PDB-5he8: Bacterial initiation protein

ID or keywords:

Entry

Database: PDB / ID: 5he8

Title

Bacterial initiation protein

Components

Helicase loader

Keywords

PROTEIN BINDING / Helicase loader

Function / homology

Function and homology information

DNA strand elongation involved in DNA replication /

DNA replication /

nucleotide binding
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Hood, I.V. / Berger, J.M.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01-GM071747	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	T32 GM 007232	United States
Department of Energy (DOE, United States)	Department of Energy Office of Science Graduate Fellowship	United States

Citation

Journal: To Be Published
Title: Bacterial initiation protein
Authors: Hood, I.V. / Berger, J.M.

History

Deposition	Jan 5, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 8, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5he8.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb5he8.ent.gz	1009.8 KB	Display	PDB format
PDBx/mmJSON format	5he8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/he/5he8 ftp://data.pdbj.org/pub/pdb/validation_reports/he/5he8	HTTPS FTP

-
Related structure data

Related structure data	5he9
Similar structure data	3let-1 4qpl-1 5wbs-3 5wbs-1 3kp9-d 5dqw-d 2f1r-d 3kcq-2 2d22-1 4nv6-d 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) 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

5he9

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#168 - Dec 2013 DNA Helicase similarity (4)

Deposited unit

A: Helicase loader

B: Helicase loader

C: Helicase loader

D: Helicase loader

E: Helicase loader

F: Helicase loader

G: Helicase loader

H: Helicase loader

I: Helicase loader

J: Helicase loader

L: Helicase loader

K: Helicase loader

hetero molecules

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

1

A: Helicase loader

F: Helicase loader

hetero molecules

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

2

B: Helicase loader

E: Helicase loader

hetero molecules

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

3

C: Helicase loader

H: Helicase loader

hetero molecules

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

4

D: Helicase loader

G: Helicase loader

hetero molecules

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

5

I: Helicase loader

K: Helicase loader

hetero molecules

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

6

J: Helicase loader

L: Helicase loader

hetero molecules

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

Unit cell

Length a, b, c (Å)	113.099, 126.261, 183.344
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Helicase loader / Primosomal protein DnaI Mass: 19700.461 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: dnaI / Production host: Escherichia coli (E. coli) / References: UniProt: W8TSU2, UniProt: Q2FXP5*PLUS
#2: Chemical	... ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.92 Å³/Da / Density % sol: 57.85 %
Crystal grow	Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 25% glycerol, 0.1 M citric acid pH 4.0, 0.8 M ammonium sulfate, 50 mM HEPES-KOH pH 7.5, 10 mM MgCl2, 10% glycerol, 2 mM ADP-BeF3

-
Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.5 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5 Å / Relative weight: 1
Reflection	Resolution: 2.6→48.13 Å / Num. obs: 81324 / % possible obs: 99.9 % / Redundancy: 13.2 % / Net I/σ(I): 3.4

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→47.241 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2697	3975	4.91 %	Random selection
R_work	0.2251	-	-	-
obs	0.2273	81007	99.62 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.6→47.241 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15757	0	140	207	16104

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	16195
X-RAY DIFFRACTION	f_angle_d	0.509	21838
X-RAY DIFFRACTION	f_dihedral_angle_d	8.428	9662
X-RAY DIFFRACTION	f_chiral_restr	0.039	2401
X-RAY DIFFRACTION	f_plane_restr	0.003	2764

