PDB-6ojm: Crystal structure of 1,4-dihydroxy-2-naphthoyl-CoA synthase Eliza...

ID or keywords:

Entry

Database: PDB / ID: 6ojm

Title

Crystal structure of 1,4-dihydroxy-2-naphthoyl-CoA synthase Elizabethkingia anophelis NUHP1

Components

1,4-dihydroxy-2-naphthoyl-CoA synthase

Keywords

LYASE / SSGCID /

Structural Genomics / DHNA-CoA synthase / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase activity / menaquinone biosynthetic process
Similarity search - Function

Biological species

Elizabethkingia anophelis NUHP1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of 1,4-dihydroxy-2-naphthoyl-CoA synthase Elizabethkingia anophelis NUHP1
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Apr 11, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 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	6ojm.cif.gz	661.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6ojm.ent.gz	544.8 KB	Display	PDB format
PDBx/mmJSON format	6ojm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oj/6ojm ftp://data.pdbj.org/pub/pdb/validation_reports/oj/6ojm	HTTPS FTP

-
Related structure data

Related structure data	3t8aS S: Starting model for refinement
Similar structure data	2ppy-d 2qq3-1 4jcs-1 4eml-d 4i4z-1 4elx-d 4izd-1 4i4z-2 1uiy-1 5k45-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-ElanA.01530.a

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 1,4-dihydroxy-2-naphthoyl-CoA synthase

B: 1,4-dihydroxy-2-naphthoyl-CoA synthase

C: 1,4-dihydroxy-2-naphthoyl-CoA synthase

D: 1,4-dihydroxy-2-naphthoyl-CoA synthase

E: 1,4-dihydroxy-2-naphthoyl-CoA synthase

F: 1,4-dihydroxy-2-naphthoyl-CoA synthase

192 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 1,4-dihydroxy-2-naphthoyl-CoA synthase

B: 1,4-dihydroxy-2-naphthoyl-CoA synthase

A: 1,4-dihydroxy-2-naphthoyl-CoA synthase

B: 1,4-dihydroxy-2-naphthoyl-CoA synthase

A: 1,4-dihydroxy-2-naphthoyl-CoA synthase

B: 1,4-dihydroxy-2-naphthoyl-CoA synthase

defined by author&software
192 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: 1,4-dihydroxy-2-naphthoyl-CoA synthase

D: 1,4-dihydroxy-2-naphthoyl-CoA synthase

C: 1,4-dihydroxy-2-naphthoyl-CoA synthase

D: 1,4-dihydroxy-2-naphthoyl-CoA synthase

C: 1,4-dihydroxy-2-naphthoyl-CoA synthase

D: 1,4-dihydroxy-2-naphthoyl-CoA synthase

defined by author&software
192 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: 1,4-dihydroxy-2-naphthoyl-CoA synthase

F: 1,4-dihydroxy-2-naphthoyl-CoA synthase

E: 1,4-dihydroxy-2-naphthoyl-CoA synthase

F: 1,4-dihydroxy-2-naphthoyl-CoA synthase

E: 1,4-dihydroxy-2-naphthoyl-CoA synthase

F: 1,4-dihydroxy-2-naphthoyl-CoA synthase

defined by author&software
192 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	138.490, 138.490, 141.430
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	150
Space group name H-M	P321

Components on special symmetry positions

ID	Model	Components
1	1	F-70- ASP
2	1	A-493- HOH
3	1	A-516- HOH
4	1	A-542- HOH
5	1	A-555- HOH
6	1	A-557- HOH
7	1	B-493- HOH
8	1	B-526- HOH
9	1	B-535- HOH
10	1	B-536- HOH
11	1	C-473- HOH
12	1	C-508- HOH
13	1	C-509- HOH
14	1	C-518- HOH
15	1	C-519- HOH
16	1	D-474- HOH
17	1	D-507- HOH
18	1	D-515- HOH
19	1	D-516- HOH
20	1	E-483- HOH
21	1	E-506- HOH
22	1	E-535- HOH
23	1	E-549- HOH
24	1	E-550- HOH
25	1	E-551- HOH
26	1	F-467- HOH
27	1	F-487- HOH
28	1	F-493- HOH
29	1	F-508- HOH
30	1	F-543- HOH
31	1	F-556- HOH
32	1	F-557- HOH

