PDB-3q15: Crystal Structure of RapH complexed with Spo0F

ID or keywords:

Entry

Database: PDB / ID: 3q15

Title

Crystal Structure of RapH complexed with Spo0F

Components

Response regulator aspartate phosphatase H
Sporulation initiation phosphotransferase F

Keywords

HYDROLASE/KINASE / Tetratricopeptide repeat / 3-helix bundle / Phosphorelay signal transduction / Phosphatase / Response regulator receiver / HYDROLASE-KINASE complex

Function / homology

Function and homology information

Transferases; Transferring phosphorus-containing groups / sporulation resulting in formation of a cellular spore / phosphorelay signal transduction system / phosphoprotein phosphatase activity / kinase activity / Hydrolases; Acting on ester bonds / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.192 Å

Authors

Parashar, V. / Neiditch, M.B.

Citation

Journal: Plos Biol. / Year: 2011
Title: Structural basis of response regulator dephosphorylation by Rap phosphatases.
Authors: Parashar, V. / Mirouze, N. / Dubnau, D.A. / Neiditch, M.B.

History

Deposition	Dec 16, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 23, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3q15.cif.gz	399.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3q15.ent.gz	333.7 KB	Display	PDB format
PDBx/mmJSON format	3q15.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q1/3q15 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/3q15	HTTPS FTP

-
Related structure data

Similar structure data	3nhq-4 4az5-1 1jg8-d 2fm1-d 5x2h-d 3c2w-2 3c2w-3 1orr-d 4our-d 1yoe-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 - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#230 - Feb 2019 Initiation Factor eIF4E similarity (6) #190 - Oct 2015 Two-component Systems similarity (5) #245 - May 2020 Spliceosomes similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (4) #166 - Oct 2013 Proteasome similarity (3) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Response regulator aspartate phosphatase H

B: Response regulator aspartate phosphatase H

C: Sporulation initiation phosphotransferase F

D: Sporulation initiation phosphotransferase F

hetero molecules

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

1

A: Response regulator aspartate phosphatase H

C: Sporulation initiation phosphotransferase F

hetero molecules

A: Response regulator aspartate phosphatase H

C: Sporulation initiation phosphotransferase F

hetero molecules

defined by author&software
118 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Response regulator aspartate phosphatase H

D: Sporulation initiation phosphotransferase F

hetero molecules

B: Response regulator aspartate phosphatase H

D: Sporulation initiation phosphotransferase F

hetero molecules

defined by author&software
118 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	95.064, 157.452, 84.715
Angle α, β, γ (deg.)	90.00, 110.57, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-407- HOH

-
Protein , 2 types, 4 molecules ABCD

#1: Protein	Response regulator aspartate phosphatase H / PSP28 Mass: 44204.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU06830, rapH, yeeH, yzqA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q59HN8, Hydrolases; Acting on ester bonds
#2: Protein	Sporulation initiation phosphotransferase F / Stage 0 sporulation protein F Mass: 14388.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU37130, spo0F / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P06628, Transferases; Transferring phosphorus-containing groups

#1: Protein

Response regulator aspartate phosphatase H / PSP28

Mass: 44204.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus subtilis (bacteria) / Gene: BSU06830, rapH, yeeH, yzqA / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q59HN8, Hydrolases; Acting on ester bonds

#2: Protein

Sporulation initiation phosphotransferase F / Stage 0 sporulation protein F

Mass: 14388.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus subtilis (bacteria) / Gene: BSU37130, spo0F / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P06628, Transferases; Transferring phosphorus-containing groups

-
Non-polymers , 4 types, 242 molecules

#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.53 Å³/Da / Density % sol: 51.43 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% [w/v] PEG 3350, 200 mM lithium sulphate, and 100 mM Bis-Tris (pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2009
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 58465 / Observed criterion σ(I): 1.8 / Redundancy: 3.69 %
Reflection shell	Resolution: 2.2→2.24 Å

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.6.4_486)	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.192→31.246 Å / SU ML: 0.35 / σ(F): 0 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2683	3408	6.21 %	Random
R_work	0.2203	-	-	-
obs	0.2234	54906	92.09 %	-
all	-	54906	-	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 49.994 Å² / k_sol: 0.357 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	8.0083 Å²	0 Å²	-16.7902 Å²
2-	-	-6.4788 Å²	0 Å²
3-	-	-	-1.5296 Å²

Refinement step

Cycle: LAST / Resolution: 2.192→31.246 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7521	0	24	236	7781

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7704
X-RAY DIFFRACTION	f_angle_d	0.548	10373
X-RAY DIFFRACTION	f_dihedral_angle_d	11.741	2876
X-RAY DIFFRACTION	f_chiral_restr	0.042	1127
X-RAY DIFFRACTION	f_plane_restr	0.002	1314

