PDB-5odu: PllA lectin, monosaccharide complex

ID or keywords:

Entry

Database: PDB / ID: 5odu

Title

PllA lectin, monosaccharide complex

Components

PllA

Keywords

SUGAR BINDING PROTEIN / PllA / Complex / Lectin / CARBOHYDRATE

Function / homology

Function and homology information

carbohydrate binding / metal ion binding
Similarity search - Function

Biological species

Photorhabdus luminescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.56 Å

Authors

Koehnke, J. / Sikandar, A.

Funding support

Germany, 1items

Citation

Journal: J. Biol. Chem. / Year: 2017
Title: Photorhabdus luminescens lectin A (PllA): A new probe for detecting alpha-galactoside-terminating glycoconjugates.
Authors: Beshr, G. / Sikandar, A. / Jemiller, E.M. / Klymiuk, N. / Hauck, D. / Wagner, S. / Wolf, E. / Koehnke, J. / Titz, A.

History

Deposition	Jul 6, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 4, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2017	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Dec 13, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5odu.cif.gz	400.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5odu.ent.gz	329.4 KB	Display	PDB format
PDBx/mmJSON format	5odu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	5ofiC 5ofxC 5ofzC 1l7lS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4zt7-1 6p5v-d 4c8z-d 4daf-2 2dwy-d 4owr-d 5ofi-1 5b4d-d 6cml-1 5j58-1 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) 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

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PllA

B: PllA

C: PllA

D: PllA

E: PllA

F: PllA

G: PllA

H: PllA

hetero molecules

106 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

F: PllA

G: PllA

hetero molecules

A: PllA

C: PllA

hetero molecules

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

2

A: PllA

C: PllA

hetero molecules

F: PllA

G: PllA

hetero molecules

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

3

E: PllA

hetero molecules

B: PllA

D: PllA

H: PllA

hetero molecules

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

4

B: PllA

D: PllA

H: PllA

hetero molecules

E: PllA

hetero molecules

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

Unit cell

Length a, b, c (Å)	62.904, 103.342, 76.086
Angle α, β, γ (deg.)	90.00, 93.05, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

PllA

Mass: 12969.544 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Photorhabdus luminescens (bacteria) / Gene: plu2096 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7N561

#2: Sugar

ChemComp-AMG / methyl alpha-D-galactopyranoside / ALPHA-METHYL-D-GALACTOSIDE / methyl alpha-D-galactoside / methyl D-galactoside / methyl galactoside

Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₇H₁₄O₆

#3: Chemical

ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1263 / 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: 2.38 Å³/Da / Density % sol: 48.32 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium acetate,0.1M BIS-Tris ph 5.5, 25 % w/v PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9677 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 22, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 1.56→51.67 Å / Num. all: 597157 / Num. obs: 133175 / % possible obs: 96.18 % / Redundancy: 4.5 % / B_iso Wilson estimate: 14.93 Å² / R_merge(I) obs: 0.09883 / R_pim(I) all: 0.05232 / R_rim(I) all: 0.1121 / Net I/σ(I): 11.19
Reflection shell	Resolution: 1.56→1.616 Å / Redundancy: 4.6 % / R_merge(I) obs: 1.261 / Mean I/σ(I) obs: 1.22 / Num. measured obs: 60933 / Num. unique obs: 13311 / R_pim(I) all: 0.6619 / R_rim(I) all: 1.427 / % possible all: 95.63

-
Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1L7L

1l7l

Resolution: 1.56→51.671 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2277	6492	4.9 %
R_work	0.1984	-	-
obs	0.1999	132564	96.15 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.56→51.671 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7264	0	112	1263	8639

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7544
X-RAY DIFFRACTION	f_angle_d	0.575	10304
X-RAY DIFFRACTION	f_dihedral_angle_d	10.017	4392
X-RAY DIFFRACTION	f_chiral_restr	0.053	1176
X-RAY DIFFRACTION	f_plane_restr	0.005	1344

