	0.1522	5141	89
1.5862-1.6429	0.1717	256	0.1534	5189	90
1.6429-1.7086	0.1801	279	0.1463	5180	90
1.7086-1.7863	0.173	271	0.151	5158	89
1.7863-1.8804	0.1854	267	0.1503	4989	86
1.8804-1.9981	0.1728	263	0.1452	4995	86
1.9981-2.1521	0.1704	251	0.1407	5175	89
2.1521-2.3682	0.1614	270	0.1474	5157	90
2.3682-2.7099	0.1914	267	0.1581	4923	85
2.7099-3.4103	0.1912	248	0.1498	4429	76
3.4103-17.896	0.2023	230	0.1624	4421	75

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	2.127	-0.5574	-1.2845	1.9021	-1.0305	3.0074	-0.0619	-0.0425	-0.2384	-0.2024	-0.0526	-0.0314	0.5609	-0.0611	0.0935	0.3261	-0.0191	0.038	0.0869	-0.0172	0.1565	64.1685	-22.8961	15.4706
2	1.7801	0.3732	-0.1339	2.5343	0.7068	8.0074	-0.0231	0.0621	0.084	-0.4222	-0.1482	-0.1778	0.2393	0.2347	0.1499	0.2881	0.034	0.0638	0.087	-0.0018	0.1543	69.7127	-14.4604	11.6796
3	4.0601	4.3276	-2.586	5.1088	-3.7728	3.7657	0.1184	-0.2567	-0.155	0.1626	0.0497	0.4295	0.1964	-0.0255	-0.0728	0.2859	-0.0292	0.0375	0.0927	0.0244	0.2192	59.8791	-22.345	23.7169
4	4.8968	-0.8524	-1.4781	1.7235	-0.9323	2.1221	-0.033	-0.1406	-0.3346	-0.1222	0.0051	-0.0146	0.3051	0.0038	0.0397	0.1988	-0.0202	0.0001	0.0907	-0.0052	0.1198	62.7621	-18.4175	24.6598
5	5.4062	5.4175	-0.1355	9.3273	-1.964	7.3614	0.0138	-0.0472	-0.1098	-0.3871	-0.1739	-0.5559	-0.2457	0.4278	0.0982	0.2245	0.0289	0.0879	0.1475	0.0294	0.2229	75.061	-9.8583	18.1635
6	2.2206	-0.099	0.9171	6.2935	0.3744	7.9256	-0.0341	0.2852	-0.8183	-0.2668	-0.0308	-1.2041	0.4479	0.503	-0.0208	0.1774	0.0329	0.0566	0.137	-0.0115	0.2851	75.3709	-14.5264	24.077
7	8.2344	1.8047	0.1862	1.378	0.1207	0.3694	-0.1431	-0.1333	-0.0318	-0.0744	0.0645	-0.0444	0.237	-0.0793	0.0817	0.1277	-0.0209	-0.0069	0.087	0.0181	0.0993	60.3884	-15.2953	27.0908
8	2.6846	0.7762	0.8446	0.7139	0.624	0.5577	-0.084	0.1411	-0.5206	-0.1791	0.0949	0.1741	0.2028	-0.1777	-0.0478	0.2904	-0.1337	-0.0373	0.1567	0.0132	0.2242	48.0894	-21.0709	20.5199
9	2.1922	1.7398	2.1504	1.5382	1.615	2.1625	-0.0939	0.0639	-0.074	-0.1594	-0.2823	0.7648	0.2584	-0.4218	0.2942	0.3851	-0.329	-0.1316	0.0845	-0.0935	0.2285	46.2746	-20.0942	13.017
10	5.9025	-1.4775	-1.6482	0.6625	0.4676	0.5577	-0.1676	0.0471	-0.2033	-0.2144	0.0857	0.0523	0.2727	-0.111	0.0306	0.1299	-0.0348	-0.0157	0.0554	0.0177	0.0757	60.2905	-12.5046	21.8093
11	3.0639	-0.4	4.645	5.5783	2.649	9.0206	-0.1023	-0.1064	-0.1419	0.1586	0.1169	-0.3022	0.0975	0.3392	-0.0463	0.0702	-0.0087	-0.0057	0.1089	0.016	0.1248	72.9007	-9.377	28.0955