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 (%)
2.1921-2.2234	0.3353	88	0.3028	1846	X-RAY DIFFRACTION	78
2.2234-2.2566	0.314	125	0.2869	1956	X-RAY DIFFRACTION	85
2.2566-2.2918	0.3044	149	0.2698	1996	X-RAY DIFFRACTION	85
2.2918-2.3294	0.3517	136	0.2748	1928	X-RAY DIFFRACTION	85
2.3294-2.3695	0.3682	161	0.2702	2007	X-RAY DIFFRACTION	88
2.3695-2.4126	0.3191	114	0.2663	2097	X-RAY DIFFRACTION	89
2.4126-2.459	0.337	149	0.2697	2095	X-RAY DIFFRACTION	91
2.459-2.5092	0.3127	129	0.276	2150	X-RAY DIFFRACTION	91
2.5092-2.5637	0.3193	132	0.252	2135	X-RAY DIFFRACTION	92
2.5637-2.6233	0.3527	136	0.2516	2143	X-RAY DIFFRACTION	92
2.6233-2.6889	0.3211	133	0.2526	2180	X-RAY DIFFRACTION	94
2.6889-2.7615	0.3059	151	0.2446	2186	X-RAY DIFFRACTION	94
2.7615-2.8427	0.2696	149	0.2516	2219	X-RAY DIFFRACTION	96
2.8427-2.9344	0.2789	152	0.2316	2255	X-RAY DIFFRACTION	97
2.9344-3.0392	0.2947	156	0.2415	2260	X-RAY DIFFRACTION	97
3.0392-3.1608	0.2969	155	0.2417	2284	X-RAY DIFFRACTION	98
3.1608-3.3045	0.2806	156	0.2372	2290	X-RAY DIFFRACTION	99
3.3045-3.4785	0.3055	155	0.2214	2315	X-RAY DIFFRACTION	99
3.4785-3.6961	0.263	156	0.2102	2317	X-RAY DIFFRACTION	99
3.6961-3.981	0.2154	155	0.1916	2267	X-RAY DIFFRACTION	98
3.981-4.3807	0.2035	148	0.1738	2233	X-RAY DIFFRACTION	96
4.3807-5.0123	0.2241	144	0.1732	2166	X-RAY DIFFRACTION	93
5.0123-6.3064	0.2664	153	0.2094	2298	X-RAY DIFFRACTION	98
6.3064-31.2487	0.2489	126	0.2203	1875	X-RAY DIFFRACTION	79

