PDB-6kbz: Crystal structure of yedK with ssDNA containing a tetrahydrofuran...

ID or keywords:

Entry

Database: PDB / ID: 6kbz

Title

Crystal structure of yedK with ssDNA containing a tetrahydrofuran abasic site

Components

5'-D (*CP*GP*GP*TP* (3DR) P*GP*AP*TP*TP*C)-3'
SOS response-associated protein

Keywords

DNA BINDING PROTEIN /

DNA repair /

abasic site / DNA BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

protein-DNA covalent cross-linking activity / : /

Lyases /

Hydrolases; Acting on peptide bonds (peptidases) /

SOS response /

single-stranded DNA binding /

peptidase activity / DNA damage response /

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.653 Å

Authors

Wang, N. / Bao, H. / Huang, H.

Funding support

China, 3items

Organization	Grant number	Country
Ministry of Science and Technology (China)	2018YFC1004500	China
National Natural Science Foundation of China	the Thousand Young Talents Program	China
National Natural Science Foundation of China	31800619	China

Citation

Journal: Nucleic Acids Res. / Year: 2019
Title: Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK.
Authors: Wang, N. / Bao, H. / Chen, L. / Liu, Y. / Li, Y. / Wu, B. / Huang, H.

History

Deposition	Jun 26, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 10, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 22, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6kbz.cif.gz	429.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6kbz.ent.gz	345 KB	Display	PDB format
PDBx/mmJSON format	6kbz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	6kbsSC 6kbuC 6kbxC 6kcqC 6kijC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1zg6-d 4r3b-d 1axb-d 4fd8-d 5iq8-3 1tgs-d 3llc-d 4oq0-d 3my0-11 1zg4-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6kbsSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: SOS response-associated protein

A: 5'-D (*CP*GP*GP*TP* (3DR) P*GP*AP*TP*TP*C)-3'

D: SOS response-associated protein

C: 5'-D (*CP*GP*GP*TP* (3DR) P*GP*AP*TP*TP*C)-3'

F: SOS response-associated protein

E: 5'-D (*CP*GP*GP*TP* (3DR) P*GP*AP*TP*TP*C)-3'

H: SOS response-associated protein

G: 5'-D (*CP*GP*GP*TP* (3DR) P*GP*AP*TP*TP*C)-3'

hetero molecules

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

1

B: SOS response-associated protein

A: 5'-D (*CP*GP*GP*TP* (3DR) P*GP*AP*TP*TP*C)-3'

hetero molecules

defined by author
Evidence: gel filtration
28.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: SOS response-associated protein

C: 5'-D (*CP*GP*GP*TP* (3DR) P*GP*AP*TP*TP*C)-3'

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

3

F: SOS response-associated protein

E: 5'-D (*CP*GP*GP*TP* (3DR) P*GP*AP*TP*TP*C)-3'

hetero molecules

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

4

H: SOS response-associated protein

G: 5'-D (*CP*GP*GP*TP* (3DR) P*GP*AP*TP*TP*C)-3'

hetero molecules

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

Unit cell

Length a, b, c (Å)	40.530, 111.391, 104.102
Angle α, β, γ (deg.)	90.000, 96.140, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	SOS response-associated protein / E.coli yedK Mass: 25606.893 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: yedK, C4J69_22885, ECTO6_01993, EFV06_12905, EFV16_12155, SAMEA3472108_01185, SAMEA3752559_04370 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A2S5ZH06, UniProt: P76318*PLUS, Hydrolases; Acting on peptide bonds (peptidases)
#2: DNA chain	5'-D (CPGPGPTP* (3DR) PGPAPTPTPC)-3' / ssDNA_THF Mass: 2926.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Escherichia coli* (E. coli)
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1086 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.04 Å³/Da / Density % sol: 39.69 %
Crystal grow	Temperature: 293 K / Method: evaporation Details: 0.02 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 22% w/v Poly(acrylic acid sodium salt) 5,100