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 (%)
1.5596-1.5774	0.3389	205	0.3538	4117	X-RAY DIFFRACTION	94
1.5774-1.5959	0.3699	196	0.3501	4165	X-RAY DIFFRACTION	96
1.5959-1.6154	0.3623	202	0.3502	4228	X-RAY DIFFRACTION	96
1.6154-1.6358	0.3744	220	0.3418	4152	X-RAY DIFFRACTION	97
1.6358-1.6574	0.3464	201	0.337	4257	X-RAY DIFFRACTION	96
1.6574-1.6801	0.3954	209	0.3339	4173	X-RAY DIFFRACTION	97
1.6801-1.7041	0.3664	225	0.3289	4201	X-RAY DIFFRACTION	97
1.7041-1.7295	0.3623	200	0.3058	4229	X-RAY DIFFRACTION	97
1.7295-1.7565	0.3315	261	0.2956	4181	X-RAY DIFFRACTION	97
1.7565-1.7853	0.3239	233	0.2744	4223	X-RAY DIFFRACTION	97
1.7853-1.8161	0.3139	206	0.2705	4206	X-RAY DIFFRACTION	97
1.8161-1.8491	0.3216	212	0.253	4293	X-RAY DIFFRACTION	97
1.8491-1.8847	0.2875	204	0.2405	4235	X-RAY DIFFRACTION	97
1.8847-1.9232	0.294	218	0.2291	4221	X-RAY DIFFRACTION	97
1.9232-1.965	0.2664	198	0.218	4280	X-RAY DIFFRACTION	97
1.965-2.0107	0.2508	209	0.212	4248	X-RAY DIFFRACTION	97
2.0107-2.061	0.2283	207	0.1916	4254	X-RAY DIFFRACTION	97
2.061-2.1167	0.2209	227	0.1821	4228	X-RAY DIFFRACTION	97
2.1167-2.179	0.2176	215	0.1746	4251	X-RAY DIFFRACTION	97
2.179-2.2493	0.2048	207	0.1739	4213	X-RAY DIFFRACTION	96
2.2493-2.3297	0.2319	186	0.1741	4130	X-RAY DIFFRACTION	94
2.3297-2.423	0.2291	169	0.1807	3616	X-RAY DIFFRACTION	82
2.423-2.5333	0.2283	185	0.1724	3509	X-RAY DIFFRACTION	80
2.5333-2.6668	0.2057	229	0.1757	4280	X-RAY DIFFRACTION	98
2.6668-2.8339	0.204	227	0.1706	4333	X-RAY DIFFRACTION	99
2.8339-3.0527	0.2087	264	0.1685	4322	X-RAY DIFFRACTION	99
3.0527-3.3599	0.1944	209	0.1636	4392	X-RAY DIFFRACTION	100
3.3599-3.8459	0.1786	272	0.1559	4336	X-RAY DIFFRACTION	100
3.8459-4.8449	0.1555	240	0.1468	4398	X-RAY DIFFRACTION	100
4.8449-51.6994	0.1872	256	0.1842	4401	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	0.061	0.0945	0.0906	0.1477	0.1477	0.1472	-0.1023	-0.133	-0.0461	-0.0255	-0.0616	0.1225	-0.0277	0.027	-0.0597	0.1132	0.0193	0.0729	0.1912	0.0658	0.1927	-33.529	-6.3598	-21.4611
2	0.0129	-0.0087	-0.011	0.0028	0.0073	0.0062	0.0457	0.0431	0.0634	0.1368	-0.0854	0.1131	-0.0579	-0.1139	-0.0224	0.1694	0.051	0.0908	0.152	0.067	0.2609	-33.5215	4.2751	-23.4226
3	0.2674	-0.0393	-0.1517	0.5177	-0.1011	0.111	0.0753	0.1404	0.1055	0.0738	0.0248	0.0496	-0.0675	-0.0988	0.1879	0.1052	0.0277	0.0276	0.144	0.0459	0.1378	-25.8534	-0.6223	-32.2482
4	0.0168	0.0039	0.0059	-0.0008	0.0015	0.0128	0.0894	0.1788	0.2287	0.1266	0.0312	-0.0483	-0.2196	-0.0291	0.0181	0.1959	0.0098	0.0197	0.0635	0.0088	0.2021	-22.2021	3.9855	-21.1341
5	0.2217	-0.0103	-0.0322	0.4319	0.1112	0.085	0.0459	0.1243	0.0923	0.1633	-0.0211	0.0035	-0.0263	-0.0775	0.0821	0.1113	0.0199	0.0246	0.0976	0.0357	0.1334	-26.5086	-1.2065	-24.1899