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	4.1067	-1.0934	-0.5777	4.158	-1.6022	3.1432	0.0407	0.5702	0.1483	-0.1591	-0.1552	-0.4052	-0.0611	0.3454	0.0001	0.4331	0.0962	0.1425	0.5318	0.0042	0.368	45.1544	120.4959	15.7227
2	0.0414	-0.0249	0.0664	0.0587	-0.0013	0.0099	-0.7375	-0.1843	-0.8555	0.8492	0.2343	-0.738	0.642	0.4247	-0.0014	0.7111	0.1142	0.0432	0.6562	-0.0602	1.0564	43.9856	101.8411	12.3271
3	0.0016	-0.032	-0.0976	-0.009	0.0947	0.0697	-1.0556	-0.0839	0.4637	-1.3162	0.7762	0.6439	0.8962	0.1735	-0.0001	0.5591	0.0284	0.0134	0.5427	-0.1205	0.9421	32.5474	102.7666	16.2315
4	0.3616	-0.0618	-0.1826	0.1521	0.2343	0.5349	0.1264	-0.1509	-0.6276	0.6337	-0.0545	0.0642	1.1186	-0.1292	0.0003	0.6519	0.0865	0.0768	0.4302	0.0034	0.5766	41.0272	108.0421	25.8081
5	1.483	-1.1938	0.2723	1.0173	1.0991	1.4177	-0.3034	0.1123	0.0772	0.1767	0.1294	0.0064	0.2259	-0.0741	0.0001	0.5808	0.0875	0.0641	0.3665	0.0161	0.3304	36.3956	128.511	28.4892
6	0.1131	-0.0693	-0.0971	0.0506	0.0379	0.0557	0.1287	-0.2915	-2.3553	0.2005	-0.2879	0.2483	0.4373	0.3456	-0.0006	1.1009	0.3437	-0.0153	0.5565	-0.0621	0.8704	45.2856	116.6507	38.2202
7	1.7568	-0.0177	0.8111	0.5177	0.6955	1.7002	-0.0654	0.4138	0.1375	0.1357	-0.125	-0.045	0.418	0.4039	-0	0.4831	0.0238	0.0789	0.4165	0.032	0.3404	41.339	133.3338	38.1553
8	-0.0299	-0.067	-0.1562	0.0978	-0.099	0.0681	0.4579	-0.361	-0.5452	1.6735	0.0963	-0.4931	2.0312	0.9091	0.0003	1.0954	0.386	-0.0702	0.5586	-0.0185	0.3772	48.8982	127.9764	45.7177
9	1.9893	0.8098	-0.2911	0.3268	-0.4469	1.9883	0.456	-0.0144	0.2421	-0.1285	-0.2678	-0.4536	0.2864	0.5998	0.0001	0.5547	0.0965	-0.0468	0.4129	0.032	0.4503	49.6138	138.0462	43.6753
10	0.1469	0.2061	0.3441	0.5021	-0.2656	0.7086	-0.1138	0.3714	0.0578	0.8112	-0.423	-0.3688	-0.176	0.0674	-0	0.4353	0.044	-0.0531	0.4933	0.05	0.466	52.3143	143.2637	50.0861
11	0.0669	0.1142	0.0845	0.1681	-0.1108	0.053	-0.094	-1.7695	-0.4821	0.8737	-0.8635	-0.7223	-0.0913	1.2943	0.0007	0.7214	0.3266	-0.2578	1.0642	0.0616	0.8149	63.951	137.1931	46.7158
12	0.9772	0.9695	1.1205	1.3419	0.229	1.0693	0.2658	0.0316	0.1048	-0.5476	-0.3123	0.0709	0.0682	0.9846	-0	0.4661	0.088	0.0675	0.6551	0.1042	0.4405	58.8218	146.1287	42.0614
13	0.1763	0.0785	-0.2003	-0.039	-0.0051	0.1502	-0.7701	-0.6135	0.8047	0.5641	-0.0126	0.0281	0.1821	0.8412	-0.0008	0.694	-0.1382	-0.1706	0.6237	0.0003	0.9253	52.9954	156.9286	49.7077
14	0.6127	-0.4177	0.0451	0.579	-0.1667	0.2073	0.1113	0.114	0.2104	0.4232	-0.135	-0.6961	0.6288	0.8618	-0.0001	0.4948	0.0004	-0.0036	0.8748	0.1631	0.6099	64.3496	151.7932	39.3092
15	1.7354	-0.2676	0.4752	1.9086	-1.3157	1.5308	0.0572	0.0885	0.2555	0.2953	-0.0561	-0.2638	-0.2534	0.6469	0	0.4348	-0.0679	-0.0176	0.5673	0.0947	0.5707	58.2786	161.9483	35.3738