12	2.3464	1.6421	1.1899	1.9874	-1.0986	5.5395	-0.1209	0.0298	0.0646	-0.1107	0.0566	-0.9142	0.2683	0.573	-0.0237	0.1093	0.006	0.0101	0.1779	-0.0038	0.229	77.3864	-7.4848	27.6808
13	3.478	3.65	3.0649	4.338	3.6332	3.8923	-0.0159	-0.0456	-0.1085	-0.0498	0.0473	-0.0797	0.1527	-0.0664	-0.0186	0.1248	-0.0215	-0.0147	0.0701	0.0087	0.0853	63.2087	-6.9725	20.8247
14	2.2098	-0.0625	0.1767	0.5909	-0.2828	0.461	-0.0651	0.2932	-0.6431	-0.441	0.1736	-0.0513	0.2619	-0.0253	-0.2266	0.412	-0.2348	-0.0893	-0.004	-0.0894	0.1979	54.1468	-20.5145	10.7219
15	1.2413	-0.4246	-0.0285	2.1891	-0.434	0.0968	-0.0399	0.3242	-0.3911	-0.3555	0.0185	-0.0226	0.2694	-0.0493	-0.1391	0.3725	-0.0912	-0.03	0.1088	-0.0584	0.172	58.5994	-17.6391	9.6107
16	5.1392	2.2418	-0.6024	4.3672	5.2746	9.4204	-0.0742	0.0015	0.0944	-0.0889	0.0195	0.0255	-0.0913	0.0323	0.0687	0.111	-0.0047	-0.0321	0.0368	0.015	0.0878	63.3068	-2.4866	18.5583
17	5.5701	0.9772	3.5516	5.8024	-3.9826	6.033	-0.0526	-0.5358	0.6343	0.5504	-0.1122	0.3048	-0.6831	-0.1568	0.1627	0.2485	-0.0578	-0.0222	0.1409	-0.0529	0.1841	66.586	11.1914	25.9365
18	1.0982	0.8487	-0.5489	6.6806	1.0968	0.6643	-0.0645	-0.0519	0.3014	-0.1247	-0.0022	-0.1535	-0.4807	0.1642	0.0233	0.1613	-0.0295	-0.0227	0.073	-0.0033	0.1277	64.7486	5.813	17.8553
19	1.6163	-1.787	-0.8914	3.6279	2.2896	1.518	0.0037	0.131	-0.0644	-0.6702	-0.06	0.0513	0.2341	-0.0749	0.0313	0.2559	-0.0368	0.0098	0.0677	-0.0104	0.1099	62.6666	-11.2517	10.6155
20	1.7366	-1.3093	0.0554	7.935	4.0345	2.5049	0.1028	0.2558	-0.0452	-0.6259	0.064	-0.662	-0.2257	0.1147	-0.1022	0.6362	0.1099	0.094	0.1532	0.0043	0.2484	68.4545	-21.5253	8.4648
21	3.0369	-2.6804	4.5424	3.175	-2.7588	8.7267	-0.0734	-0.8274	0.2907	0.2721	0.0425	-0.317	-0.4763	0.5819	0.0149	0.1581	-0.0053	-0.003	0.2046	-0.0466	0.1163	59.1111	-1.6594	40.0848
22	4.6299	-0.9625	4.9407	4.8934	-0.4889	5.3354	-0.1368	0.726	0.6257	-0.5469	-0.0565	0.2471	-0.499	0.0934	0.3178	0.1724	0.0051	-0.0318	0.2394	0.0467	0.1239	48.5767	2.9176	32.9715
23	5.8724	-5.7433	5.6668	5.6881	-5.4945	5.5106	-0.1455	-0.4106	-0.3796	-0.0973	0.5421	0.4961	-0.5275	-0.4724	-0.3086	0.16	0.0158	-0.008	0.1368	0.0144	0.1518	50.1328	-3.8645	35.1732
24	7.2241	7.5235	-0.0173	8.5768	-1.8094	4.3292	-0.0707	0.1497	-0.9961	-0.101	0.0552	-0.7021	1.0748	1.4772	0.0004	0.2566	0.1375	0.0039	0.4506	-0.0111	0.1691	64.8098	-10.3093	38.3164
25	0.6584	-0.848	0.8851	4.711	-0.7735	4.9235	-0.1582	-0.5057	0.1545	0.0485	0.1799	0.5526	-0.1031	-0.4832	0.0487	0.1279	-0.0048	-0.0096	0.1401	0.0044	0.1564	50.3566	-7.6752	34.2986