6	0.0038	0.0056	-0.0003	0.0095	-0.0109	0.0072	0.0386	-0.0688	0.0312	0.0905	0.0524	-0.0583	-0.123	-0.0005	0.0101	0.2712	-0.0229	-0.0278	0.1065	0.0106	0.1543	-14.9527	-9.3407	-3.4263
7	0.0105	0.0013	0.018	0.0308	0.0053	0.0148	0.0217	-0.0733	0.1689	0.0649	-0.0169	-0.2193	-0.1765	0.1667	0.0001	0.1743	-0.0329	-0.004	0.1468	-0.0121	0.1533	-46.5404	5.7682	-61.5232
8	0.1672	0.0496	-0.1956	0.1135	0.0717	0.2428	0.0328	-0.0537	0.0039	-0.0802	0.0456	0.0191	-0.0235	0.016	0.0884	0.119	-0.005	-0.0053	0.0703	0.0125	0.1254	-55.273	1.1612	-69.1798
9	0.0056	-0.0021	0.0025	0.0096	0.0047	0.0121	0.0013	0.073	-0.0413	-0.1047	0.0179	-0.0052	-0.029	0.1846	0	0.1336	0.0151	0.0024	0.1339	-0.0104	0.1447	-46.1287	-6.1957	-64.685
10	0.1851	-0.1716	-0.0137	0.0067	-0.011	0.1514	0.0154	-0.089	0.0048	-0.0288	0.0275	-0.0192	-0.0192	0.1485	0.0298	0.1154	-0.0036	0.0059	0.1078	0.0151	0.1228	-50.337	-0.3292	-62.9114
11	0.0088	0.0104	-0.0086	0.0045	-0.0061	0.0052	0.0809	-0.0904	0.091	-0.0287	0.0142	-0.0934	0.0285	0.0912	-0	0.173	0.0044	-0.0239	0.1983	0.027	0.145	-46.5635	-15.629	-43.0224
12	0.0146	0.0003	-0.0141	0.0515	0.0092	0.0308	-0.0607	-0.1354	-0.1086	-0.0669	-0.0347	-0.0851	0.0056	0.0119	-0.0011	0.1032	0.0152	0.0076	0.2121	0.0194	0.1789	-12.5979	-18.1669	-32.0688
13	0.001	-0.0061	-0.0017	0.0014	-0.0049	0.0039	0.0432	0.1049	-0.1473	-0.1035	0.0066	-0.1187	0.1272	0.036	-0	0.1543	0.0148	0.0171	0.199	-0.0344	0.1859	-15.2307	-23.2897	-41.149
14	0.0045	0.0017	-0.0006	0.0045	-0.0116	0.0124	0.0565	0.07	-0.046	0.0434	-0.0418	0.1024	0.1043	0.0283	0.0007	0.2258	0.0204	0.0021	0.1152	-0.0244	0.1869	-19.2264	-30.783	-24.4357
15	0.0188	-0.0036	0.0076	0.3648	0.0274	0.0196	0.0612	0.2165	-0.0165	0.1211	-0.0002	0.0473	0.0212	-0.1269	-0.007	0.0388	-0.0001	-0.0007	0.172	0.0234	0.0935	-21.7578	-11.3948	-40.4798
16	0.0388	-0.0196	-0.0284	0.0288	0.0075	0.0199	0.0152	0.1793	0.014	0.0391	0.0419	0.1177	0.0003	-0.2239	0.0006	0.0951	-0.0032	-0.0062	0.2265	0.0117	0.1294	-28.9922	-11.8647	-44.0496
17	0.0118	-0.0023	-0.0123	0.008	-0.0058	0.0108	0.0989	0.1882	-0.0239	-0.0021	-0.0093	0.0243	0.1849	-0.0052	0.0104	0.1519	-0.0287	-0.0058	0.1385	-0.05	0.1648	-24.7984	-26.7941	-35.4451
18	-0.0214	0.014	-0.0031	0.1524	-0.0296	0.0257	0.0092	0.0981	-0.0597	0.026	-0.0063	-0.0237	0.0628	-0.1151	0.001	0.1243	-0.0108	0.0039	0.1578	-0.0258	0.1366	-22.496	-21.7071	-36.9151
19	0.0185	0.0156	-0.0015	0.0148	0.0123	0.0144	0.022	0.0573	0.0004	0.0546	-0.0195	0.0175	0.0181	0.0717	0	0.1329	-0.0122	-0.0068	0.1419	0.0066	0.1353	-16.6046	-16.9149	-28.8929
20	0.0293	0.001	-0.0096	0.0039	0.0079	0.0215	-0.1171	0.0319	-0.007	0.0016	-0.0562	0.0507	0.0868	0.0406	-0.003	0.191	-0.0066	0.0168	0.1079	0.0051	0.1901	-22.5339	-32.9149	-13.0029