16	0.0677	0.097	0.0578	0.0723	0.0213	0.0751	0.8769	0.4371	-1.814	-0.9438	1.53	0.1162	0.5002	-0.2129	0.0013	1.1447	-0.0633	-0.0074	0.7107	-0.2838	1.2745	55.4877	149.6333	21.1349
17	1.7527	-0.1597	-1.3782	0.2982	0.3812	1.5728	-0.0534	0.4779	0.4919	-0.3291	-0.0932	-0.2932	-0.6311	0.3178	0	0.5346	-0.1473	-0.1249	0.5283	0.2301	0.7212	48.0418	165.8662	27.8298
18	0.0059	-0.0825	-0.0028	0.0019	0.0078	0.0329	-0.7233	1.1541	0.7471	-0.6003	-0.4331	1.1892	-0.4413	-0.8881	0.0001	0.5921	-0.0062	-0.0455	0.6287	-0.0065	0.7294	39.6334	155.5832	22.0494
19	1.573	0.2465	-1.3568	0.419	0.0503	2.2441	-0.2456	-0.015	0.6119	-0.2042	0.1058	-0.3023	-0.4124	0.1607	0	0.416	-0.0246	-0.0594	0.3314	0.0572	0.7711	37.89	166.0462	35.6725
20	0.1023	0.2718	-0.0067	0.1987	0.2096	0.1895	-0.2196	0.1831	0.4355	-0.4107	0.2542	0.1526	0.0841	-0.1052	-0.0002	0.5476	0.0197	-0.0153	0.3066	0.0128	0.4346	28.694	145.6631	28.8503
21	-0.0275	0.0048	-0.0524	0.0338	0.0031	-0.0755	-1.2116	1.069	1.5738	-1.9225	-1.0085	0.2008	-0.0765	-0.1246	-0.0007	0.5829	0.1126	0.2061	1.3175	0.2458	0.8376	23.8378	92.7668	-6.3057
22	-0.0733	0.151	-0.0426	0.014	0.003	0.0779	0.5184	0.4754	-0.4138	-1.0883	-0.4224	0.356	0.2925	1.3305	-0.0005	1.161	0.506	-0.2606	0.8293	0.0417	0.8468	20.2534	80.4816	-10.3847
23	-0.0066	0.1145	0.0316	0.0769	0.0938	0.0105	0.1126	1.747	0.387	0.1427	-0.2443	0.838	0.777	-0.8438	-0.0004	1.4212	0.3339	-0.1005	1.0058	-0.2679	0.9483	20.1176	71.2201	-13.4235
24	0.0782	0.0576	0.0214	0.118	-0.0386	0.0157	1.4986	-0.1467	1.1308	0.6353	-2.3401	0.5805	-0.1393	0.7819	0.0007	0.7966	0.2141	0.0647	1.2453	-0.0118	0.7106	23.5935	87.5961	3.3691
25	0.2018	0.061	-0.0656	0.1	-0.0211	0.221	1.1719	0.1528	-2.178	-1.393	-0.5471	-0.1601	1.5027	-0.5878	0.0006	1.4436	0.8807	-0.3275	1.2511	-0.3303	0.6836	24.0975	76.4646	-2.0792
26	0.3767	0.2707	0.3527	0.2638	0.536	0.446	0.9822	0.6814	-1.318	-0.5901	-0.8476	0.319	0.6769	0.2437	-0.0001	1.2081	0.402	-0.4148	0.7239	-0.3207	1.0756	17.3896	71.9211	-1.9772
27	0.399	-0.0593	0.5578	0.2241	-0.9585	0.6541	1.0106	1.1982	-0.6595	-1.2819	-0.5123	-0.1513	1.0263	1.5787	-0.0004	0.6016	0.2763	0.0287	0.7803	-0.1117	0.4151	11.4091	93.9155	-6.613
28	1.1154	-0.1162	-0.894	0.5772	0.0615	0.5429	0.8813	0.2129	-1.0165	-1.4116	0.1001	1.225	1.8488	0.6322	0.0011	1.0817	0.0185	-0.5171	0.4856	-0.0018	0.9026	8.6129	82.5881	5.4269
29	1.3416	-0.0834	1.1726	0.3435	0.2501	1.159	0.5692	0.1105	-0.7294	-0.1191	-0.0483	-0.0723	0.3984	0.2673	0.0002	0.4571	0.0094	0.0271	0.3658	-0.021	0.3906	5.938	97.4872	5.2534
30	2.9129	0.9605	1.5168	0.7066	-0.4681	1.2163	0.1203	-0.8873	-0.258	0.1459	0.1578	0.1016	0.0851	-0.319	0.0001	0.3759	-0.049	0.079	0.5432	0.0376	0.2908	8.0058	99.2611	16.7214
