PDB-5yse: Crystal structure of beta-1,2-glucooligosaccharide binding protei...

ID or keywords:

Entry

Database: PDB / ID: 5yse

Title

Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophorotetraose

Components

Lin1841 protein

Keywords

SUGAR BINDING PROTEIN / solute-binding protein / protein-carbohydrate complex / beta-1 / 2-glucooligosaccharide / sophorooligosaccharide / alpha/beta domain

Function / homology

Function and homology information

maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / metal ion binding
Similarity search - Function

Biological species

Listeria innocua serovar 6a

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Abe, K. / Nakajima, M. / Taguchi, H. / Arakawa, T. / Fushinobu, S.

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Structural and thermodynamic insights into beta-1,2-glucooligosaccharide capture by a solute-binding protein inListeria innocua.
Authors: Abe, K. / Sunagawa, N. / Terada, T. / Takahashi, Y. / Arakawa, T. / Igarashi, K. / Samejima, M. / Nakai, H. / Taguchi, H. / Nakajima, M. / Fushinobu, S.

History

Deposition	Nov 14, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 2, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 20, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5yse.cif.gz	340.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5yse.ent.gz	277 KB	Display	PDB format
PDBx/mmJSON format	5yse.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5yse_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	5yse_full_validation.pdf.gz	1.3 MB	Display
Data in XML	5yse_validation.xml.gz	17.5 KB	Display
Data in CIF	5yse_validation.cif.gz	29.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ys/5yse ftp://data.pdbj.org/pub/pdb/validation_reports/ys/5yse	HTTPS FTP

-
Related structure data

Related structure data	5ysbSC 5ysdC 5ysfC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ysd-1 5ysf-2 7c6x-8 7c6z-1 6dtq-3 6dna-1 4kp1-d 6g83-2 2zym-d 5ysf-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	#205 - Jan 2017 Nuclear Pore Complex similarity (2) #221 - May 2018 Human Papillomavirus and Vaccines similarity (2) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (2) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#205 - Jan 2017
Nuclear Pore Complex
similarity (2)
#221 - May 2018
Human Papillomavirus and Vaccines
similarity (2)
#243 - Mar 2020
Voltage-gated Sodium Channels
similarity (2)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#22 - Oct 2001
Photosystem I
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#29 - May 2002
Penicillin-binding Proteins
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Lin1841 protein

B: Lin1841 protein

hetero molecules

90.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Lin1841 protein

hetero molecules

defined by author&software
Evidence: gel filtration
45.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Lin1841 protein

hetero molecules

defined by author&software
45.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	36.014, 63.280, 87.451
Angle α, β, γ (deg.)	89.99, 82.24, 86.08
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	0	1	0	A	9 - 393
2	0	1	0	B	9 - 393

#1: Protein

Lin1841 protein / beta-1 / 2-glucooligosaccharide binding protein

Mass: 44582.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria)
Strain: ATCC BAA-680 / CLIP 11262 / Gene: lin1841 / Plasmid: pET30a / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92AS8

#2: Polysaccharide

beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-alpha-D-glucopyranose

Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpa1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,4,3/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2/a2-b1_b2-c1_c2-d1	WURCS	PDB2Glycan 1.1.0
[][a-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL

Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM

#4: Chemical

ChemComp-MG / MAGNESIUM ION

Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 632 / 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: 2.26 Å³/Da / Density % sol: 45.65 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.3 / Details: 0.1M MES-NaOH, pH 5.3, 42% (v/v) MPD

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 28, 2015
Radiation	Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 98051 / % possible obs: 96 % / Redundancy: 3.4 % / R_merge(I) obs: 0.068 / R_pim(I) all: 0.043 / Net I/σ(I): 20.7
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.737 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4453 / CC_1/2: 0.617 / R_pim(I) all: 0.474 / % possible all: 87

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-2000		data processing
MOLREP		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5YSB

5ysb

Resolution: 1.6→43.32 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.963 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18763	4783	4.9 %	RANDOM
R_work	0.1575	-	-	-
obs	0.15902	92359	96.38 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 46.917 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0 Å²
2-	-	0 Å²	-0.01 Å²
3-	-	-	0 Å²