#1: Protein	1,4-dihydroxy-2-naphthoyl-CoA synthase / DHNA-CoA synthase Mass: 32083.297 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria) Gene: menB, BD94_2634 / Plasmid: ElanA.01530.a.B1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) References: UniProt: A0A077EJG6, 1,4-dihydroxy-2-naphthoyl-CoA synthase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1449 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

1,4-dihydroxy-2-naphthoyl-CoA synthase / DHNA-CoA synthase

Mass: 32083.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Elizabethkingia anophelis NUHP1 (bacteria)
Gene: menB, BD94_2634 / Plasmid: ElanA.01530.a.B1
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)
References: UniProt: A0A077EJG6, 1,4-dihydroxy-2-naphthoyl-CoA synthase

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 1449 / 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: 2.04 Å³/Da / Density % sol: 39.65 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Molecular Dimensions Morpheus screen, C7: 10% (w/v) PEG 4000, 20% (v/v) glycerol, 30mM of each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate: 100mM MOPS/HEPES-Na pH 7.5: ...Details: Molecular Dimensions Morpheus screen, C7: 10% (w/v) PEG 4000, 20% (v/v) glycerol, 30mM of each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate: 100mM MOPS/HEPES-Na pH 7.5: ElanA.01530.a.B1.PW38414 at 20.1 mg/ml: cryo: direct: tray 298241c7: puck uya9-1

Crystal

Density Matthews: 2.04 Å³/Da / Density % sol: 39.65 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Molecular Dimensions Morpheus screen, C7: 10% (w/v) PEG 4000, 20% (v/v) glycerol, 30mM of each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate: 100mM MOPS/HEPES-Na pH 7.5: ...

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 12, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.6→43.876 Å / Num. obs: 204876 / % possible obs: 99.7 % / Redundancy: 6.191 % / B_iso Wilson estimate: 23.947 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.053 / R_rim(I) all: 0.057 / Χ²: 1.029 / Net I/σ(I): 21.94

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.6-1.64	6.25	0.5	3.46	14987	0.887	0.545	99.4
1.64-1.69	6.255	0.414	4.2	14631	0.914	0.451	99.5
1.69-1.74	6.254	0.345	5.01	14283	0.941	0.376	99.7
1.74-1.79	6.258	0.276	6.36	13796	0.961	0.301	99.6
1.79-1.85	6.263	0.224	7.96	13472	0.972	0.244	99.7
1.85-1.91	6.237	0.173	10.26	12984	0.985	0.188	99.8
1.91-1.98	6.209	0.137	12.95	12615	0.991	0.15	99.9
1.98-2.07	6.208	0.109	16.01	12129	0.994	0.119	99.9
2.07-2.16	6.183	0.087	19.9	11662	0.996	0.095	99.9
2.16-2.26	6.16	0.072	23.41	11101	0.999	0.079	99.9
2.26-2.39	6.192	0.061	27.28	10622	0.998	0.066	100
2.39-2.53	6.215	0.054	29.99	10042	0.998	0.059	99.9
2.53-2.7	6.192	0.048	33.7	9454	0.998	0.052	99.9
2.7-2.92	6.194	0.039	39.55	8775	0.999	0.043	99.9
2.92-3.2	6.149	0.032	45.46	8156	0.999	0.035	99.9
3.2-3.58	6.075	0.027	52.41	7342	0.999	0.03	99.8
3.58-4.13	6.016	0.024	58.23	6530	0.999	0.026	99.6
4.13-5.06	5.992	0.022	61.91	5513	1	0.024	99.4
5.06-7.16	5.981	0.023	57.55	4339	0.999	0.026	99.4
7.16-43.876	5.691	0.021	60.93	2443	0.999	0.024	97.4

-
Processing

Software

Name	Version	Classification
PHENIX		refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
MoRDa		phasing
PHASER		phasing
ARP/wARP		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3t8a, chain A

3t8a

Resolution: 1.6→43.876 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1753	1983	0.97 %	0
R_work	0.145	-	-	-
obs	0.1453	204839	99.71 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 73.18 Å² / B_iso mean: 21.7539 Å² / B_iso min: 3.72 Å²

Refinement step

Cycle: final / Resolution: 1.6→43.876 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12518	0	0	1470	13988
B_iso mean	-	-	-	32.73	-
Num. residues	-	-	-	-	1616

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	13146
X-RAY DIFFRACTION	f_angle_d	0.91	17833
X-RAY DIFFRACTION	f_dihedral_angle_d	13.551	7873
X-RAY DIFFRACTION	f_chiral_restr	0.059	1884
X-RAY DIFFRACTION	f_plane_restr	0.006	2348