31	0.5917	-0.2083	0.2407	0.8565	0.7257	0.3494	0.2566	-0.7605	-0.6553	0.0774	0.2831	-0.3225	0.5144	-0.2307	-0.0001	0.4748	-0.0036	-0.025	0.6962	-0.005	0.3957	19.6998	101.0979	24.5955
32	0.1313	0.3089	0.4431	0.2004	0.4436	0.4166	-0.3566	-0.7442	0.6974	-0.1099	0.0177	-0.0197	-0.2886	-0.5086	0.0003	0.4495	-0.0394	0.0401	0.5525	-0.1258	0.4124	11.8369	112.3293	19.0121
33	0.0134	0.0421	0.0391	0.101	0.0463	0.0511	-0.0911	-0.7053	1.4756	1.8785	-0.5558	1.3788	-2.6878	0.6794	-0.0005	0.8076	0.0428	0.0712	0.9354	-0.392	0.7851	9.084	120.2633	23.9861
34	0.7327	0.2708	0.3936	1.6242	-0.5714	0.964	-0.1187	-0.9109	0.1551	0.3209	-0.0362	-0.0568	-0.0466	0.0203	-0	0.5314	0.0425	-0.1074	0.6127	-0.2134	0.5612	23.2901	113.7604	21.68
35	0.1531	0.0976	-0.2735	0.3884	-0.5959	0.6713	-0.1087	0.1708	0.6197	-0.7762	-0.1869	1.1056	-0.8462	-0.0412	0.0002	0.5958	0.0631	-0.1603	0.4676	-0.2018	0.7776	15.5459	122.6297	15.5776
36	1.3483	0.59	0.6648	1.105	-1.0664	1.7352	0.0823	-0.3879	0.2663	0.1301	-0.3693	-0.2226	-0.6998	0.5158	-0.0001	0.5532	-0.0214	-0.1045	0.5409	-0.0973	0.7399	24.4144	125.1726	15.7752
37	0.9718	-0.36	0.0552	0.3125	-0.7275	1.6969	-0.2332	-0.2068	0.8497	-0.8054	0.3956	0.4531	-0.1191	0.4128	-0.0001	0.639	-0.1539	-0.2304	0.5321	0.0414	0.8943	19.3572	127.0444	7.0238
38	0.0385	0.0318	-0.0297	0.0637	-0.0002	0.0018	0.169	-0.0771	1.273	-1.9127	-0.0666	1.2213	-1.7872	-0.4136	0.0008	0.9295	-0.4052	-0.0647	1.0615	0.1853	1.1056	17.7832	132.8827	-1.5477
39	2.2489	0.2527	2.1393	1.4503	-0.3771	2.142	-0.2825	0.4015	0.9502	-0.066	0.1315	-0.2399	-0.2485	0.3299	0.0001	0.4933	-0.0731	-0.1695	0.3937	0.1102	0.9672	9.7428	127.1241	0.129
40	0.7485	-0.4907	0.0835	0.1702	0.443	0.5551	-0.24	0.811	0.3906	-0.4036	-0.1404	0.168	-0.0871	0.3659	0.0001	0.3597	-0.0021	0.0988	0.4719	0.0324	0.495	5.0664	112.0999	-8.4249
41	0.2915	0.32	-0.0377	0.2482	-0.3405	0.3815	0.5649	2.1688	-0.9097	0.2073	-0.7743	-0.6514	0.0121	1.5966	0.0004	0.7125	0.3288	-0.3496	0.7368	-0.2115	1.1902	63.1492	107.8574	30.3697
42	0.0929	-0.1694	-0.0761	0.1636	0.1755	0.1468	-0.438	-0.4517	1.3981	0.5285	0.0817	-0.3296	0.9262	-0.1209	-0.0005	0.7125	0.0257	-0.1535	0.6693	0.0214	0.7652	53.5004	117.5205	31.1104
43	0.2005	-0.0392	-0.0402	0.0039	0.0026	0.0969	-0.3658	-0.635	-0.2137	1.3958	-1.1127	0.8718	1.5558	-0.3453	-0.0009	0.7482	0.2045	-0.0932	0.7591	0.0294	0.6006	53.6317	109.9643	27.9024
44	0.0226	-0.0106	0.1278	0.0658	-0	0.0201	0.0049	0.8523	0.0308	-0.2219	0.1254	-0.5863	0.7378	0.5663	0.0002	0.9137	0.0421	-0.0542	0.9288	-0.2769	1.0116	57.6201	102.3073	23.4838
45	0.0948	-0.03	0.0028	-0.0188	0.0283	0.0273	-0.4101	0.3702	-0.9724	0.3107	0.1541	0.578	-0.2278	0.2568	0.0001	0.7566	0.0941	-0.0792	0.6444	0.0845	0.8934	59.8366	106.7857	33.7782
46	0.0405	-0.0286	0.0485	0.0235	0.0154	0.0733	-0.41	-0.4513	0.0369	1.2381	0.2866	1.4975	0.5608	-0.0126	0.0004	1.1127	0.1036	-0.2528	0.4952	-0.0647	0.8006	64.7745	114.1632	40.6469