Refinement step

Cycle: 1 / Resolution: 1.6→43.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6124	0	115	632	6871

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.02	6430
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	5825
X-RAY DIFFRACTION	r_angle_refined_deg	1.855	1.974	8726
X-RAY DIFFRACTION	r_angle_other_deg	3.626	3	13649
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.959	5	780
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.468	25.69	290
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.559	15	1102
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.856	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.125	0.2	952
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	7021
X-RAY DIFFRACTION	r_gen_planes_other	0.016	0.02	1233
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.007	1.435	3105
X-RAY DIFFRACTION	r_mcbond_other	1.007	1.436	3104
X-RAY DIFFRACTION	r_mcangle_it	1.502	2.149	3881
X-RAY DIFFRACTION	r_mcangle_other	1.502	2.149	3882
X-RAY DIFFRACTION	r_scbond_it	1.631	1.642	3325
X-RAY DIFFRACTION	r_scbond_other	1.631	1.643	3326
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.451	2.384	4843
X-RAY DIFFRACTION	r_long_range_B_refined	5.385	18.371	7512
X-RAY DIFFRACTION	r_long_range_B_other	5.385	18.378	7513
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 26248 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 1.6→1.642 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.269	320	-
R_work	0.265	6762	-
obs	-	-	94.78 %