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 (%)
2.6-2.6317	0.6216	147	0.711	2593	X-RAY DIFFRACTION	95
2.6317-2.665	0.6723	141	0.5907	2677	X-RAY DIFFRACTION	99
2.665-2.7001	0.5602	119	0.5241	2753	X-RAY DIFFRACTION	99
2.7001-2.7371	0.4899	135	0.4191	2706	X-RAY DIFFRACTION	99
2.7371-2.7762	0.3576	145	0.3682	2700	X-RAY DIFFRACTION	99
2.7762-2.8176	0.36	124	0.3386	2733	X-RAY DIFFRACTION	100
2.8176-2.8616	0.3726	140	0.32	2722	X-RAY DIFFRACTION	100
2.8616-2.9085	0.3697	149	0.3172	2714	X-RAY DIFFRACTION	100
2.9085-2.9587	0.3866	128	0.2968	2714	X-RAY DIFFRACTION	100
2.9587-3.0125	0.3164	133	0.2847	2760	X-RAY DIFFRACTION	100
3.0125-3.0704	0.3267	150	0.2833	2727	X-RAY DIFFRACTION	100
3.0704-3.1331	0.3384	144	0.289	2738	X-RAY DIFFRACTION	100
3.1331-3.2012	0.3405	146	0.2753	2730	X-RAY DIFFRACTION	100
3.2012-3.2756	0.3037	145	0.2484	2739	X-RAY DIFFRACTION	100
3.2756-3.3575	0.3039	156	0.2392	2709	X-RAY DIFFRACTION	100
3.3575-3.4483	0.3149	161	0.2331	2735	X-RAY DIFFRACTION	100
3.4483-3.5497	0.2774	133	0.2178	2767	X-RAY DIFFRACTION	100
3.5497-3.6642	0.2395	165	0.2004	2731	X-RAY DIFFRACTION	100
3.6642-3.7951	0.2283	143	0.1976	2746	X-RAY DIFFRACTION	100
3.7951-3.947	0.2526	150	0.1959	2768	X-RAY DIFFRACTION	100
3.947-4.1266	0.2239	134	0.1897	2768	X-RAY DIFFRACTION	100
4.1266-4.344	0.1965	153	0.1665	2783	X-RAY DIFFRACTION	100
4.344-4.6159	0.2213	132	0.1607	2769	X-RAY DIFFRACTION	100
4.6159-4.972	0.2183	154	0.1743	2773	X-RAY DIFFRACTION	100
4.972-5.4716	0.225	127	0.1886	2829	X-RAY DIFFRACTION	100
5.4716-6.2619	0.2544	143	0.2253	2820	X-RAY DIFFRACTION	100
6.2619-7.8833	0.2455	128	0.2193	2867	X-RAY DIFFRACTION	100
7.8833-47.2489	0.2319	150	0.1959	2961	X-RAY DIFFRACTION	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	6.9465	6.6873	-1.6093	7.4409	1.098	10.0025	0.0823	-0.089	0.2409	-0.8703	0.5574	-0.1326	-2.3801	0.4119	-0.5678	0.8364	0.0645	0.2235	0.4904	-0.1086	0.7447	9.6242	151.3231	56.5602
2	3.8087	0.5826	-0.2456	0.8865	-1.1938	2.7507	-0.0027	-0.0875	-0.0789	-0.1306	-0.0277	-0.1634	-0.2236	0.0735	-0.0364	0.5639	0.0429	0.136	0.4965	-0.0641	0.5309	11.163	143.1683	53.524
3	6.2714	-3.3281	-6.1702	7.7116	3.1854	7.3286	0.0134	0.229	-0.4887	-0.8169	-0.3511	0.1584	0.0574	-0.7814	0.1905	0.871	-0.1539	0.0999	0.738	-0.0201	0.6013	10.1713	133.9691	40.9858
4	3.837	5.7605	2.9782	9.4313	2.8466	9.7971	0.2213	0.4207	-0.5741	-0.2549	0.345	-0.4984	0.4882	0.0931	-0.4543	0.9421	-0.0489	0.1595	0.7645	-0.0279	0.8271	12.685	134.6744	29.6925
5	3.0927	0.4205	-1.2718	1.8768	0.1577	4.228	-0.0747	0.3266	-0.1365	-0.3901	-0.0104	-0.3248	0.2779	-0.2168	0.0457	0.657	-0.1076	0.2226	0.5624	-0.0385	0.6443	20.5227	139.0501	42.1932
6	5.5504	-0.8876	-2.7858	2.2728	2.7437	8.1496	-0.0929	-0.331	-0.0623	-0.5166	0.3424	-0.2559	-0.04	1.5146	-0.1421	0.5812	-0.0713	0.2491	0.6273	-0.0855	0.8388	27.7372	139.6582	45.0023
7	4.4325	-0.6798	-0.3235	9.8845	-0.8753	2.0411	0.2762	0.2273	-0.7829	-0.5457	0.2151	1.0388	0.6057	-0.4358	-0.5181	0.7778	0.1228	-0.309	0.5244	-0.0024	0.8607	10.5913	101.431	39.3255