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.64	0.2301	151	0.1916	14300	14451	99
1.64-1.6844	0.2178	155	0.1721	14344	14499	99
1.6844-1.7339	0.1705	147	0.1603	14378	14525	100
1.7339-1.7899	0.2176	162	0.1536	14329	14491	100
1.7899-1.8539	0.1823	126	0.152	14409	14535	100
1.8539-1.9281	0.1913	157	0.1529	14423	14580	100
1.9281-2.0159	0.2073	115	0.1443	14480	14595	100
2.0159-2.1221	0.1656	151	0.1428	14445	14596	100
2.1221-2.2551	0.1889	138	0.1415	14465	14603	100
2.2551-2.4292	0.1789	158	0.1425	14524	14682	100
2.4292-2.6736	0.1613	137	0.1463	14576	14713	100
2.6736-3.0604	0.1797	110	0.1445	14600	14710	100
3.0604-3.8555	0.1557	131	0.1338	14670	14801	100
3.8555-43.892	0.1587	145	0.1412	14913	15058	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	2.0775	0.1128	-0.2085	2.9531	0.532	1.624	0.0141	-0.0294	0.1557	0.1097	0.0213	-0.2879	-0.055	0.1987	-0.0347	0.0806	0.0084	-0.0324	0.1732	-0.022	0.1934	-38.6235	40.6801	16.3831
2	0.9264	-0.4958	-0.8658	2.5911	1.2603	3.4922	0.1575	0.6233	0.4198	-0.547	0.205	-0.4183	-0.7514	0.4412	-0.3077	0.295	-0.0963	0.0718	0.391	0.0557	0.3092	-43.8931	52.6458	11.7193
3	0.5698	-0.1458	0.0624	0.6173	-0.0731	0.5645	0.0002	-0.0259	0.01	0.0394	0.0205	-0.0545	0.0127	0.078	-0.0207	0.0703	0.0023	-0.0031	0.0941	-0.0063	0.1055	-55.1542	39.5049	14.6638
4	4.1925	0.8216	-2.2504	3.5696	-0.9723	4.6991	-0.2331	0.2522	-0.5758	-0.1989	0.1804	-0.3007	0.4374	0.2737	0.1213	0.3315	0.0777	-0.0299	0.1828	-0.0721	0.3062	-55.8315	10.1761	-14.3324
5	2.4706	-0.3636	0.0589	4.4537	0.3923	1.1213	0.035	0.1334	0.1174	-0.2205	-0.0633	-0.5096	-0.0487	0.3907	0.0078	0.129	-0.0134	0.0522	0.3023	-0.0462	0.2281	-34.2047	42.554	-19.6042
6	2.1473	-0.4929	-0.1153	4.5966	-0.3919	2.0712	0.0116	0.1317	-0.1959	-0.3061	0.0488	-0.1719	0.2208	0.2678	-0.0391	0.1189	0.0222	0.0092	0.2435	-0.0461	0.1831	-39.9854	33.5662	-21.0987
7	1.4984	-0.1321	0.0473	2.9856	-0.1358	1.6446	0.0147	-0.0996	0.0774	0.1767	0.0266	-0.1817	-0.0453	0.2519	-0.0539	0.1058	-0.0022	0.0191	0.2428	-0.029	0.1762	-40.6508	41.6998	-12.1476
8	1.512	-0.1163	-0.2346	1.8437	-0.0339	2.1348	-0.0266	-0.0579	-0.3416	0.0683	0.0133	-0.0886	0.4313	0.379	-0.0055	0.1418	0.0598	-0.0094	0.2077	-0.0013	0.2289	-44.2025	28.5091	-12.9977
9	1.0655	0.4338	-0.1867	0.9508	0.1197	0.7865	-0.0179	0.1344	-0.0633	-0.1213	0.0455	-0.0618	0.0381	0.0614	-0.0264	0.1116	0.0105	0.0049	0.1294	-0.0161	0.1025	-57.1911	33.4333	-21.5118
10	1.4699	-1.9155	-1.8824	6.3577	5.781	5.5204	0.0813	0.1111	0.0688	-0.4279	0.0975	-0.2838	-0.3284	0.2273	-0.1962	0.1693	-0.0282	0.0464	0.1852	0.0168	0.1496	-47.8053	50.2481	-26.7384
11	0.7728	-1.153	-0.5367	2.0997	0.0155	2.5305	0.0305	-0.0651	0.1179	0.0755	0.0181	-0.1441	-0.2425	0.1824	-0.0549	0.093	-0.0173	0.0007	0.1137	-0.0104	0.1098	-56.2192	51.7868	-3.8228
12	6.7596	-1.8752	3.3875	3.8444	-0.6634	7.4532	-0.1988	0.19	0.3393	-0.0395	0.1701	-0.5628	-0.34	0.833	0.1037	0.2297	-0.0852	0.0361	0.2669	-0.0478	0.3187	-50.0096	67.5911	10.8812
13	6.2358	-3.4555	4.0278	2.031	-2.5645	3.6969	-0.4122	-0.0935	0.5817	0.272	0.1998	-0.2334	-0.5651	0.0902	0.2179	0.2807	-0.0437	0.0166	0.1574	-0.0467	0.2364	-59.1157	70.9351	12.9369
14	3.0652	-0.6182	-0.6421	2.8449	0.9936	2.0904	0.1271	0.013	0.171	-0.0029	0.0139	-0.4072	-0.2432	0.2557	-0.0981	0.2288	-0.0783	0.0325	0.1445	0.0174	0.2163	-52.9252	65.0278	53.6787