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	0.7597	0.1348	-0.2412	7.2841	-0.4162	3.2545	0.0271	0.0165	-0.1161	-0.2429	0.0729	0.2342	0.1314	-0.178	-0.0999	0.0208	-0.0344	-0.0021	0.1218	-0.0308	0.1866	-9.621	-19.017	-3.65
2	0.1841	0.584	-0.3315	6.7534	1.3474	2.0311	0.0206	-0.0098	-0.0196	-0.0207	-0.1283	0.4582	-0.0943	-0.0264	0.1077	0.0076	-0.0164	0.004	0.1081	-0.0349	0.1931	-10.218	-15.234	2.5
3	0.7096	0.4757	0.119	3.0473	0.3915	0.807	0.2416	-0.1912	-0.1773	0.7424	-0.157	-0.2806	0.1615	0.0056	-0.0845	0.2264	-0.0856	-0.067	0.1251	0.0155	0.1481	-0.982	-13.324	11.269
4	7.2052	-6.3357	-1.9974	12.7146	0.9966	10.9928	0.2403	-0.2612	-0.3719	-0.2885	-0.0886	-0.0679	0.2413	0.3095	-0.1517	0.0324	0.0027	-0.0561	0.0534	-0.0025	0.1728	11.265	-23.861	2.711
5	5.4365	4.5731	3.598	6.3428	2.3103	8.0228	0.079	0.3092	-0.5527	-0.1379	0.1273	-0.534	0.4064	0.6168	-0.2062	0.0383	0.0324	0.0329	0.123	-0.0416	0.2385	11.499	-14.936	-5
6	0.6261	-0.3409	0.2861	3.3196	-1.0194	0.8217	-0.0217	-0.0132	-0.0581	0.151	-0.0058	-0.2557	-0.0304	0.0267	0.0275	0.0278	-0.0276	0.0158	0.1305	-0.0481	0.172	3.258	-1.348	-3.026
7	4.0574	-0.3273	3.745	2.3557	-1.468	6.5528	-0.0791	0.2686	0.1822	-0.2858	0.0396	-0.0108	-0.0399	0.2185	0.0395	0.0579	-0.0409	0.0368	0.1141	-0.0191	0.1552	2.084	21.218	-12.316
8	1.2444	-0.027	0.5255	2.6349	-0.7065	0.8213	-0.0156	-0.0605	0.171	0.0949	0.0175	0.2048	-0.0898	-0.0474	-0.0018	0.0357	-0.0206	0.0453	0.1078	-0.0681	0.1652	-5.076	17.966	-1.823
9	1.4422	0.2361	-0.2094	2.7615	0.2831	5.7225	0.0238	-0.2389	-0.0923	0.5111	-0.1053	-0.4205	0.3082	0.3257	0.0814	0.1155	-0.033	-0.0594	0.1585	-0.0307	0.191	12.778	9.721	11.91
10	1.7592	-0.2509	0.8878	1.7006	-0.0628	1.1734	0.0271	-0.0782	0.1723	0.1977	-0.0605	-0.025	-0.1147	0.0004	0.0333	0.0572	-0.0346	0.0351	0.1261	-0.0745	0.1467	-0.571	19.728	6.043
11	4.2095	1.4022	-2.2831	0.5432	-1.3903	6.927	-0.1529	0.1119	-0.0855	-0.0495	0.0332	-0.0157	0.1323	-0.2632	0.1197	0.0188	-0.0307	0.0265	0.1267	-0.0612	0.1931	-15.431	11.942	-7.693
12	1.668	-0.4513	0.2071	2.0729	0.247	0.3564	-0.0042	0.0924	-0.0316	0.0092	-0.0004	0.1195	0.0053	-0.0706	0.0047	0.0157	-0.0376	0.0342	0.1302	-0.0466	0.1385	-8.185	6.369	-9.8
13	3.3986	0.4479	1.874	1.2708	0.0423	2.5868	-0.0169	0.1258	0.0344	-0.0974	0.0174	-0.0644	-0.0487	0.0221	-0.0005	0.0286	-0.0208	0.0421	0.1245	-0.0509	0.1554	1.741	12.078	-10.236
14	0.4735	1.1439	0.0839	5.7466	-0.8997	0.4545	0.1867	-0.0623	-0.1669	0.5154	-0.1291	-0.3349	0.0153	0.0199	-0.0575	0.0966	-0.044	-0.03	0.1079	-0.0213	0.1727	1.58	-13.444	5.429
15	0.9612	1.0279	-0.8492	6.2109	-4.3101	7.8956	0.0706	0.0414	-0.3192	0.0586	-0.0096	-0.2747	0.1892	-0.0547	-0.0609	0.0333	-0.0112	-0.0043	0.0599	-0.0413	0.2086	0.104	-22.798	-3.646
16	0.9497	-0.1843	-0.591	3.0277	-0.5821	0.616	-0.0397	0.0946	-0.0887	-0.2598	-0.0219	-0.0881	0.0974	0.0465	0.0616	0.0508	-0.0139	0.0473	0.1583	-0.0685	0.1296	3.882	-4.818	-15.061
17	0.7662	0.3884	-1.5934	2.9557	-3.3907	11.9188	-0.0007	-0.0178	-0.1317	0.144	-0.1205	-0.1887	0.0673	0.5895	0.1213	0.0221	-0.0201	-0.006	0.1405	-0.0426	0.1583	9.976	1.408	-1.041
18	1.217	-0.0502	0.0566	1.3316	0.1254	1.031	0.1042	-0.1898	0.073	0.3807	-0.1101	0.0143	-0.0055	-0.1142	0.006	0.1316	-0.0698	0.0291	0.1533	-0.0701	0.0693	-0.307	10.945	15.633
19	4.5258	-3.6655	1.812	16.6617	-7.2014	6.6742	-0.0559	-0.2585	0.118	0.078	0.1366	-0.6358	0.1812	-0.13	-0.0806	0.1951	-0.0838	-0.0378	0.1269	-0.0159	0.0686	7.506	0.414	24.187
20	13.9418	0.6699	0.6755	10.5921	-1.5326	11.7575	-0.2081	0.2833	-0.1729	0.723	0.1737	-0.0347	-0.4161	0.7302	0.0345	0.1169	-0.0418	-0.0837	0.0847	0.0383	0.1302	10.422	-8.948	27.205