8	9.2717	1.0195	-0.3114	2.7701	0.1536	4.4097	-0.1824	0.4087	-0.4456	-0.5524	0.2636	0.1738	0.8234	0.2082	-0.2449	0.6175	0.0104	-0.1518	0.4526	-0.0089	0.6442	11.3282	108.3694	43.1179
9	4.7604	1.5507	1.36	8.6977	1.6946	6.5643	0.4545	-0.8975	0.6176	-0.1651	-0.1407	0.5792	0.3268	-0.693	-0.262	0.3879	0.0485	-0.0254	0.6199	0.1689	0.6787	9.2122	117.0321	54.4627
10	2.4444	-0.4714	-0.8412	4.0621	-0.4479	4.1234	0.1202	-0.7925	0.1045	0.3887	0.1608	-0.0866	-0.3753	-0.0841	-0.3283	0.6789	0.0878	-0.1049	0.723	0.037	0.6577	13.767	116.5899	60.6847
11	5.8354	-1.7545	3.3161	1.4083	-0.0517	8.5775	-0.1202	-0.4039	-0.0821	0.0946	0.0219	-0.2288	-0.0244	0.0493	0.1255	0.3979	-0.0271	-0.0663	0.4281	0.0701	0.5186	21.8601	111.6809	55.6634
12	4.1549	-1.6153	1.7489	7.5962	1.9046	6.2976	-0.581	0.1838	1.522	-0.4919	0.8885	-0.5164	-1.7155	0.3514	-0.1819	0.8605	-0.2	-0.2561	0.8957	0.0185	1.1578	33.2631	122.0793	60.2878
13	6.894	0.5971	3.4234	2.5952	1.549	2.5071	0.2785	-0.0381	-0.6898	0.1181	-0.1176	-0.3179	0.0359	1.0615	-0.1469	0.531	-0.0186	-0.0957	0.5307	0.0159	0.6148	25.4529	109.138	49.0342
14	6.2429	-4.4124	2.4289	4.0139	-3.8292	7.0048	0.4905	-0.1177	0.5101	-0.4718	-0.4725	-1.4257	-0.0577	0.041	0.0514	0.5487	0.0351	0.1204	0.5338	-0.054	0.5531	-21.0943	111.1686	31.5271
15	3.7854	-0.0232	1.2727	4.0495	0.4226	5.9003	0.2494	0.0343	-0.0843	-0.396	-0.2413	-0.1722	0.0426	-0.1444	-0.0653	0.4538	-0.0512	0.0185	0.3836	0.0212	0.4121	-25.8911	110.1078	38.8972
16	6.193	-4.3339	-2.8592	9.6519	5.3823	9.9033	-0.5914	-0.1645	-0.4582	0.9298	0.4302	0.3548	1.8962	0.0004	-0.1324	0.7036	-0.0351	-0.0864	0.5742	0.0344	0.6036	-28.5299	100.4925	42.735
17	5.2127	-5.1865	-0.0385	5.4488	-0.8463	8.5329	-0.2646	-0.6254	-0.7763	-0.0863	0.1483	0.7524	0.4687	-1.2586	0.0753	0.5549	-0.1358	-0.0512	0.6038	0.0089	0.7533	-28.6931	100.7962	60.6096
18	2.2071	-0.6425	1.3578	2.5326	0.0145	4.9929	-0.0812	0.0777	0.1054	-0.0556	0.1039	-0.0344	0.0418	-0.0115	-0.0728	0.4169	-0.0591	-0.0073	0.4234	-0.0034	0.4226	-20.8005	113.176	54.5385
19	2.7546	0.218	4.7293	5.7735	-1.9706	8.8809	-0.307	0.5389	1.69	-0.7993	0.6232	0.2063	-1.9283	0.2312	-0.6364	0.807	-0.1086	0.1688	0.9587	0.0296	0.8188	-28.1636	125.989	28.993
20	5.9318	4.8203	1.0816	9.1737	-2.5869	8.1152	-0.0708	0.1386	-0.4587	1.1986	0.9769	-0.9345	0.1298	0.2419	-0.9039	0.5972	0.0031	-0.025	0.7646	-0.1805	0.6331	-22.9989	141.6836	64.5169
21	4.1694	-0.3509	-1.2533	4.9139	1.2379	5.2911	0.2177	-0.1428	0.2951	-0.1812	0.0207	-0.3445	-0.4876	-0.2206	-0.2336	0.5698	-0.029	0.1248	0.5994	-0.0304	0.5675	-27.9266	145.0392	57.3882
22	0.946	-0.5829	-0.7935	4.3513	-2.8065	4.5497	0.1265	0.1864	0.4492	-0.0403	0.2785	0.587	-0.1724	-0.7282	-0.318	0.471	0.0027	0.0861	0.6111	0.0078	0.6101	-29.898	148.3113	38.9821
23	3.3725	0.7136	-1.7581	3.6399	-1.9494	6.2238	0.1386	-0.126	0.189	-0.1594	-0.0341	-0.2453	-0.2153	-0.0506	-0.0885	0.3848	-0.0123	0.0372	0.3118	-0.035	0.4271	-20.0739	139.5881	41.4745