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 8, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.65→40 Å / Num. obs: 108392 / % possible obs: 99 % / Redundancy: 6.1 % / B_iso Wilson estimate: 12.97 Å² / R_merge(I) obs: 0.084 / R_pim(I) all: 0.036 / R_rim(I) all: 0.092 / Χ²: 0.934 / Net I/σ(I): 5.6 / Num. measured all: 660240

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.65-1.71	4.8	0.76	10777	0.46	0.371	0.849	0.797	98.4
1.71-1.78	5.5	0.632	10779	0.689	0.288	0.696	0.841	99.1
1.78-1.86	5.6	0.494	10789	0.799	0.224	0.544	0.889	98.7
1.86-1.96	6.1	0.38	10859	0.896	0.164	0.415	0.946	99.6
1.96-2.08	6.1	0.269	10881	0.951	0.116	0.293	0.97	99.6
2.08-2.24	6	0.191	10815	0.974	0.083	0.209	1.007	98.7
2.24-2.46	6.6	0.14	10882	0.988	0.058	0.152	1.029	99.7
2.46-2.82	6.4	0.095	10823	0.993	0.04	0.103	1.042	98.8
2.82-3.55	7	0.052	10920	0.998	0.021	0.057	1.014	99.6
3.55-40	6.8	0.033	10867	0.999	0.013	0.036	0.756	97.8

-
Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.12_2829	refinement
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6KBS

6kbs

Resolution: 1.653→36.265 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 19.47

	R_factor	Num. reflection	% reflection
R_free	0.1961	5191	5.17 %
R_work	0.1598	-	-
obs	0.1617	100370	91.56 %

Solvent computation

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

Displacement parameters

B_iso max: 90.3 Å² / B_iso mean: 19.7322 Å² / B_iso min: 3.88 Å²

Refinement step

Cycle: final / Resolution: 1.653→36.265 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7111	708	4	1086	8909
B_iso mean	-	-	35.17	29.12	-
Num. residues	-	-	-	-	931

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	8112
X-RAY DIFFRACTION	f_angle_d	0.831	11170
X-RAY DIFFRACTION	f_chiral_restr	0.05	1158
X-RAY DIFFRACTION	f_plane_restr	0.005	1355
X-RAY DIFFRACTION	f_dihedral_angle_d	20.446	4674

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6527-1.6714	0.3083	64	0.2957	1202	1266	35
1.6714-1.6911	0.3266	95	0.256	1667	1762	48
1.6911-1.7117	0.2922	105	0.2579	2022	2127	59
1.7117-1.7334	0.3042	117	0.2415	2489	2606	72
1.7334-1.7562	0.2805	151	0.2256	2889	3040	82
1.7562-1.7803	0.2712	176	0.2244	2983	3159	88
1.7803-1.8057	0.2677	175	0.2124	3084	3259	91
1.8057-1.8326	0.2318	174	0.2076	3317	3491	94
1.8326-1.8613	0.2488	169	0.1991	3411	3580	99
1.8613-1.8918	0.2254	172	0.1894	3417	3589	99
1.8918-1.9244	0.2141	220	0.1863	3428	3648	99
1.9244-1.9594	0.2445	169	0.178	3432	3601	100
1.9594-1.9971	0.2023	180	0.175	3463	3643	100
1.9971-2.0378	0.2378	204	0.1728	3456	3660	100
2.0378-2.0822	0.2112	182	0.1707	3403	3585	100
2.0822-2.1306	0.2046	185	0.1601	3470	3655	100
2.1306-2.1839	0.2095	159	0.1579	3365	3524	97
2.1839-2.2429	0.2159	194	0.1518	3472	3666	99
2.2429-2.3089	0.1773	181	0.1461	3415	3596	100
2.3089-2.3834	0.1866	191	0.148	3492	3683	100
2.3834-2.4686	0.1931	192	0.1502	3405	3597	100
2.4686-2.5674	0.2066	204	0.1623	3457	3661	100
2.5674-2.6842	0.2062	193	0.1603	3450	3643	100
2.6842-2.8257	0.206	183	0.1639	3368	3551	97
2.8257-3.0026	0.1891	185	0.1602	3437	3622	100
3.0026-3.2343	0.2003	192	0.1486	3473	3665	100
3.2343-3.5595	0.167	211	0.1356	3432	3643	99
3.5595-4.074	0.1411	180	0.1236	3434	3614	98
4.074-5.1305	0.1345	203	0.1145	3428	3631	99
5.1305-36.2732	0.1769	185	0.1614	3418	3603	97