15	0.691	-0.1309	-0.0141	0.8541	-0.1445	0.9155	0.0268	-0.0016	0.0772	0.0152	0.0223	0.031	-0.1705	-0.021	-0.057	0.1325	-0.0066	0.0109	0.0948	-0.0001	0.1073	-66.7777	54.4189	58.8371
16	3.8283	-1.1807	0.5002	2.8818	-0.3751	1.3533	-0.0608	-0.1276	0.3575	-0.0241	0.0473	-0.1306	-0.3117	0.1009	0.0143	0.2713	-0.0897	0.0221	0.1601	-0.043	0.1873	-54.9001	67.0065	86.349
17	4.0372	0.1035	-0.3979	3.2604	1.4522	6.2438	0.0409	-0.1627	0.3695	-0.0629	0.0633	0.3506	-0.7007	-0.3046	-0.0845	0.3618	0.0169	0.0432	0.1776	-0.0189	0.2525	-67.4367	69.0776	92.5094
18	1.0924	0.1593	-0.0541	0.254	-0.0371	0.684	0.0318	-0.1287	0.0652	0.0627	0.0034	-0.0206	-0.1245	0.0241	-0.0332	0.1865	-0.0106	0.005	0.1384	-0.0208	0.116	-65.1457	54.2049	90.3429
19	0.5463	-0.9274	0.1973	1.8915	0.5468	2.636	-0.0457	0.0138	0.0541	-0.0488	0.0783	-0.1579	-0.0582	0.3628	-0.0316	0.1196	-0.0216	0.0054	0.1612	-0.0114	0.1131	-52.4167	45.7955	73.3339
20	1.9213	0.565	-0.2131	6.671	-2.3636	3.5248	0.156	-0.1589	0.1131	-0.2296	-0.2115	-0.4211	-0.1239	0.5167	0.0731	0.164	-0.0022	0.0332	0.4065	-0.0578	0.2682	-36.4869	38.317	57.795
21	3.1814	0.5486	0.1883	3.3021	-0.2158	1.0377	0.0829	-0.238	0.0686	0.2355	0.0068	0.3836	-0.1026	-0.1922	-0.0567	0.1553	0.0563	0.0906	0.2185	-0.002	0.1716	-27.8803	15.6799	54.2371
22	1.9687	0.476	0.0199	1.6759	-0.2123	0.9297	0.0044	-0.0901	0.0409	0.0797	0.0543	0.2909	-0.0776	-0.1435	-0.0812	0.1292	0.0589	0.0643	0.187	0.0072	0.1904	-25.3139	13.7313	50.3397
23	2.3079	-0.1127	0.2052	2.144	-1.8869	6.4883	0.3873	0.4627	-0.2735	-0.3529	0.1595	0.5325	0.2791	-0.701	-0.5184	0.206	0.0415	-0.0411	0.3745	0.0249	0.295	-27.9443	2.2151	48.0069
24	0.4867	-0.1997	-0.1512	1.0165	-0.0095	0.6971	0.0022	-0.1346	-0.0076	0.1524	0.0334	0.0707	-0.0102	-0.0991	-0.035	0.114	0.0085	0.0246	0.1484	0.0146	0.0913	-14.1041	1.6902	53.4109
25	1.8998	1.1688	-1.5894	1.6524	-1.1567	1.7799	0.121	-0.2602	0.1776	0.3474	-0.053	0.1672	-0.2543	-0.0242	-0.0861	0.2276	0.0378	0.0529	0.2027	-0.0492	0.1439	-12.7478	19.8847	60.07
26	1.067	0.4704	-0.2207	0.3295	0.2854	1.6727	0.0398	-0.0087	0.1911	-0.0377	0.0144	-0.0146	-0.2874	-0.0428	-0.0601	0.1293	0.016	0.0227	0.0898	-0.0006	0.1117	-4.9019	17.4142	37.1449
27	7.6904	-2.8584	2.6063	4.6574	-0.9857	4.2926	-0.0422	0.3784	0.6192	-0.0008	0.027	-0.0784	-0.3695	-0.0519	0.0155	0.2723	-0.0172	0.0525	0.1115	0.0336	0.241	3.6389	32.4507	21.585
28	4.0119	-0.2211	-1.1664	1.9865	-1.5976	1.7438	-0.0007	0.0337	0.1975	-0.1465	-0.1154	0.6218	-0.0263	-0.3312	0.0977	0.0927	0.0644	-0.0205	0.1806	0.0331	0.2137	-32.5067	16.0733	15.5524
29	1.8107	0.5828	-0.0422	3.3574	0.234	1.4313	-0.0238	-0.0481	0.1369	-0.0419	0.0463	0.1288	-0.0879	-0.1155	-0.0278	0.0696	0.0498	0.0023	0.1294	0.021	0.1362	-24.7715	15.6237	19.7477
30	1.1317	-0.0004	-0.0022	1.2478	0.1109	1.2379	0.0155	-0.0916	0.3272	0.1401	0.0711	-0.0545	-0.5157	-0.0539	-0.0789	0.2186	0.0405	0.0305	0.1278	-0.0154	0.2279	-15.7488	22.705	23.3382
31	0.9698	0.1867	0.0726	0.4304	-0.0192	0.4715	0.0142	0.0934	0.0372	-0.0421	0.0098	0.0254	-0.0531	-0.0374	-0.018	0.0996	0.0145	0.0045	0.1012	0.011	0.1015	-10.0617	9.9557	13.5789
32	0.0846	-0.2272	0.3257	2.0556	0.0006	1.7981	0.0238	-0.0948	-0.0709	0.0631	-0.0134	0.1653	0.1208	-0.2518	-0.028	0.0763	-0.0048	0.0081	0.1186	0.0149	0.0979	-17.2001	-3.5808	32.2154
33	5.5556	0.0373	-1.6893	2.7728	-0.1947	3.2494	-0.0584	-0.0767	-0.2931	0.4848	0.33	0.703	0.0021	-0.7238	-0.1953	0.2597	-0.0339	0.0479	0.4498	0.1804	0.35	-26.9816	-18.5639	47.8322

