PDB-4zwt: Crystal Structure of the Bacteriophage T4 recombination mediator ...

ID or keywords:

Entry

Database: PDB / ID: 4zwt

Title

Crystal Structure of the Bacteriophage T4 recombination mediator protein UvsY, Lattice Type IV

Components

Recombination protein uvsY

Keywords

VIRAL PROTEIN / recombination / DNA binding / homo-heptamer / asymmetry / alpha barrel

Function / homology

Recombination, repair and ssDNA binding protein UvsY / Recombination, repair and ssDNA binding protein UvsY / DNA biosynthetic process / DNA recombination / DNA binding / Recombination protein uvsY

Function and homology information

Biological species

Enterobacteria phage T4 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 4.2 Å

Authors

Gajewski, S. / White, S.W.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM066934	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	CA21765	United States
American Lebanese-Syrian Associated Charities (ALSAC)		United States

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure and mechanism of the phage T4 recombination mediator protein UvsY.
Authors: Gajewski, S. / Waddell, M.B. / Vaithiyalingam, S. / Nourse, A. / Li, Z. / Woetzel, N. / Alexander, N. / Meiler, J. / White, S.W.

History

Deposition	May 19, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 2, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 23, 2016	Group: Database references
Revision 1.2	Apr 20, 2016	Group: Database references
Revision 1.3	Sep 6, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4zwt.cif.gz	636.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4zwt.ent.gz	522.7 KB	Display	PDB format
PDBx/mmJSON format	4zwt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4zwt_validation.pdf.gz	544.2 KB	Display	wwPDB validaton report
Full document	4zwt_full_validation.pdf.gz	557.3 KB	Display
Data in XML	4zwt_validation.xml.gz	56.3 KB	Display
Data in CIF	4zwt_validation.cif.gz	76.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zw/4zwt ftp://data.pdbj.org/pub/pdb/validation_reports/zw/4zwt	HTTPS FTP

-
Related structure data

Related structure data	4zwqC 4zwrSC 4zwsC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4zwr-d 4zwq-d 6dtd-d 3fhq-2 5znn-d 3kjx-d 7526 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

Deposited unit

A: Recombination protein uvsY

B: Recombination protein uvsY

C: Recombination protein uvsY

D: Recombination protein uvsY

E: Recombination protein uvsY

F: Recombination protein uvsY

G: Recombination protein uvsY

H: Recombination protein uvsY

I: Recombination protein uvsY

J: Recombination protein uvsY

K: Recombination protein uvsY

L: Recombination protein uvsY

M: Recombination protein uvsY

N: Recombination protein uvsY

251 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Recombination protein uvsY

B: Recombination protein uvsY

C: Recombination protein uvsY

D: Recombination protein uvsY

E: Recombination protein uvsY

F: Recombination protein uvsY

G: Recombination protein uvsY

defined by author&software
125 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

H: Recombination protein uvsY

I: Recombination protein uvsY

J: Recombination protein uvsY

K: Recombination protein uvsY

L: Recombination protein uvsY

M: Recombination protein uvsY

N: Recombination protein uvsY

defined by author&software
125 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	184.380, 184.380, 615.010
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	97
Space group name H-M	I422

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
3	1	chain C
4	1	chain D
5	1	chain E
6	1	chain F
7	1	chain G
8	1	chain H
9	1	chain I
10	1	chain J
11	1	chain K
12	1	chain L
13	1	chain M
14	1	chain N

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	ARG	ARG	ALA	ALA	chain A	A	A	2 - 135	22 - 155
2	MET	MET	ALA	ALA	chain B	B	B	1 - 135	21 - 155
3	MET	MET	GLU	GLU	chain C	C	C	1 - 134	21 - 154
4	MET	MET	ALA	ALA	chain D	D	D	1 - 135	21 - 155
5	MET	MET	ALA	ALA	chain E	E	E	1 - 135	21 - 155
6	MET	MET	ALA	ALA	chain F	F	F	1 - 135	21 - 155
7	ARG	ARG	ALA	ALA	chain G	G	G	2 - 135	22 - 155
8	MET	MET	ALA	ALA	chain H	H	H	1 - 135	21 - 155
9	MET	MET	ALA	ALA	chain I	I	I	1 - 135	21 - 155
10	MET	MET	ALA	ALA	chain J	J	J	1 - 135	21 - 155
11	MET	MET	ALA	ALA	chain K	K	K	1 - 135	21 - 155
12	MET	MET	ALA	ALA	chain L	L	L	1 - 135	21 - 155
13	MET	MET	ALA	ALA	chain M	M	M	1 - 135	21 - 155
14	MET	MET	ALA	ALA	chain N	N	N	1 - 135	21 - 155