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	0.7106	-0.1038	0.0544	2.6961	-0.2867	1.2523	-0.0286	0.2754	0.4519	-0.2257	0.0424	0.1162	-0.2686	-0.0914	-0.0093	0.2016	-0.0308	0.0055	0.1713	0.0949	0.2383	20.3322	22.2066	19.933
2	1.2941	-0.3435	-0.2259	1.8962	0.2444	1.3313	-0.048	0.1715	0.4803	-0.0005	0.0477	-0.4474	-0.2284	0.1678	0.0006	0.141	-0.0369	0.014	0.1203	0.0525	0.1909	24.6182	21.1285	25.8058
3	1.9206	-0.0465	-0.0944	1.1856	-0.0227	1.7931	0.0051	-0.1524	0.2169	0.3095	-0.0363	0.162	-0.1739	-0.1493	0.0238	0.172	0.0077	0.0247	0.077	-0.0225	0.1149	11.7036	16.8969	36.2129
4	1.3928	-0.6365	-0.4951	1.229	0.4061	1.7662	-0.0559	0.2052	-0.0324	0.0755	-0.055	0.1138	0.1192	-0.0654	0.0809	0.0945	-0.0328	0.0116	0.102	0.0087	0.0688	14.6088	9.1036	24.6061
5	2.5571	-0.3033	-0.4201	3.6006	0.6479	2.5147	-0.0512	0.2567	0.3241	-0.174	-0.0679	0.4695	-0.3024	-0.3916	0.1207	0.1386	0.042	-0.0133	0.1967	0.0309	0.1529	5.3307	19.8403	25.3176
6	1.7073	-0.045	0.4996	1.4296	0.2432	1.6	-0.0426	0.2851	-0.1035	-0.0558	0.0316	-0.0171	0.1088	-0.004	0.0249	0.1085	-0.0138	0.0077	0.2064	0.0033	0.0508	20.9365	2.3943	16.2382
7	1.1579	0.6704	1.4425	1.8865	-0.4137	3.1439	0.2221	0.2195	-0.2759	-0.0206	-0.183	0.2078	0.1547	-0.0081	-0.0142	0.1792	-0.0425	0.019	0.0301	0.0114	0.0731	17.0814	0.3756	34.9336
8	1.3873	0.2151	-0.1272	2.8042	0.3669	1.2461	0.0155	0.1217	0.3309	-0.3818	0.0634	0.2059	-0.1853	-0.0675	-0.0481	0.1322	-0.0041	-0.002	0.1124	0.0191	0.1102	33.564	20.84	70.5027
9	1.2865	-0.0867	-0.4466	1.3528	-0.0617	1.2185	0.0418	0.0074	0.167	0.1214	-0.0562	-0.1322	-0.1777	0.1265	-0	0.1181	-0.0131	-0.0106	0.0967	-0.0083	0.0688	37.8301	20.1735	76.3629
10	1.4704	0.4705	-0.463	1.4396	-0.282	1.7904	0.0593	-0.2254	0.088	0.348	-0.0342	0.0324	-0.2609	0.0333	-0.0413	0.2081	0.0112	0.0149	0.1061	-0.0319	0.0488	30.2008	17.2866	88.5959
11	1.7536	0.6876	-0.4566	1.3017	-0.615	1.8068	0.1194	-0.1496	0.157	0.3041	0.0002	0.253	-0.2351	-0.2092	-0.0758	0.1623	0.0401	0.0677	0.1039	-0.0134	0.1101	20.3001	16.4912	85.8947
12	2.5259	-1.2843	0.4767	1.6241	0.438	1.5167	0.0177	-0.1505	-0.2629	0.1786	0.0432	0.3281	0.3007	-0.0964	-0.0925	0.1252	-0.0256	0.0085	0.0784	0.0117	0.0796	29.4011	-0.8552	71.7759
13	1.0074	0.1694	-0.3062	1.3119	0.0396	1.5337	-0.0218	-0.0243	0.1306	0.1065	-0.0249	0.1697	-0.1363	-0.0216	0.0275	0.1129	0.0165	0.0102	0.063	0.0042	0.0716	26.6967	14.2365	79.2691
14	1.6859	-0.3762	-0.216	4.1164	0.725	2.1392	-0.017	0.086	0.2377	0.149	0.049	0.4997	-0.2194	-0.1715	-0	0.0877	0.0276	0.0361	0.1102	0.0203	0.1144	20.7426	18.3161	75.588
15	3.5975	1.2969	0.3365	6.4664	2.2061	7.9815	0.0011	-0.0322	0.1872	-0.0062	-0.0229	0.5968	-0.2596	-0.4495	0.0677	0.1207	0.0889	0.0553	0.2502	0.0585	0.2568	12.3786	21.4276	78.5253