26	2.4254	-0.1603	1.4074	7.3655	1.4255	1.7114	0.1948	-0.6729	0.3546	0.6535	-0.1719	0.6375	-0.0115	-0.0039	-0.046	0.1739	-0.0519	0.0012	0.2036	0.0654	0.372	39.2625	-10.9193	34.3321
27	4.139	4.1099	-1.1429	4.2086	-0.9084	0.6939	0.046	-0.2199	0.025	-0.0168	0.0316	0.1221	0.1383	-0.1287	-0.0453	0.0924	-0.024	-0.0139	0.1238	0.0288	0.068	54.4181	-11.3621	30.6739
28	4.076	5.6566	-0.3186	7.8805	-0.7559	6.8035	0.1687	-0.6755	0.2507	0.4353	-0.26	-0.3107	-0.2462	0.3093	0.0157	0.1424	-0.0061	-0.0269	0.1759	-0.0169	0.1644	69.363	-2.8543	33.9402
29	7.6649	2.1514	2.4283	2.5206	0.957	5.5911	0.0812	-0.4107	0.5345	0.4616	-0.0256	-0.6928	-0.6341	0.4264	0.0174	0.219	-0.069	-0.0404	0.1627	-0.0613	0.2277	70.1154	5.1309	32.0988
30	7.7821	-0.0863	-1.2153	3.4876	-2.3398	3.6466	-0.0927	-0.1982	-0.0379	-0.0042	0.135	0.0425	0.0256	-0.1413	-0.0159	0.0784	-0.0132	-0.0118	0.0753	0.0091	0.0425	56.8435	-6.3604	27.887
31	3.8525	3.44	-4.8094	8.9944	-0.5927	8.8939	-0.4007	-0.152	-0.3245	0.103	0.0568	0.3252	0.3081	0.0202	0.3181	0.1043	-0.0272	-0.0201	0.1229	0.0613	0.1687	43.4326	-15.7196	27.9752
32	1.765	1.4316	0.7232	4.9973	1.4443	1.1063	-0.1262	0.0116	-0.2445	-0.1801	-0.0061	0.3144	-0.0933	-0.2556	0.129	0.2388	-0.1174	-0.0757	0.1974	0.0491	0.1831	42.4514	-14.5491	21.6663
33	6.8839	5.3458	2.438	7.0633	3.0833	1.3558	-0.14	0.0551	-0.1293	-0.2097	0.1801	-0.0466	0.1535	-0.0958	-0.0451	0.1334	-0.0483	-0.0249	0.096	0.0191	0.0624	54.7133	-5.0281	23.6122
34	1.3967	-0.356	0.0992	5.4983	1.3019	0.9373	-0.0266	-0.6469	0.6624	0.5511	0.0794	0.0149	-0.843	0.0861	-0.1697	0.2509	-0.022	-0.0143	0.2387	-0.0964	0.1612	61.7131	6.0339	34.7344
35	3.4308	1.2468	1.6107	6.0144	3.6177	2.4114	0.0877	-0.4279	0.5052	0.0592	0.0202	0.0152	-0.8514	-0.2105	-0.1277	0.2182	0.0159	0.018	0.1347	-0.0568	0.1242	57.3324	7.0798	32.7804
36	4.831	0.8928	3.9843	7.6833	5.6666	6.5258	0.0536	-0.0923	-0.0385	-0.0407	0.0233	0.0019	0.1178	-0.2007	-0.0804	0.1059	-0.0413	-0.0101	0.0872	0.0199	0.0496	53.3264	-1.4402	20.4551
37	5.7436	6.2643	5.0878	7.4613	4.7516	5.5114	-0.1111	0.4013	-0.3415	-0.6247	0.4109	-0.3356	0.2853	0.0412	-0.3676	0.3774	-0.1421	-0.0626	0.181	0.0107	0.1799	48.2109	-13.7687	10.1396
38	0.0923	0.5707	0.5158	4.7003	4.1786	3.714	-0.1304	0.2075	-0.0846	-0.6818	0.0819	0.3908	0.0408	-0.3816	0.1511	0.2746	-0.0909	-0.0699	0.17	0.0114	0.1403	48.1704	-7.1887	8.6836