21	0.8842	1.1692	1.028	7.1517	0.3243	4.5045	-0.0931	0.0287	-0.0616	-0.8281	0.1672	-0.1786	-0.6525	0.3582	-0.0742	0.3391	-0.108	0.0808	0.1182	-0.051	0.0752	-5.601	6.633	-48.179
22	0.6616	0.8275	0.1608	2.0612	0.3981	3.9456	0.1733	-0.1415	0.0237	0.1595	0.0392	-0.0896	-0.157	0.159	-0.2126	0.0624	-0.0621	0.0198	0.1149	-0.0729	0.0807	-8.223	-1.423	-33.525
23	3.8518	1.3049	-2.7086	7.5703	-9.1005	19.0501	0.236	-0.3931	0.6323	0.2227	0.1511	1.0505	-1.2174	-1.1105	-0.3872	0.2915	0.1485	0.0205	0.2873	-0.1061	0.4476	-24.969	10.261	-35.732
24	4.3825	2.7453	-2.1666	13.2905	-1.5828	7.3713	0.105	0.2987	0.3929	-0.2828	-0.0351	1.1269	-0.8363	-1.055	-0.0699	0.1214	0.1289	-0.0669	0.249	-0.0497	0.2343	-25.9	3.358	-43.353
25	0.5731	-0.0699	-0.4561	4.4943	1.8956	2.9703	0.0165	0.0018	0.0352	-0.1683	-0.0486	0.3101	0.1852	-0.2694	0.0322	0.1242	-0.0541	-0.0287	0.1568	-0.0233	0.0958	-17.775	-12.906	-45.334
26	2.6404	-1.6141	-6.299	5.9158	2.8591	15.5549	-0.1155	0.1082	-0.1461	-0.0864	-0.1622	0.1964	0.6387	-0.3194	0.2777	0.3545	-0.1111	-0.0257	0.0995	-0.0636	0.0896	-19.294	-34.02	-53.845
27	10.8214	-2.5784	1.0623	4.9105	-0.1219	4.3024	-0.2933	0.0021	-0.098	-0.2308	0.0533	-0.0038	1.0475	0.0059	0.2401	0.5621	-0.0253	0.0309	0.0249	-0.0235	0.0541	-14.617	-37.088	-49.548
28	5.588	0.1177	-3.8943	4.4968	7.8679	16.8707	-0.1731	-0.0582	-1.0472	0.8109	0.518	-0.5974	1.551	1.067	-0.3449	0.7273	0.2059	-0.0214	0.2164	-0.0751	0.3746	-2.767	-37.589	-51.67
29	1.8016	0.5247	-0.599	2.0537	1.2145	4.8274	-0.0065	-0.1204	0.009	0.3961	-0.092	0.1196	1.0955	-0.2372	0.0986	0.4429	-0.1279	-0.0089	0.0755	-0.0194	0.0418	-17.997	-25.809	-33.026
30	2.7714	0.0109	0.4849	2.8543	-0.776	5.5347	-0.1801	0.1672	0.063	0.0626	0.1226	-0.8301	0.8315	0.8897	0.0575	0.6771	0.119	-0.0458	0.2587	-0.0817	0.3502	-3.32	-29.542	-48.654
31	0.1558	0.2217	-0.2354	1.8297	1.152	3.1364	-0.0242	0.0305	0.0261	-0.1523	0.0546	0.0451	0.2812	-0.0857	-0.0305	0.1718	-0.0751	-0.0209	0.1184	-0.026	0.0711	-13.997	-15.697	-48.704
32	6.2935	2.6688	3.6793	12.6647	2.4927	11.6237	0.1371	-0.1731	0.2376	0.5769	-0.1925	0.3217	-0.5933	-0.1281	0.0554	0.358	-0.0194	0.0632	0.0262	-0.0449	0.0808	-11.942	14.358	-38.397
33	3.6293	2.2226	2.8896	8.9209	4.8528	13.8392	-0.0305	0.1201	0.3486	-1.0403	-0.0405	0.3481	-0.877	-0.1393	0.071	0.2808	0.0913	-0.0341	0.0474	0.0009	0.0472	-17	5.867	-50.937
34	2.0649	-0.3293	-1.7098	5.0031	2.1414	6.0918	0.0909	0.1446	0.183	-1.0412	-0.1522	0.4225	-0.3401	-0.7795	0.0612	0.2718	0.008	-0.1193	0.1729	-0.0291	0.0939	-20.711	-4.417	-53.72
35	12.4779	4.2126	16.1434	15.2474	-4.8901	28.6534	-0.8069	-0.7342	0.0915	0.5275	0.6872	0.1307	-1.7566	-1.6697	0.1198	0.5487	0.1901	-0.1698	0.5608	-0.1455	0.3076	-24.971	-8.729	-60.463
36	3.5697	0.001	1.1487	4.6487	-1.7056	6.8117	-0.0395	0.1209	-0.0262	-0.5812	0.0042	0.3353	0.1028	-0.4008	0.0352	0.2086	-0.093	-0.071	0.1799	-0.0433	0.0695	-21.894	-15.734	-56.5
37	2.4048	1.4077	2.832	3.8297	6.3307	16.9453	0.1671	-0.2536	-0.0211	-0.033	-0.3996	0.363	0.0452	-1.43	0.2325	0.0726	-0.0577	-0.0069	0.1871	-0.0281	0.1089	-23.253	-14.376	-39.364
38	0.5928	-1.8786	-0.7448	7.208	1.841	5.2036	0.0526	-0.0907	0.1399	0.2949	0.1232	-0.4693	1.0546	0.5016	-0.1758	0.6129	0.0383	-0.0534	0.2283	-0.0403	0.145	-7.733	-22.143	-30.122
39	13.5763	0.1989	-9.5114	3.4995	-0.4633	6.9429	-0.6783	-0.2089	-0.587	1.1253	0.2053	-0.2578	0.7771	0.1653	0.473	1.1987	0.0775	-0.1477	0.2363	-0.0004	0.1965	-10.1	-33.541	-26.376
40	1.2597	-4.3122	-1.0111	15.964	4.9426	4.283	-0.0482	-0.0844	0.0267	0.2637	0.285	0.1608	0.7759	0.0815	-0.2367	0.3523	-0.0669	-0.1112	0.2083	-0.0388	0.2595	-14.559	-14.699	-17.417