24	0.0092	0.0498	-0.0334	0.0148	-0.0347	0.025	-0.8805	-1.7782	-0.3998	2.3822	0.7024	0.0824	1.1576	-0.6827	0.216	1.1689	0.2925	0.2771	1.1644	0.0977	0.8254	-30.052	126.7285	64.5979
25	7.9404	4.3569	0.3496	2.4471	-0.1334	8.257	0.7344	0.0812	-0.524	-0.5076	0.0516	0.8148	-0.8218	0.5803	-0.8835	0.6494	-0.0044	-0.111	0.4528	0.0242	0.633	8.6785	118.6925	31.426
26	4.2605	-0.0066	1.0258	1.7006	2.6693	4.3455	0.0778	0.0054	0.27	0.1514	0.1292	-0.3	0.0637	0.3274	-0.2581	0.4533	0.0893	-0.0859	0.3262	0.0469	0.5266	-0.4132	109.9081	28.8975
27	9.614	-3.2711	-1.0649	7.0236	-0.8083	8.4944	0.1591	0.1417	-0.6649	0.925	-0.4081	1.0672	0.5643	-0.7169	0.1452	0.4671	0.043	0.0033	0.351	-0.0061	0.5581	-17.8025	106.6255	18.7331
28	2.5349	-0.3882	0.6052	2.7356	1.2099	4.7298	-0.0154	0.0647	0.181	0.1356	0.0605	-0.3064	0.0129	0.2801	-0.0711	0.4107	0.0323	-0.0426	0.3777	0.0277	0.5159	-0.1873	107.466	15.2346
29	1.0637	0.2211	0.0066	2.1725	-0.2029	4.3682	-0.0551	-0.1181	-0.1624	-0.3036	-0.1459	-0.1559	0.2936	0.246	0.2109	0.4303	0.0023	0.0844	0.3756	-0.0224	0.4869	4.9859	136.2412	67.2078
30	3.5964	-1.1546	-3.2932	2.268	0.7681	4.8491	0.1268	0.3567	-0.1101	-0.1179	-0.1853	0.2155	-0.2413	-0.0951	0.1245	0.521	-0.119	0.0055	0.4632	-0.0133	0.5139	-5.4788	143.907	64.8455
31	8.8974	5.6284	2.514	5.9427	1.8432	2.2801	-0.2378	0.1455	1.6842	-0.2395	0.0515	0.158	-1.3497	-0.2762	-0.1929	0.669	0.113	-0.0733	0.3963	-0.0539	0.6632	-19.9871	146.7021	77.6123
32	4.0285	0.031	-0.2287	2.6307	0.1919	3.2901	-0.035	0.0516	-0.049	-0.0485	0.0303	0.0085	-0.131	0.0204	-0.0236	0.3327	-0.0408	0.0403	0.3243	-0.0131	0.4097	-4.9005	143.9027	78.9478
33	6.6121	-0.4446	-1.7414	4.4358	2.2115	7.6968	0.1286	-0.3543	0.0226	0.0856	-0.2098	-0.1708	-0.1479	0.1528	0.0398	0.3674	-0.0003	-0.0249	0.3102	0.019	0.46	1.4169	144.5869	83.5484
34	4.2387	-1.5749	-1.7214	3.8785	0.9064	6.3129	-0.0326	0.7546	-0.4173	-0.2959	0.0394	0.4529	0.2387	-0.7423	-0.0544	0.4536	-0.0881	0.0114	0.586	-0.0769	0.5194	-39.7138	139.2556	66.9027
35	3.8777	2.2029	3.8582	2.8249	3.8015	8.5952	-0.2532	0.0565	0.3752	-0.0647	-0.1398	0.0175	-1.0619	-0.4175	0.2949	0.4822	0.0491	0.0955	0.5723	0.0909	0.6159	-39.2115	153.6667	78.8621
36	2.5831	0.5222	-1.7436	3.9802	2.9742	9.8266	0.0788	0.4265	0.3578	-0.1991	-0.1682	0.1428	-0.5757	-0.0866	0.0664	0.5711	0.0289	0.0837	0.6479	0.0395	0.6213	-42.8669	152.2604	84.0433
37	1.9642	-0.9746	-2.7962	2.1633	2.1072	7.8148	-0.2362	0.1972	-0.236	0.1735	0.2046	0.0424	0.2732	0.2234	0.0095	0.3926	0.0191	0.0683	0.4552	0.0216	0.466	-41.2696	139.5634	85.9017
38	0.5257	-0.1588	0.9649	2.0085	-0.8013	1.5513	0.2406	-0.3646	1.2317	0.5183	-0.4587	1.208	-0.213	-0.939	0.0199	0.6295	0.1125	0.014	0.8472	0.0243	0.6946	-39.396	117.1454	32.4988
39	4.1657	0.8579	1.7407	2.2907	0.3378	4.3108	0.086	-0.6943	0.4719	0.2982	0.0844	0.3199	0.185	-0.5258	-0.1464	0.4735	-0.0366	-0.0061	0.4551	-0.0268	0.4686	-36.5266	111.6231	26.4905
40	3.1135	-0.0719	-2.4359	5.8446	3.1373	6.7797	0.1829	-0.3582	-0.0767	-0.0723	-0.1936	-0.5248	0.7136	-0.2444	0.1474	0.5471	0.0037	-0.1041	0.6409	0.2059	0.6422	-37.6626	99.9358	19.3806