47	0.0265	-0.0197	0.0343	0.0461	0.0225	0.0482	0.4804	-0.0128	0.1217	0.46	0.4152	-0.1749	0.0206	-0.6912	-0.0003	0.9422	0.1428	-0.2256	0.6372	0.1201	0.9154	67.6223	105.487	39.4523
48	0.2226	0.1066	-0.2406	0.107	-0.0054	0.2818	-0.2675	-0.3556	-0.499	1.5179	-0.3969	0.1001	-0.0612	1.0904	0.0003	0.841	0.2584	-0.1201	0.6952	0.0987	1.0039	67.6148	109.7412	30.341
49	0.0523	0.0242	-0.1337	0.063	0.043	0.0505	-0.154	-1.393	1.2416	-0.3565	0.0684	-0.8166	0.462	0.5138	-0.0002	0.9964	0.2525	-0.1487	0.7515	0.1281	1.2132	63.8269	123.7157	34.1998
50	0.0918	0.0736	0.0151	0.0221	0.0904	0.021	0.9537	-0.0869	0.8277	0.5316	1.053	0.7546	-2.3963	0.1552	0.0009	1.2843	0.0002	-0.0474	0.8636	-0.1064	1.1343	71.6977	121.1725	34.4509
51	0.1002	0.041	-0.0146	0.0042	-0.005	0.016	-0.6663	-0.6568	0.0831	1.2624	-0.621	-0.2894	-0.7168	1.2961	-0.0014	1.2668	-0.1055	-0.3753	0.9063	0.1188	1.2251	75.0181	113.7541	36.8995
52	0.0792	-0.0637	-0.0495	0.0541	-0.0102	0.0068	-0.4732	1.1174	-1.0739	0.0438	-0.6494	-0.3065	-0.5424	-0.0561	0.0001	0.7858	0.2062	-0.1181	1.1834	0.4927	1.4619	76.8041	108.1114	30.0942
53	0.1373	0.0515	0.0683	0.1278	0.0479	0.0513	-0.4457	0.0406	0.9443	0.7968	0.2676	1.4942	-0.3205	0.5403	0.0007	0.8213	0.0942	-0.3596	0.7676	0.1059	1.2236	65.6203	118.1172	24.8803
54	0.0193	-0.0095	0.0202	-0.0349	0.0015	-0.0577	-0.2592	-0.3463	0.208	1.2538	-0.9806	-1.1297	-0.5381	1.9649	-0.0008	0.9105	-0.0801	-0.0054	1.2044	0.5293	1.7077	66.4454	129.2981	22.8256
55	0.0068	-0.0312	0.0526	0.0856	-0.0228	0.0378	-0.2813	-0.8301	1.1104	1.2057	0.5245	-0.0186	-0.2862	-0.5558	0.0001	0.6715	-0.1702	-0.0163	1.1557	0.2838	1.3318	73.4397	124.489	24.8109
56	-0.004	0.0207	0.0162	0.0827	0.0649	-0.0134	-1.0594	0.0635	1.331	-0.7982	0.0858	-0.6108	-1.6604	1.4675	-0.0002	0.6531	0.0319	-0.1385	1.3473	0.0318	1.0877	74.2325	117.8981	22.8679
57	-0.014	0.01	-0.0384	-0.0392	0.0132	0.0116	0.3756	0.1855	-0.1876	0.1662	0.1397	-0.7678	1.0035	0.8898	-0.0003	0.8381	0.0627	-0.0325	0.8304	-0.0691	0.8005	59.9016	118.7989	19.8829
58	0.0169	0.0216	0.0365	-0.009	0.0126	0.1027	0.0474	1.0424	-1.3205	-1.5822	-0.4256	0.1873	0.7623	-0.4597	-0.0003	1.0014	-0.0094	-0.0478	1.0142	-0.1307	0.7593	59.6757	110.3095	15.6955
59	0.002	-0.0123	-0.007	-0.0033	-0.0188	-0.0077	0.3	-0.0939	0.1035	0.2049	-0.2045	0.3582	-0.0988	0.4726	0	0.9813	0.0575	0.1842	1.0979	-0.1627	1.3925	68.7236	106.0381	18.9407
60	0.0519	0.0509	0.054	0.0295	-0.0139	0.026	-0.0114	-1.1359	-1.3081	0.8101	0.1175	-1.0236	0.7301	0.4785	0.0007	0.5226	0.438	0.0729	0.9282	0.203	0.8354	28.4288	67.018	17.1638
61	0.0804	-0.1438	0.0442	0.0498	0.0777	0.1122	-0.8209	1.1835	0.384	-2.4575	0.5877	1.9354	-0.6653	-0.1648	-0.0022	0.8922	-0.0603	-0.2926	0.8064	0.1765	0.7896	21.4638	79.8954	12.4473