39	7.161	-6.5565	-5.6571	6.0093	5.1312	4.9506	-0.2107	-0.1488	0.1159	0.093	-0.0392	0.329	-0.3011	-0.5542	0.2514	0.126	0.0054	-0.0092	0.1034	-0.007	0.0788	51.8135	4.079	24.9573
40	2.904	-0.2291	-1.7304	9.9143	5.5633	4.0093	-0.0224	-0.469	0.1164	0.4277	-0.099	0.5308	0.3101	-0.1952	-0.0101	0.1821	-0.0001	0.0171	0.1757	-0.0186	0.1213	50.2684	4.5108	36.567
41	9.0598	4.6378	-0.2146	6.9234	-2.1241	4.1618	0.0558	-0.0924	-0.1055	-0.0841	-0.0157	-0.0641	0.0627	0.0297	-0.066	0.0795	0.0105	0.0106	0.088	-0.0178	0.0678	60.1405	0.6419	-9.9122
42	7.62	4.7683	-0.8782	3.4955	-2.0543	4.5446	-0.0098	-0.3803	-0.5146	0.0539	-0.1481	-0.1265	0.8908	0.1123	0.2459	0.2099	-0.0057	0.0469	0.1439	-0.0118	0.226	54.3005	-3.1869	-6.6073
43	4.0504	5.8651	2.4255	8.9732	3.0647	2.8696	-0.0611	0.2181	0.3207	-0.5258	0.0529	0.3061	-0.6488	0.0549	0.1277	0.1896	-0.0192	0.0365	0.0994	-0.0068	0.1568	60.103	11.1182	-10.3344
44	4.649	5.8982	3.8151	7.5245	4.7721	3.4318	-0.1808	0.1588	0.0479	-0.2774	0.0402	0.0433	-0.1653	-0.0031	0.1706	0.0816	0.0087	0.003	0.076	0.0007	0.0884	54.7546	8.7234	-7.5625
45	9.5955	-3.6212	3.4411	5.5507	2.3889	6.1915	0.0381	1.2542	-1.749	-1.7215	0.085	1.9454	1.3769	-1.7744	-0.1336	0.5086	-0.1779	-0.0741	0.4752	-0.1082	0.619	45.188	-2.5402	-10.7315
46	7.6456	4.0526	1.8642	2.7404	1.8494	2.2521	-0.1342	0.5653	-0.2382	-0.4859	0.059	0.3765	0.2121	-0.2362	0.0134	0.1517	-0.0192	-0.0458	0.1693	-0.0284	0.1694	44.1024	3.5915	-8.7935
47	7.726	4.7688	3.9485	7.4259	1.8398	7.784	-0.1403	0.0008	0.2013	-0.3658	0.0668	0.1911	-0.0943	-0.3017	0.0841	0.0593	-0.0014	-0.0142	0.0624	0.0137	0.0754	55.6621	11.6632	-3.5403
48	6.7658	-0.1969	3.3609	1.7247	0.3378	3.9726	-0.0671	0.3448	0.1199	-0.0667	-0.0352	-0.4596	-0.0947	0.394	0.1214	0.0922	-0.026	0.0143	0.1131	0.0278	0.1765	69.8508	12.0275	-2.9593
49	5.1257	-1.1431	2.6672	5.393	1.3909	5.4905	0.0129	0.3191	0.0222	-0.1832	0.0094	-0.6801	0.0478	0.6541	-0.0677	0.0665	-0.0124	0.0307	0.1551	0.0162	0.1822	74.4802	5.5134	-0.3548
50	8.1739	1.6645	0.0728	2.0299	-0.1728	1.3767	-0.0287	0.0349	-0.0704	-0.0803	0.0296	0.0537	0.0109	-0.0729	0.0102	0.06	-0.0005	-0.0099	0.0639	0.0114	0.0712	53.419	6.4159	-0.5086
51	6.5126	2.1161	1.6811	2.7579	2.1122	3.5636	-0.0639	0.5236	-0.1108	-0.4954	-0.0388	0.6915	-0.0849	-0.5976	0.0609	0.1047	0.0192	-0.042	0.2062	0.0037	0.1683	38.6032	6.5581	-6.43
52	2.0007	-0.3926	1.4455	1.706	0.1143	1.7228	-0.0307	-0.1402	-0.1277	0.0499	-0.0013	0.1882	0.0139	-0.245	0.0536	0.0587	0.008	0.0059	0.1117	0.0163	0.1255	42.2775	5.3781	3.2061