41	8.9993	2.3576	-0.9526	4.9864	0.914	3.1939	-0.3607	-0.5119	-1.7041	0.0671	0.5238	0.0537	2.2355	1.2525	-0.0713	0.9369	-0.0044	-0.1311	0.578	0.1132	0.8565	-43.762	94.7553	8.4069
42	4.1614	0.1259	1.783	2.2238	1.0179	7.9916	0.2747	-0.5045	0.0318	0.039	-0.0221	0.1646	0.6033	-0.4965	-0.2166	0.4304	-0.0688	-0.0414	0.4372	0.0488	0.4779	-41.8073	107.0299	12.6197
43	2.7191	1.2408	1.8654	2.7626	2.0516	8.3762	-0.1834	0.0646	0.3431	-0.2615	0.166	0.0392	-0.1855	0.0783	0.0507	0.4101	-0.0123	-0.0445	0.3415	0.0596	0.5214	-35.8277	116.4201	8.7386
44	5.3636	-2.8681	0.2126	4.7769	-1.2341	7.2234	-0.1736	0.1648	-0.5377	-0.7495	-0.2581	-1.66	0.9412	1.3035	0.214	0.7029	0.121	0.2541	1.0858	-0.0301	1.0129	12.3726	139.6464	11.4655
45	3.7222	0.7598	0.3257	2.6346	1.2321	4.26	-0.1935	0.379	-0.788	-0.1655	-0.0549	-0.826	0.6255	0.8162	0.2229	0.6548	0.035	0.2304	0.7567	-0.0204	0.7988	4.0013	139.8679	10.7802
46	6.2619	3.8027	-2.5787	5.0727	-1.2995	6.7202	-0.3422	1.0053	0.0426	-1.0928	0.3133	0.1819	0.2828	-1.0159	0.0098	0.9021	-0.0371	0.0898	0.6565	-0.0166	0.5321	-17.0081	137.7565	14.7762
47	5.9171	2.207	-0.3903	2.1314	-1.2369	5.3897	-0.1041	0.1272	-0.0933	-0.0638	0.1022	0.0797	0.2975	0.1545	-0.0029	0.5204	0.0018	0.0668	0.3176	-0.0239	0.4326	-8.9144	145.3401	21.3654
48	2.8265	-0.7805	-2.2257	5.5819	1.382	5.9639	-0.6257	-0.4071	-0.0266	0.0161	0.222	-0.359	0.4284	0.6227	0.3187	0.4575	-0.0374	-0.0141	0.5313	0.0611	0.4523	-0.1273	149.146	22.4697
49	6.9391	4.9059	2.2945	7.5976	-3.2928	8.8239	-0.2784	0.2145	1.087	0.3567	-0.339	-1.4469	-0.3047	1.0426	0.6543	0.7502	-0.1608	-0.2656	0.9015	0.1211	0.9373	9.9601	116.8817	87.5288
50	4.842	-2.4728	1.5682	1.0263	-1.2839	3.8509	-0.4617	-0.0733	0.466	0.4201	0.2036	-0.4552	-0.4336	0.2179	0.2816	0.7066	0.062	-0.0884	0.5514	-0.104	0.5754	-2.9594	114.4967	87.991
51	3.7443	-1.5909	-0.0286	4.1254	-0.2789	1.992	-0.2436	-0.1891	0.0978	0.2173	0.3212	-0.133	0.0746	0.0936	-0.0797	0.4614	0.0214	-0.052	0.4167	-0.0267	0.3914	-9.7489	110.2998	76.3393
52	5.4871	-1.9836	-0.3206	2.2283	0.3017	7.9421	0.3032	0.6409	-0.5223	0.3189	0.3723	-0.0445	2.0535	-0.1375	-0.5881	0.9557	-0.1159	-0.3928	0.979	-0.0536	0.8762	7.5654	106.5549	103.0031
53	2.0827	-0.9452	0.5602	0.7865	0.2923	5.502	0.0444	-0.0863	0.4281	0.0945	-0.3466	0.0115	-0.7559	0.2171	0.306	0.9497	-0.0377	-0.2926	1.0458	-0.034	0.8564	12.3589	122.1217	110.7126
54	4.5485	0.0486	4.7589	2.627	0.8912	8.2137	0.062	0.872	-0.3275	-0.0001	0.0706	-0.2622	0.5244	0.7548	-0.0629	0.7784	-0.0136	-0.2912	0.9082	-0.0789	0.7457	21.7222	111.4447	111.2415
55	2.1526	-2.2709	-2.9537	3.2	3.3775	4.6356	0.009	-0.2478	-0.1264	0.0586	-0.1614	0.0305	-0.146	0.0939	0.1401	0.8683	-0.0419	0.1963	1.0712	-0.0442	0.7889	11.7615	139.6348	-7.32
56	4.6851	-1.5338	-2.643	4.0802	3.5094	8.1123	0.0373	-0.8942	0.0283	0.2878	-0.1088	0.1084	0.1517	-0.0598	0.0463	0.6123	-0.0935	0.1485	0.7765	-0.0611	0.5983	22.0965	141.4394	-14.6668