62	0.0542	-0.0205	0.0599	0.0732	0.0063	-0.005	-1.0828	0.9643	0.9453	0.9718	-0.7465	-1.1403	-0.6562	0.9515	0.0023	0.5438	0.1643	-0.0713	0.7018	0.0854	0.7773	22.6943	74.2688	8.7773
63	0.0008	-0.0002	-0.0384	0.02	0.0324	0.0448	-0.2599	-0.7988	-0.6367	-0.1569	0.2516	1.0121	0.1649	-0.0453	0.0001	1.018	0.3483	-0.0424	0.9253	0.041	1.016	25.7104	66.1366	6.8465
64	0.0036	-0.0282	0.004	0.0389	0.0697	0.0352	-0.5609	0.3213	-0.9185	-0.6506	0.2098	-0.0314	0.8041	0.3597	-0.0001	1.0412	0.3782	-0.0705	0.8558	0.0474	1.103	27.8293	63.0949	11.7593
65	0.082	0.0839	-0.1588	0.144	-0.1416	0.0291	-0.0346	0.2767	-0.4318	-0.2679	0.3552	0.5842	0.4467	0.4808	-0.0003	0.4443	0.0991	0.0015	1.0217	-0.0681	0.5985	21.5314	74.5141	18.8576
66	-0.033	-0.0014	0.0367	0.0624	0.0808	0.0623	0.1564	-1.2715	-0.8219	0.3926	-0.5593	-0.3627	0.2707	1.5951	0.0005	0.3986	0.0081	0.2352	0.8603	0.2125	0.4933	22.8989	73.6613	25.9591
67	0.0571	0.0028	0.0142	-0.0827	-0.058	-0.0296	0.0776	0.9374	0.6753	0.137	-0.2656	-0.347	0.7295	0.6307	-0.0003	0.8686	0.2721	-0.031	1.0484	0.3022	0.7497	27.0752	65.2618	24.7419
68	0.0649	0.0744	-0.0409	0.0562	-0.0552	0.024	-0.4211	0.1103	0.3384	-0.4282	-0.011	0.2477	0.0546	0.0673	0.0013	0.3778	0.2203	0.0206	1.0524	0.0586	0.6644	30.6908	75.7208	17.0469
69	0.0694	-0.1374	-0.0235	0.15	0.123	-0.0091	-1.4153	-0.088	-0.5521	1.2183	-0.176	-0.7176	-0.5049	1.4882	0	0.7083	-0.082	-0.031	0.9511	0.1493	0.7489	25.9356	86.2686	19.0899
70	-0.0051	-0.0193	-0.0026	0.0093	0.0679	0.0262	-0.4859	-1.1241	0.6506	0.4393	-0.4159	0.9806	-1.2324	0.2024	-0.0009	1.0742	-0.2557	0.1394	1.1275	-0.0669	1.178	30.7339	83.961	24.2453
71	0.0384	0.0011	-0.011	-0.0097	0.0065	0.03	0.2192	-1.5303	0.6868	-0.0097	-1.2242	-0.1436	0.2146	1.0048	-0.0003	0.7438	0.1229	-0.0368	2.5049	-0.4809	0.8455	31.8677	78.044	29.2936
72	0.0284	-0.0005	-0.0108	-0.0132	0.0003	0.004	0.6301	-0.1191	0.9441	-0.141	-0.169	-1.843	0.4506	0.8996	0.0023	0.6631	0.2298	0.1312	2.779	0.7066	0.9644	35.3652	70.1334	28.6649
73	0.1127	0.0116	0.0239	0.0749	0.1304	0.1389	0.2905	-0.8662	0.3948	-0.4031	-0.6554	-0.8396	-0.0484	1.7195	-0.0001	0.5763	0.0894	-0.0025	1.0139	0.0665	0.8021	34.9124	76.9797	16.3254
74	0.0179	0.0571	0.0003	0.0087	-0.061	-0.0177	-0.0355	0.0193	-1.6579	-1.1776	0.6129	-0.6908	-0.3764	1.4165	0.0001	0.7086	-0.0389	-0.0602	1.28	0.1105	1.1113	36.9657	79.2713	11.5988
75	-0.016	-0.0063	-0.0075	0.0352	-0.0297	0.004	-0.2475	0.6209	-1.2312	0.0223	-0.7328	-0.3058	0.0267	0.5847	0.0007	1.0147	0.2816	0.2251	1.7391	0.1139	1.05	33.0572	75.7703	2.8339
76	0.077	-0.044	0.108	0.0091	-0.0295	0.086	-0.5073	0.1609	-1.3119	-0.9062	0.0368	-1.4672	-0.3655	2.2243	-0.0001	0.8483	0.3105	0.105	1.0939	-0.0672	1.1883	38.1646	69.1129	9.5043