16	3.6089	-3.0415	-1.3617	5.2012	1.9254	2.1852	-0.0419	0.0376	0.1656	-0.1026	-0.0582	0.2698	-0.1391	-0.2722	0.0745	0.122	0.0079	-0.0349	0.0995	-0.0104	0.0904	22.5809	6.8967	65.6582
17	3.1928	1.1697	2.1727	3.2953	1.8782	7.8463	-0.0027	0.1364	-0.1488	0.0448	0.2597	-0.3706	0.2677	0.4724	-0.1867	0.087	0.0398	-0.0164	0.1278	-0.0064	0.0593	39.9082	-0.1949	70.7555
18	1.0062	0.4224	1.1819	1.6057	-0.2525	2.5115	0.0751	-0.0284	-0.221	0.1592	-0.0143	0.1853	0.0549	0.0212	-0.0399	0.1846	-0.0232	0.0155	0.0809	0.0215	0.0486	30.4847	0.3569	87.1161
19	1.0602	0.556	-0.3113	1.9621	0.6424	1.1421	-0.0222	0.0176	-0.3092	0.0404	0.1006	-0.3221	0.1061	0.0718	-0.0554	0.0294	0.0163	-0.0234	0.0643	-0.03	0.1585	24.3292	-20.7939	44.2012
20	2.1882	0.4796	0.2991	1.3346	0.33	1.1156	0.0624	-0.1311	-0.0261	0.099	-0.0885	0.1259	0.0055	-0.0422	0.0127	0.035	0.0169	0.0004	0.0517	-0.0051	0.0563	19.6007	-11.5287	51.0413
21	0.2982	-0.5192	0.3956	1.8082	0.4523	3.4848	0.1647	-0.0674	0.2171	-0.0116	-0.1632	0.1669	-0.3107	0.0302	0.0598	0.0514	0.0519	-0.0231	0.037	0.005	0.0858	18.5692	-1	39.6631
22	2.0728	0.4742	0.1925	2.9694	-1.7999	3.0891	0.076	-0.182	-0.3758	0.0876	-0.1106	-0.0877	0.1489	0.1407	0.0219	0.0465	-0.0018	0.0011	0.1239	0.0191	0.1145	43.3867	-17.4455	103.3667
23	1.3187	0.0087	0.3751	0.5395	0.3283	1.5851	0.0699	-0.0078	-0.5158	0.0491	0.0069	-0.1121	0.4158	0.1599	-0.0608	0.1318	0.0377	-0.0004	0.1269	0.0101	0.2215	44.9503	-20.6332	98.6299
24	2.6974	-0.1156	-0.0462	6.1357	-2.5573	5.0728	0.0075	0.1075	-0.6317	-0.2113	0.0377	0.103	0.5346	-0.0688	-0.03	0.0995	0.0085	-0.0079	0.0886	-0.0331	0.1868	35.1051	-25.9278	96.316
25	5.3815	1.5823	1.4613	2.4311	1.5966	1.5971	0.0052	0.2389	0.0689	-0.2272	0.0132	0.1421	-0.1322	-0.054	-0.0222	0.0752	0.0037	0.0018	0.1174	0.0061	0.0465	25.7642	-10.1427	87.6956
26	2.9073	-0.5065	0.6194	1.0404	-0.2355	1.0384	0.0585	-0.1033	-0.1352	0.0263	-0.002	0.1336	0.0411	-0.0958	-0.0436	0.0478	-0.0134	0.023	0.0983	0.02	0.0678	22.7829	-15.9727	98.9764
27	2.4237	0.961	-0.1816	1.8829	-0.6391	2.9682	0.0546	-0.0653	0.2174	0.1126	-0.1546	0.2177	-0.4073	-0.0704	0.0764	0.1032	0.0227	-0.0135	0.1331	-0.0202	0.0594	39.3587	0.281	105.5435
28	1.7522	0.2191	0.6703	1.5322	0.3409	1.3878	0.0098	-0.1038	-0.0536	0.1177	-0.0427	0.0261	0.0722	-0.0124	0.0244	0.0496	0.0015	0.0233	0.0897	0.0199	0.0611	31.9847	-14.3465	100.9766
29	1.4634	0.7541	0.5227	1.8259	0.2909	0.7168	0.1253	-0.4173	-0.1703	0.2346	-0.0957	0.1703	0.103	-0.112	-0.0346	0.1056	-0.0111	0.0188	0.2146	0.0524	0.0976	29.2191	-15.5254	109.7306
30	3.242	0.8096	1.8115	2.9661	1.2562	7.1815	0.0097	-0.1688	0.0853	0.0513	-0.041	-0.1617	-0.4313	0.1972	0.0332	0.0729	-0.0191	0.0129	0.1253	0.0072	0.0573	48.5072	-0.6931	101.2002
31	1.897	0.8413	1.1015	1.6596	0.8768	1.6447	-0.1267	0.0281	0.1824	-0.1951	0.0702	0.0873	-0.1816	0.0689	0.0421	0.1032	0.0175	-0.0073	0.0931	0.024	0.0651	31.9203	-0.6918	91.8221