53	7.4576	0.5268	-1.7388	2.3169	0.2895	4.2136	-0.0534	-0.1575	-0.062	-0.0126	0.0583	-0.1295	-0.0885	0.1197	0.003	0.0492	-0.0072	-0.0046	0.045	0.0091	0.0681	59.3124	3.7111	2.6189
54	2.9323	-3.6344	-0.6246	4.9948	2.4975	6.2256	-0.0774	0.8518	-1.0193	-0.637	0.1224	-0.5581	1.1551	0.5687	-0.0916	0.2849	0.0373	0.0785	0.2754	-0.131	0.3114	69.9469	-1.9697	-6.9049
55	8.0247	0.2414	-3.6176	1.1958	-0.7633	2.1455	-0.2698	0.2359	-0.4492	-0.1606	0.0637	-0.1616	0.4409	0.0177	0.2661	0.1012	-0.0012	0.0147	0.0752	-0.0146	0.1063	61.2725	-1.6804	0.678
56	7.726	-3.6356	-5.4153	4.3172	3.0656	5.8559	-0.1133	0.1923	-0.2061	0.2328	-0.0461	0.4233	0.0027	-0.6011	0.1967	0.0841	0.0126	0.0192	0.1527	0.0259	0.1199	44.3655	4.8119	10.5988
57	6.1008	-4.7801	2.7876	4.9683	-1.0373	2.9584	-0.494	-0.883	-0.2241	1.0809	0.2812	0.4895	0.1775	-0.5144	0.1559	0.2423	0.022	0.0798	0.3613	0.0554	0.2074	40.6767	3.8035	19.407
58	7.6902	-4.8217	-1.8808	3.3672	2.4209	7.2846	-0.2553	-0.0429	-0.4121	0.2811	0.0821	0.2995	0.222	-0.4348	0.2635	0.103	-0.0271	0.0232	0.1046	0.0246	0.1284	48.0181	-0.1679	12.1651
59	7.3017	3.3078	-5.5397	1.8916	-2.8137	4.4416	-0.0602	-0.0391	-0.2271	0.1279	-0.1364	0.316	0.6935	-0.0193	0.1733	0.1575	-0.0157	0.0258	0.0709	-0.0038	0.1001	58.2649	-4.4713	1.0748
60	8.3411	-1.6643	5.8756	5.1103	2.1477	7.8057	-0.1227	0.7126	-1.679	-0.9132	0.0803	0.0373	1.3874	-0.6158	-0.063	0.3465	-0.0348	0.0147	0.2233	-0.0863	0.2685	60.6555	-7.1191	-10.6915
61	0.3675	1.0882	0.963	4.6371	1.9817	7.3874	-0.0072	0.0071	0.2735	0.0076	-0.0655	0.2342	-0.3573	-0.5064	0.0877	0.1631	0.0561	0.0038	0.1437	-0.0172	0.1695	47.4034	23.0532	9.5539
62	6.7801	-1.0373	3.2703	9.5508	-5.6864	7.4925	0.0868	-0.1222	-0.1244	0.1531	0.0117	-0.1401	-0.1188	0.5733	-0.1164	0.2354	0.0394	-0.0194	0.1873	-0.0591	0.1656	56.2467	20.2309	18.4493
63	7.6781	-1.8478	5.8282	2.7116	-1.8265	7.616	-0.0152	0.0506	-0.0527	0.0065	0.0898	0.1322	-0.2986	0.0143	-0.1015	0.1823	0.0493	-0.0012	0.1319	-0.0362	0.1793	51.503	22.3631	6.2849
64	5.6835	0.3584	0.885	4.8549	-0.0724	4.9928	-0.1089	0.1618	0.4567	-0.3502	0.016	0.2247	-0.3207	-0.191	0.1226	0.1295	0.0465	0.0137	0.0714	0.0076	0.1245	50.2486	19.2052	1.0379
65	6.64	-2.3045	-4.5691	4.8602	6.4909	9.1121	0.5088	-1.3116	1.039	0.9799	-0.2179	-0.6699	-0.999	0.6396	-0.3694	0.8112	-0.111	0.0965	0.6735	-0.3175	1.1204	65.2576	26.5214	11.7204