21	-0.0005	0.011	0.008	0.1597	0.0592	0.0234	0.0537	0.0625	-0.0467	0.0737	0.0759	-0.1146	-0.0446	0.0282	0.0099	0.1052	-0.0149	0.0223	0.1986	0.0251	0.1345	-44.8475	-2.1598	-31.4567
22	0.0022	-0.016	0.0251	0.0445	0.0169	0.021	-0.1367	0.0602	0.0618	0.1138	-0.0849	0.0026	-0.2496	0.0186	-0	0.146	0.0095	-0.0122	0.2055	-0.0128	0.1437	-49.8764	5.6358	-28.7002
23	0.0645	-0.0718	-0.0067	0.1318	0.0401	0.0371	0.0775	-0.0494	0.0133	0.0527	-0.0688	-0.0404	0.0862	-0.0759	0.0336	0.1472	-0.0727	-0.0403	0.1814	0.0443	0.1282	-48.8011	-9.1649	-19.678
24	0.2619	0.0242	0.1291	-0.0013	0.02	0.0592	0.2203	-0.1069	-0.0023	0.2803	0.0327	0.1277	-0.0076	-0.2587	0.2207	-0.3802	-0.4128	0.0761	0.2573	0.0767	0.1253	-54.1542	-8.9949	-13.5343
25	0.0777	-0.0107	0.0101	0.0415	-0.0181	0.0055	-0.0193	-0.1589	-0.0987	0.0467	-0.1428	0.0037	-0.2209	-0.1244	-0.0072	0.1683	0.0235	0.0042	0.3547	-0.0492	0.1198	-56.2389	4.6734	-24.0781
26	0.0562	0.0969	0.1181	0.0926	0.0577	0.0811	-0.0238	-0.1932	-0.0203	-0.035	-0.0282	-0.0032	0	-0.3297	-0.0039	0.1234	0.0079	-0.004	0.222	0.01	0.1195	-51.7851	-0.9177	-25.7618
27	0.0096	0.0026	0.0082	0.0011	-0.0043	0.0073	0.0353	-0.0428	0.0314	-0.0215	-0.0383	-0.075	-0.035	-0.0437	0.0001	0.1969	0.054	-0.03	0.2145	-0.0151	0.1544	-63.5088	8.1603	-45.9782
28	0.023	0.0389	-0.0163	0.0374	-0.016	0.0177	0.0382	-0.1184	-0.1224	0.0124	0.082	0.0938	0.0578	-0.2708	-0.0015	0.1068	-0.0178	-0.0176	0.1902	0.0476	0.1486	-13.3176	-5.0321	-59.6969
29	0.0041	0.0065	-0.0048	0.0008	0.0023	0.004	-0.0157	-0.1005	-0.0039	0.0357	0.0914	0.0631	-0.0967	-0.0415	0.0044	0.1239	0.0145	0.0076	0.3472	0.0536	0.1977	-10.6828	-1.5862	-43.3515
30	0.1299	0.0018	0.0021	0.0904	-0.0851	0.0338	0.0174	-0.0434	0.0427	-0.0868	-0.0298	0.0644	-0.0191	-0.0303	-0.0194	0.1389	0.0234	-0.0219	0.0928	0.0214	0.1199	-6.4779	5.905	-68.7533
31	0.0057	0.015	-0.0083	0.051	0.0223	0.0282	-0.1835	-0.0784	0.0824	-0.0656	0.1999	0.2295	-0.0552	-0.1518	-0.0008	0.117	0.0467	0.0212	0.245	0.0228	0.1822	-13.2016	5.7193	-53.6961
32	0.0799	-0.0435	0.0439	0.127	0.056	0.0607	0.0136	-0.1741	-0.0477	-0.0304	0.0461	0.039	0.0174	-0.1963	0.0465	0.0946	0.0166	-0.0051	0.1809	0.0298	0.1174	-9.4194	0.9359	-57.8616
33	0.0017	-0.0018	0.0011	0.0113	-0.0065	0.0089	0.0062	-0.1441	0.0463	-0.0411	0.1001	0.0505	0.0959	-0.0572	-0.0001	0.1472	0.0438	-0.0025	0.4612	0.0324	0.1572	-3.8084	-0.7501	-33.3895
34	0.0062	-0.0445	-0.0148	0.0758	0.004	0.0097	0.0375	0.2813	-0.0384	-0.0059	-0.1344	-0.222	-0.0582	0.151	-0.001	0.1515	0.0439	-0.0128	0.256	-0.0105	0.1629	2.2271	-28.041	-79.7209
35	0.0218	0	0.0124	0.0161	-0.0039	0.0169	0.0033	0.0224	0.071	0.078	-0.0432	0.03	0.0223	0.203	-0.0027	0.15	-0.0615	-0.033	0.2501	0.0723	0.1853	-0.6127	-13.9589	-88.3497