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 1 through 73 )	A	1 - 73
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 74 through 99 )	A	74 - 99
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 100 through 252 )	A	100 - 252
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 253 through 278 )	A	253 - 278
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 18 )	B	1 - 18
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 19 through 36 )	B	19 - 36
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 37 through 63 )	B	37 - 63
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 64 through 109 )	B	64 - 109
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 110 through 199 )	B	110 - 199
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 200 through 218 )	B	200 - 218
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 219 through 252 )	B	219 - 252
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 253 through 264 )	B	253 - 264
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 265 through 278 )	B	265 - 278
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1 through 99 )	C	1 - 99
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 100 through 278 )	C	100 - 278
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 63 )	D	1 - 63
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 64 through 99 )	D	64 - 99
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 100 through 218 )	D	100 - 218
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 219 through 252 )	D	219 - 252
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 253 through 278 )	D	253 - 278
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 1 through 36 )	E	1 - 36
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 37 through 73 )	E	37 - 73
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 74 through 99 )	E	74 - 99
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 100 through 199 )	E	100 - 199
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 200 through 218 )	E	200 - 218
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 219 through 252 )	E	219 - 252
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 253 through 278 )	E	253 - 278
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 1 through 12 )	F	1 - 12
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 13 through 63 )	F	13 - 63
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 64 through 109 )	F	64 - 109
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 110 through 218 )	F	110 - 218
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 219 through 252 )	F	219 - 252
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 253 through 278 )	F	253 - 278

-
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