66	6.1032	-1.4883	-2.2398	6.4506	-3.5365	3.5631	-0.1128	-0.3842	0.6683	0.111	0.0197	-0.1229	-0.6714	-0.0542	0.1071	0.1431	-0.0017	0.019	0.0519	-0.0089	0.1418	60.8833	20.9441	4.136
67	3.9685	3.7848	-3.6509	4.9393	-2.4416	4.1692	0.0729	0.0018	0.2892	0.0746	0.0223	0.3813	-0.1133	-0.3243	-0.0682	0.0858	0.0218	-0.0178	0.1141	-0.0002	0.1127	41.9567	13.1455	1.8783
68	5.5383	-0.8784	-0.1309	2.8288	1.4349	0.7484	-0.1654	-0.3722	-0.0883	0.3146	0.0967	0.7039	0.1572	-0.6832	0.1025	0.1022	0.0187	0.0482	0.2921	0.0307	0.1991	36.1638	10.3966	9.9095
69	6.5237	4.0225	-0.1217	3.6374	-0.6974	2.5116	-0.0376	-0.0804	0.1524	0.0568	0.0221	0.056	-0.155	-0.1472	0.023	0.0735	0.0118	-0.0061	0.0654	0.0024	0.0783	53.0923	13.289	5.8512
70	3.1502	2.8034	-1.0274	2.765	-0.6278	2.4417	-0.0275	0.158	0.4172	-0.1394	0.0722	-0.2356	-0.4533	0.3036	-0.0251	0.1295	-0.0492	0.0142	0.106	0.0109	0.1776	67.4613	18.8068	3.1995
71	0.4593	1.3698	-0.9201	7.2063	-1.8799	2.1342	-0.0573	-0.1993	0.7369	0.3338	0.0204	-0.2243	-0.4742	0.2576	0.0028	0.1423	-0.0445	-0.0319	0.1109	-0.0145	0.2416	70.6738	16.5592	5.0977
72	7.6072	-0.6137	-2.0552	2.0268	0.329	3.3735	-0.0479	-0.1286	0.0901	0.0202	-0.0048	0.105	-0.1187	-0.1555	0.0494	0.0779	0.0185	-0.0091	0.075	-0.0016	0.078	51.0959	11.7785	9.812
73	2.8949	3.1656	0.4201	5.2513	-2.0807	3.6659	-0.001	-0.6306	0.8836	0.8471	0.0717	0.8772	-0.9038	-0.6102	-0.341	0.3225	0.1827	0.059	0.4122	-0.1605	0.3531	41.6623	18.7008	17.3104
74	8.2268	-3.7319	-0.8273	6.0892	1.4646	2.7173	-0.1125	-0.1825	-0.0951	0.2043	0.0159	0.194	-0.0752	-0.1747	0.0967	0.0614	0.0048	0.0068	0.063	0.0019	0.0468	53.405	9.3487	13.7716
75	4.393	-5.1782	-2.9063	6.5421	2.0911	5.9982	-0.0086	-0.1257	0.0722	-0.0613	-0.0153	-0.4899	0.3494	0.5204	-0.0305	0.1093	0.0173	0.0257	0.1291	0.0064	0.1767	70.3689	2.5935	6.2605
76	5.6828	-6.0188	-1.8208	8.3967	1.3591	7.8917	-0.0416	-0.0105	-0.3255	0.1596	-0.1915	-0.3523	0.4306	0.6039	0.2073	0.1159	0.0221	0.0133	0.1265	0.037	0.1647	70.1392	-0.9824	10.4162
77	5.0576	-4.5863	-5.4162	4.2942	4.7891	7.2996	-0.1952	-0.2948	0.3099	0.2232	0.1473	-0.0944	-0.175	-0.0189	0.0854	0.0971	0.0177	-0.0168	0.0937	-0.0054	0.0911	58.2118	8.04	16.4476
78	5.8648	0.0372	-1.2835	6.8498	2.2647	6.4369	-0.069	-0.3065	0.6041	0.555	0.0666	0.1581	-0.5857	-0.0797	0.032	0.232	0.0804	-0.0052	0.1359	-0.0404	0.1609	50.9745	21.6164	18.2438

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 16:22)	A	16 - 22
2	X-RAY DIFFRACTION	2	(chain A and resid 23:28)	A	23 - 28
3	X-RAY DIFFRACTION	3	(chain A and resid 29:36)	A	29 - 36