36	0.1051	0.0349	0.0594	0.0783	0.0762	0.041	0.0279	0.0112	0.0072	0.1831	0.0414	-0.052	0.0027	0.0598	0.075	0.2286	0.0039	-0.041	0.1058	0.0154	0.1204	-4.4245	-27.5135	-65.5134
37	0.0047	0.0036	0.0095	0.0118	-0.0005	0.0062	0.0416	-0.0716	-0.0428	0.1344	0.0757	-0.2263	-0.0903	0.0844	0	0.1474	-0.0475	-0.0187	0.1554	0.0064	0.1704	1.7849	-16.261	-75.8293
38	0.2153	0.1143	0.1556	0.1974	0.0463	0.0818	0.0256	0.1917	-0.0178	0.0585	0.0084	-0.0506	0.0103	0.1752	0.0325	0.1241	0.0015	-0.0208	0.1182	0.0059	0.1033	-1.6891	-22.7467	-76.5794
39	0.0115	0.0092	-0.0055	0.0043	-0.005	-0.001	-0.0458	-0.0136	-0.0066	0.0136	-0.0568	-0.0655	-0.1703	0.2605	-0.0014	0.1667	-0.0388	-0.0371	0.1342	0.0602	0.1675	-7.6574	-6.3374	-94.5835
40	0.0107	-0.0359	-0.0034	0.0339	0.0298	0.0428	-0.0671	-0.1648	-0.048	0.02	-0.0258	0.148	-0.1093	-0.1773	-0.0008	0.1994	0.023	0.0803	0.1765	0.0392	0.239	-27.5577	-22.6863	-70.4501
41	0.0717	-0.0284	0.0826	0.177	-0.0562	0.099	-0.0145	0.002	0.0238	0.103	0.0063	0.0893	0.0714	-0.068	-0.0178	0.2017	-0.0103	0.0365	0.0925	0.0186	0.1433	-18.6117	-31.0553	-68.318
42	0.0128	-0.008	-0.0023	0.0126	0.0183	0.0213	0.0361	-0.0555	-0.0236	0.1391	0.1247	0.1842	0.0883	-0.0783	0.0098	0.1399	-0.0508	0.0379	0.1488	0.034	0.2169	-27.6196	-33.2498	-76.9605
43	0.054	0.0465	-0.0008	0.0964	0.0423	0.1284	-0.0467	0.0065	0.0059	0.043	0.0193	0.1154	0.0258	0.0429	-0.0638	0.1466	-0.0086	0.0407	0.131	0.026	0.16	-23.667	-27.762	-73.8801
44	0.0025	0.0002	-0.0101	0.0139	0.0063	0.0149	-0.0436	0.087	-0.002	0.0542	0.0489	0.0215	0.0296	-0.1014	0.0011	0.1465	-0.0448	0.0031	0.1516	0.0445	0.2199	-27.5116	-23.8404	-98.4403
45	0.0225	0.0028	0.0068	0.006	0.0079	0.0116	0.1313	0.0569	-0.0964	0.0042	0.0058	0.1638	0.1611	-0.1635	0.0116	0.2036	-0.0968	-0.0759	0.3276	0.1124	0.2734	-64.2765	-23.6316	-30.8475
46	0.0193	0.0028	-0.0181	0.2142	-0.0001	0.0912	0.1177	-0.1511	-0.1586	-0.0758	0.0606	0.0549	0.1808	-0.2193	0.0326	0.1631	-0.0722	-0.0428	0.2052	0.0792	0.1505	-53.7139	-21.1322	-24.7643
47	0.1547	-0.0268	-0.1389	0.0136	0.0347	0.1257	0.3156	-0.1173	-0.0652	-0.1445	0.0646	0.0262	0.0827	0.0346	0.0387	0.2619	-0.0214	-0.1064	0.1022	0.0539	0.2346	-53.5453	-26.7373	-36.1155
48	0.1158	-0.1164	-0.0399	0.3144	-0.0172	0.0855	0.0751	-0.0945	-0.0787	-0.1017	-0.0549	-0.0098	0.1047	-0.084	0.0947	0.183	-0.065	-0.0605	0.1593	0.063	0.1487	-55.8029	-24.1652	-31.4426
49	0.0133	-0.0298	-0.0184	0.0594	0.0351	0.0454	0.0205	-0.1421	0.0299	-0.0897	-0.0911	0.1547	0.0313	-0.0982	-0.0056	0.1828	-0.0811	-0.0188	0.2605	0.0364	0.1655	-61.5902	-15.1294	-33.6687
50	0.0119	0.0196	0.0089	-0.003	-0.006	0.0125	0.0033	-0.0177	0.0806	-0.1537	-0.1114	-0.175	0.1208	-0.0371	0.0002	0.3315	0.0327	-0.0916	0.131	-0.0156	0.1833	-55.6058	-14.8244	-56.2717