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 2 through 23 )	B	2 - 23
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 24 through 50 )	B	24 - 50
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 51 through 100 )	B	51 - 100
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 101 through 158 )	B	101 - 158
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 159 through 192 )	B	159 - 192
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 193 through 227 )	B	193 - 227
7	X-RAY DIFFRACTION	7	chain 'A' and (resid -1 through 7 )	A	-1 - 7
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 2 through 23 )	D	2 - 23
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 24 through 50 )	D	24 - 50
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 51 through 74 )	D	51 - 74
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 75 through 100 )	D	75 - 100
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 101 through 120 )	D	101 - 120
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 121 through 158 )	D	121 - 158
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 159 through 181 )	D	159 - 181
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 182 through 191 )	D	182 - 191
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 192 through 203 )	D	192 - 203
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 204 through 224 )	D	204 - 224
18	X-RAY DIFFRACTION	18	chain 'C' and (resid -1 through 7 )	C	-1 - 7
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 2 through 74 )	F	2 - 74
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 75 through 227 )	F	75 - 227
21	X-RAY DIFFRACTION	21	chain 'E' and (resid -1 through 7 )	E	-1 - 7
22	X-RAY DIFFRACTION	22	chain 'H' and (resid 2 through 17 )	H	2 - 17
23	X-RAY DIFFRACTION	23	chain 'H' and (resid 18 through 42 )	H	18 - 42
24	X-RAY DIFFRACTION	24	chain 'H' and (resid 43 through 60 )	H	43 - 60
25	X-RAY DIFFRACTION	25	chain 'H' and (resid 61 through 74 )	H	61 - 74
26	X-RAY DIFFRACTION	26	chain 'H' and (resid 75 through 100 )	H	75 - 100
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 101 through 120 )	H	101 - 120
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 121 through 158 )	H	121 - 158
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 159 through 203 )	H	159 - 203
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 204 through 225 )	H	204 - 225
31	X-RAY DIFFRACTION	31	chain 'G' and (resid -1 through 7 )	G	-1 - 7

-
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