4	X-RAY DIFFRACTION	4	(chain A and resid 37:43)	A	37 - 43
5	X-RAY DIFFRACTION	5	(chain A and resid 44:50)	A	44 - 50
6	X-RAY DIFFRACTION	6	(chain A and resid 51:54)	A	51 - 54
7	X-RAY DIFFRACTION	7	(chain A and resid 55:59)	A	55 - 59
8	X-RAY DIFFRACTION	8	(chain A and resid 60:65)	A	60 - 65
9	X-RAY DIFFRACTION	9	(chain A and resid 66:72)	A	66 - 72
10	X-RAY DIFFRACTION	10	(chain A and resid 73:77)	A	73 - 77
11	X-RAY DIFFRACTION	11	(chain A and resid 78:82)	A	78 - 82
12	X-RAY DIFFRACTION	12	(chain A and resid 83:87)	A	83 - 87
13	X-RAY DIFFRACTION	13	(chain A and resid 88:93)	A	88 - 93
14	X-RAY DIFFRACTION	14	(chain A and resid 94:100)	A	94 - 100
15	X-RAY DIFFRACTION	15	(chain A and resid 101:106)	A	101 - 106
16	X-RAY DIFFRACTION	16	(chain A and resid 107:113)	A	107 - 113
17	X-RAY DIFFRACTION	17	(chain A and resid 114:119)	A	114 - 119
18	X-RAY DIFFRACTION	18	(chain A and resid 120:125)	A	120 - 125
19	X-RAY DIFFRACTION	19	(chain A and resid 126:130)	A	126 - 130
20	X-RAY DIFFRACTION	20	(chain A and resid 131:136)	A	131 - 136
21	X-RAY DIFFRACTION	21	(chain B and resid 14:20)	B	14 - 20
22	X-RAY DIFFRACTION	22	(chain B and resid 21:25)	B	21 - 25
23	X-RAY DIFFRACTION	23	(chain B and resid 26:31)	B	26 - 31
24	X-RAY DIFFRACTION	24	(chain B and resid 32:36)	B	32 - 36
25	X-RAY DIFFRACTION	25	(chain B and resid 37:47)	B	37 - 47
26	X-RAY DIFFRACTION	26	(chain B and resid 48:53)	B	48 - 53
27	X-RAY DIFFRACTION	27	(chain B and resid 54:59)	B	54 - 59
28	X-RAY DIFFRACTION	28	(chain B and resid 60:65)	B	60 - 65
29	X-RAY DIFFRACTION	29	(chain B and resid 66:72)	B	66 - 72
30	X-RAY DIFFRACTION	30	(chain B and resid 73:77)	B	73 - 77
31	X-RAY DIFFRACTION	31	(chain B and resid 78:83)	B	78 - 83
32	X-RAY DIFFRACTION	32	(chain B and resid 84:88)	B	84 - 88
33	X-RAY DIFFRACTION	33	(chain B and resid 89:94)	B	89 - 94
34	X-RAY DIFFRACTION	34	(chain B and resid 95:100)	B	95 - 100
35	X-RAY DIFFRACTION	35	(chain B and resid 101:105)	B	101 - 105
36	X-RAY DIFFRACTION	36	(chain B and resid 106:110)	B	106 - 110
37	X-RAY DIFFRACTION	37	(chain B and resid 111:116)	B	111 - 116
38	X-RAY DIFFRACTION	38	(chain B and resid 117:125)	B	117 - 125
39	X-RAY DIFFRACTION	39	(chain B and resid 126:129)	B	126 - 129
40	X-RAY DIFFRACTION	40	(chain B and resid 130:134)	B	130 - 134
41	X-RAY DIFFRACTION	41	(chain C and resid 16:23)	C	16 - 23
42	X-RAY DIFFRACTION	42	(chain C and resid 24:29)	C	24 - 29
43	X-RAY DIFFRACTION	43	(chain C and resid 30:36)	C	30 - 36