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 138 through 153 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 154 through 184 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 185 through 203 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 204 through 217 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 218 through 271 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 272 through 300 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 138 through 152 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 153 through 184 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 185 through 200 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 201 through 233 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 234 through 271 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 272 through 278 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 279 through 301 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 136 through 152 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 153 through 183 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 184 through 192 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 193 through 218 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 219 through 297 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 298 through 306 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 135 through 152 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 153 through 188 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 189 through 233 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 234 through 297 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 298 through 304 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 138 through 152 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 153 through 200 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 201 through 218 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 219 through 302 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 138 through 169 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 170 through 200 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 201 through 217 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 218 through 271 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 272 through 301 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 137 through 184 )
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 185 through 203 )
36	X-RAY DIFFRACTION	36	chain 'G' and (resid 204 through 233 )
37	X-RAY DIFFRACTION	37	chain 'G' and (resid 234 through 301 )
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 137 through 152 )
39	X-RAY DIFFRACTION	39	chain 'H' and (resid 153 through 183 )
40	X-RAY DIFFRACTION	40	chain 'H' and (resid 184 through 200 )
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 201 through 217 )
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 218 through 259 )
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 260 through 301 )
44	X-RAY DIFFRACTION	44	chain 'I' and (resid 138 through 152 )
45	X-RAY DIFFRACTION	45	chain 'I' and (resid 153 through 188 )
46	X-RAY DIFFRACTION	46	chain 'I' and (resid 189 through 217 )
47	X-RAY DIFFRACTION	47	chain 'I' and (resid 218 through 278 )
48	X-RAY DIFFRACTION	48	chain 'I' and (resid 279 through 302 )
49	X-RAY DIFFRACTION	49	chain 'J' and (resid 138 through 152 )
50	X-RAY DIFFRACTION	50	chain 'J' and (resid 153 through 200 )
51	X-RAY DIFFRACTION	51	chain 'J' and (resid 201 through 300 )
52	X-RAY DIFFRACTION	52	chain 'L' and (resid 139 through 169 )
53	X-RAY DIFFRACTION	53	chain 'L' and (resid 170 through 218 )
54	X-RAY DIFFRACTION	54	chain 'L' and (resid 219 through 301 )
55	X-RAY DIFFRACTION	55	chain 'K' and (resid 137 through 209 )
56	X-RAY DIFFRACTION	56	chain 'K' and (resid 210 through 300 )

-
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