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	35 - 58
2	X-RAY DIFFRACTION	2	A	59 - 77
3	X-RAY DIFFRACTION	3	A	78 - 109
4	X-RAY DIFFRACTION	4	A	110 - 116
5	X-RAY DIFFRACTION	5	A	117 - 130
6	X-RAY DIFFRACTION	6	A	131 - 158
7	X-RAY DIFFRACTION	7	A	159 - 172
8	X-RAY DIFFRACTION	8	A	173 - 203
9	X-RAY DIFFRACTION	9	A	204 - 222
10	X-RAY DIFFRACTION	10	A	223 - 245
11	X-RAY DIFFRACTION	11	A	246 - 258
12	X-RAY DIFFRACTION	12	A	259 - 278
13	X-RAY DIFFRACTION	13	A	279 - 296
14	X-RAY DIFFRACTION	14	A	297 - 310
15	X-RAY DIFFRACTION	15	A	311 - 330
16	X-RAY DIFFRACTION	16	A	331 - 362
17	X-RAY DIFFRACTION	17	A	363 - 372
18	X-RAY DIFFRACTION	18	A	373 - 408
19	X-RAY DIFFRACTION	19	A	409 - 417
20	X-RAY DIFFRACTION	20	A	418 - 421
21	X-RAY DIFFRACTION	21	B	36 - 67
22	X-RAY DIFFRACTION	22	B	68 - 110
23	X-RAY DIFFRACTION	23	B	111 - 115
24	X-RAY DIFFRACTION	24	B	116 - 130
25	X-RAY DIFFRACTION	25	B	131 - 159
26	X-RAY DIFFRACTION	26	B	160 - 170
27	X-RAY DIFFRACTION	27	B	171 - 181
28	X-RAY DIFFRACTION	28	B	182 - 189
29	X-RAY DIFFRACTION	29	B	190 - 234
30	X-RAY DIFFRACTION	30	B	235 - 261
31	X-RAY DIFFRACTION	31	B	262 - 310
32	X-RAY DIFFRACTION	32	B	311 - 318
33	X-RAY DIFFRACTION	33	B	319 - 331
34	X-RAY DIFFRACTION	34	B	332 - 348
35	X-RAY DIFFRACTION	35	B	349 - 353
36	X-RAY DIFFRACTION	36	B	354 - 362
37	X-RAY DIFFRACTION	37	B	363 - 373
38	X-RAY DIFFRACTION	38	B	374 - 392
39	X-RAY DIFFRACTION	39	B	393 - 401
40	X-RAY DIFFRACTION	40	B	402 - 422

-
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://pdbjlvh1.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