44	X-RAY DIFFRACTION	44	(chain C and resid 37:43)	C	37 - 43
45	X-RAY DIFFRACTION	45	(chain C and resid 44:50)	C	44 - 50
46	X-RAY DIFFRACTION	46	(chain C and resid 51:55)	C	51 - 55
47	X-RAY DIFFRACTION	47	(chain C and resid 56:59)	C	56 - 59
48	X-RAY DIFFRACTION	48	(chain C and resid 60:65)	C	60 - 65
49	X-RAY DIFFRACTION	49	(chain C and resid 66:72)	C	66 - 72
50	X-RAY DIFFRACTION	50	(chain C and resid 73:79)	C	73 - 79
51	X-RAY DIFFRACTION	51	(chain C and resid 80:84)	C	80 - 84
52	X-RAY DIFFRACTION	52	(chain C and resid 85:90)	C	85 - 90
53	X-RAY DIFFRACTION	53	(chain C and resid 91:95)	C	91 - 95
54	X-RAY DIFFRACTION	54	(chain C and resid 96:101)	C	96 - 101
55	X-RAY DIFFRACTION	55	(chain C and resid 102:108)	C	102 - 108
56	X-RAY DIFFRACTION	56	(chain C and resid 109:115)	C	109 - 115
57	X-RAY DIFFRACTION	57	(chain C and resid 116:120)	C	116 - 120
58	X-RAY DIFFRACTION	58	(chain C and resid 121:126)	C	121 - 126
59	X-RAY DIFFRACTION	59	(chain C and resid 127:130)	C	127 - 130
60	X-RAY DIFFRACTION	60	(chain C and resid 131:135)	C	131 - 135
61	X-RAY DIFFRACTION	61	(chain D and resid 16:21)	D	16 - 21
62	X-RAY DIFFRACTION	62	(chain D and resid 22:26)	D	22 - 26
63	X-RAY DIFFRACTION	63	(chain D and resid 27:34)	D	27 - 34
64	X-RAY DIFFRACTION	64	(chain D and resid 35:43)	D	35 - 43
65	X-RAY DIFFRACTION	65	(chain D and resid 44:51)	D	44 - 51
66	X-RAY DIFFRACTION	66	(chain D and resid 52:57)	D	52 - 57
67	X-RAY DIFFRACTION	67	(chain D and resid 58:65)	D	58 - 65
68	X-RAY DIFFRACTION	68	(chain D and resid 66:72)	D	66 - 72
69	X-RAY DIFFRACTION	69	(chain D and resid 73:77)	D	73 - 77
70	X-RAY DIFFRACTION	70	(chain D and resid 78:82)	D	78 - 82
71	X-RAY DIFFRACTION	71	(chain D and resid 83:89)	D	83 - 89
72	X-RAY DIFFRACTION	72	(chain D and resid 90:96)	D	90 - 96
73	X-RAY DIFFRACTION	73	(chain D and resid 97:103)	D	97 - 103
74	X-RAY DIFFRACTION	74	(chain D and resid 104:109)	D	104 - 109
75	X-RAY DIFFRACTION	75	(chain D and resid 110:117)	D	110 - 117
76	X-RAY DIFFRACTION	76	(chain D and resid 118:123)	D	118 - 123
77	X-RAY DIFFRACTION	77	(chain D and resid 124:128)	D	124 - 128
78	X-RAY DIFFRACTION	78	(chain D and resid 129:135)	D	129 - 135

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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

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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

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Yorodumi