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 9 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 10 through 19 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 20 through 63 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 64 through 74 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 75 through 116 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 117 through 122 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 19 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 20 through 63 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 64 through 74 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 75 through 116 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 117 through 122 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 2 through 9 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 10 through 19 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 20 through 26 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 27 through 43 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 44 through 63 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 64 through 74 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 75 through 106 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 107 through 116 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 117 through 122 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 2 through 9 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 10 through 26 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 27 through 43 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 44 through 63 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 64 through 74 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 75 through 116 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 117 through 122 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 2 through 19 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 20 through 26 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 27 through 63 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 64 through 74 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 75 through 116 )
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 117 through 122 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 2 through 19 )
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 20 through 26 )
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 27 through 63 )
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 64 through 74 )
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 75 through 116 )
39	X-RAY DIFFRACTION	39	chain 'F' and (resid 117 through 122 )
40	X-RAY DIFFRACTION	40	chain 'G' and (resid 2 through 19 )
41	X-RAY DIFFRACTION	41	chain 'G' and (resid 20 through 63 )
42	X-RAY DIFFRACTION	42	chain 'G' and (resid 64 through 74 )
43	X-RAY DIFFRACTION	43	chain 'G' and (resid 75 through 116 )
44	X-RAY DIFFRACTION	44	chain 'G' and (resid 117 through 122 )
45	X-RAY DIFFRACTION	45	chain 'H' and (resid 2 through 19 )
46	X-RAY DIFFRACTION	46	chain 'H' and (resid 20 through 63 )
47	X-RAY DIFFRACTION	47	chain 'H' and (resid 64 through 74 )
48	X-RAY DIFFRACTION	48	chain 'H' and (resid 75 through 106 )
49	X-RAY DIFFRACTION	49	chain 'H' and (resid 107 through 116 )
50	X-RAY DIFFRACTION	50	chain 'H' and (resid 117 through 122 )

-
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