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 4:64)
2	X-RAY DIFFRACTION	2	(chain A and resid 65:69)
3	X-RAY DIFFRACTION	3	(chain A and resid 77:83)
4	X-RAY DIFFRACTION	4	(chain A and resid 84:98)
5	X-RAY DIFFRACTION	5	(chain A and resid 99:128)
6	X-RAY DIFFRACTION	6	(chain A and resid 129:136)
7	X-RAY DIFFRACTION	7	(chain A and resid 137:161)
8	X-RAY DIFFRACTION	8	(chain A and resid 162:171)
9	X-RAY DIFFRACTION	9	(chain A and resid 172:196)
10	X-RAY DIFFRACTION	10	(chain A and resid 197:207)
11	X-RAY DIFFRACTION	11	(chain A and resid 208:213)
12	X-RAY DIFFRACTION	12	(chain A and resid 214:231)
13	X-RAY DIFFRACTION	13	(chain A and resid 232:238)
14	X-RAY DIFFRACTION	14	(chain A and resid 239:258)
15	X-RAY DIFFRACTION	15	(chain A and resid 259:290)
16	X-RAY DIFFRACTION	16	(chain A and resid 291:295)
17	X-RAY DIFFRACTION	17	(chain A and resid 296:324)
18	X-RAY DIFFRACTION	18	(chain A and resid 325:329)
19	X-RAY DIFFRACTION	19	(chain A and resid 330:364)
20	X-RAY DIFFRACTION	20	(chain A and resid 365:376)
21	X-RAY DIFFRACTION	21	(chain B and resid 4:11)
22	X-RAY DIFFRACTION	22	(chain B and resid 12:20)
23	X-RAY DIFFRACTION	23	(chain B and resid 21:26)
24	X-RAY DIFFRACTION	24	(chain B and resid 46:50)
25	X-RAY DIFFRACTION	25	(chain B and resid 51:60)
26	X-RAY DIFFRACTION	26	(chain B and resid 61:102)
27	X-RAY DIFFRACTION	27	(chain B and resid 103:122)
28	X-RAY DIFFRACTION	28	(chain B and resid 123:141)
29	X-RAY DIFFRACTION	29	(chain B and resid 142:163)
30	X-RAY DIFFRACTION	30	(chain B and resid 164:206)
31	X-RAY DIFFRACTION	31	(chain B and resid 207:218)
32	X-RAY DIFFRACTION	32	(chain B and resid 219:234)
33	X-RAY DIFFRACTION	33	(chain B and resid 235:240)
34	X-RAY DIFFRACTION	34	(chain B and resid 241:259)
35	X-RAY DIFFRACTION	35	(chain B and resid 260:273)
36	X-RAY DIFFRACTION	36	(chain B and resid 274:291)
37	X-RAY DIFFRACTION	37	(chain B and resid 295:312)
38	X-RAY DIFFRACTION	38	(chain B and resid 313:320)
39	X-RAY DIFFRACTION	39	(chain B and resid 321:358)
40	X-RAY DIFFRACTION	40	(chain B and resid 359:376)
41	X-RAY DIFFRACTION	41	(chain C and resid 4:10)
42	X-RAY DIFFRACTION	42	(chain C and resid 11:15)
43	X-RAY DIFFRACTION	43	(chain C and resid 16:21)
44	X-RAY DIFFRACTION	44	(chain C and resid 22:28)
45	X-RAY DIFFRACTION	45	(chain C and resid 29:34)
46	X-RAY DIFFRACTION	46	(chain C and resid 35:41)
47	X-RAY DIFFRACTION	47	(chain C and resid 42:46)
48	X-RAY DIFFRACTION	48	(chain C and resid 47:54)
49	X-RAY DIFFRACTION	49	(chain C and resid 55:60)
50	X-RAY DIFFRACTION	50	(chain C and resid 61:67)
51	X-RAY DIFFRACTION	51	(chain C and resid 68:72)
52	X-RAY DIFFRACTION	52	(chain C and resid 73:77)
53	X-RAY DIFFRACTION	53	(chain C and resid 78:83)
54	X-RAY DIFFRACTION	54	(chain C and resid 84:88)
55	X-RAY DIFFRACTION	55	(chain C and resid 89:93)
56	X-RAY DIFFRACTION	56	(chain C and resid 94:101)
57	X-RAY DIFFRACTION	57	(chain C and resid 102:106)
58	X-RAY DIFFRACTION	58	(chain C and resid 107:113)
59	X-RAY DIFFRACTION	59	(chain C and resid 114:119)
60	X-RAY DIFFRACTION	60	(chain D and resid 4:8)
61	X-RAY DIFFRACTION	61	(chain D and resid 9:13)
62	X-RAY DIFFRACTION	62	(chain D and resid 14:20)
63	X-RAY DIFFRACTION	63	(chain D and resid 21:25)
64	X-RAY DIFFRACTION	64	(chain D and resid 26:30)
65	X-RAY DIFFRACTION	65	(chain D and resid 31:36)
66	X-RAY DIFFRACTION	66	(chain D and resid 37:44)
67	X-RAY DIFFRACTION	67	(chain D and resid 45:49)
68	X-RAY DIFFRACTION	68	(chain D and resid 50:54)
69	X-RAY DIFFRACTION	69	(chain D and resid 55:60)
70	X-RAY DIFFRACTION	70	(chain D and resid 61:66)
71	X-RAY DIFFRACTION	71	(chain D and resid 67:71)
72	X-RAY DIFFRACTION	72	(chain D and resid 72:76)
73	X-RAY DIFFRACTION	73	(chain D and resid 77:82)
74	X-RAY DIFFRACTION	74	(chain D and resid 99:104)
75	X-RAY DIFFRACTION	75	(chain D and resid 105:109)
76	X-RAY DIFFRACTION	76	(chain D and resid 110:119)

-
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://pdbjlc1.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

-
Protein , 2 types, 4 molecules ABCD

-
Non-polymers , 4 types, 242 molecules

-
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

-Protein , 2 types, 4 molecules ABCD

-Non-polymers , 4 types, 242 molecules

-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

-
Protein , 2 types, 4 molecules ABCD

-
Non-polymers , 4 types, 242 molecules

-
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