#1: Protein	Recombination protein uvsY Mass: 17904.482 Da / Num. of mol.: 14 / Mutation: E79A, K80A, S81A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: uvsY / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04537

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 5.21 Å³/Da / Density % sol: 80.66 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1:1 UvsY (22.5 mg/mL in 0.5 M sodium chloride, 15 mM HEPES, pH 8.2, 2 mM DTT) to 2 M sodium/potassium phosphate, pH 7.0, 0.1 M sodium acetate, pH 4.5

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2011

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 4.01→50 Å / Num. obs: 25618 / % possible obs: 56 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / B_iso Wilson estimate: 129.6 Å² / R_merge F obs: 0.996 / R_merge(I) obs: 0.201 / R_rim(I) all: 0.219 / Χ²: 1.022 / Net I/σ(I): 7.35 / Num. measured all: 303824

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
4.01-4.12		4.3	0.529	0.976	1.92	454	6259	105	1.113	1.7
4.12-4.23			0.778	0.836	3.47	2484	6110	345	0.901	5.6
4.23-4.35			0.961	0.793	3.54	3980	5928	561	0.856	9.5
4.35-4.48			0.89	0.769	3.67	5719	5819	848	0.835	14.6
4.48-4.63			0.892	0.617	4.25	7374	5593	1166	0.674	20.8
4.63-4.79			0.902	0.65	4.04	9056	5396	1504	0.713	27.9
4.79-4.98			0.9	0.668	3.99	11838	5271	2016	0.734	38.2
4.98-5.18			0.873	0.795	3.34	15373	5001	2582	0.872	51.6
5.18-5.41			0.864	1.048	2.41	23812	4815	3753	1.145	77.9
5.41-5.67			0.769	1.529	1.83	30571	4647	4645	1.664	100
5.67-5.98			0.893	1.263	2.21	28716	4386	4375	1.376	99.7
5.98-6.34			0.833	1.122	2.56	27198	4147	4144	1.221	99.9
6.34-6.78			0.885	0.808	3.84	25402	3875	3874	0.879	100
6.78-7.32			0.938	0.493	5.95	23704	3631	3631	0.536	100
7.32-8.02			0.982	0.227	9.81	21849	3363	3363	0.247	100
8.02-8.97			0.995	0.108	14.84	19348	3010	3010	0.118	100
8.97-10.36			0.997	0.069	20.34	16917	2667	2667	0.075	100
10.36-12.68			0.997	0.06	21.91	14011	2233	2233	0.065	100
12.68-17.94			0.998	0.056	21.94	10707	1745	1745	0.061	100
	17.94		0.998	0.058	23.11	5311	974	920	0.064	94.5

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data scaling
PDB_EXTRACT	3.15	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZWR

4zwr

Resolution: 4.2→49.617 Å / SU ML: 0.86 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.36 / Stereochemistry target values: ML
Details: THE X-RAY DIFFRACTION DATA EXHIBITED STRONG ANISOTROPY. REFINEMENT WAS PERFORMED AGAINST ELLIPTICALLY TRUNCATED DATA (RESOLUTION LIMITS OF 1/5.4, 1/5.4, AND 1/4.0 A IN A*, B*, C*, ...

	R_factor	Num. reflection	% reflection
R_free	0.3078	1271	5 %
R_work	0.2737	24124	-
obs	0.2754	25395	64.67 %

Solvent computation

Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 274.04 Å² / B_iso mean: 140.3233 Å² / B_iso min: 63.51 Å²

Refinement step

Cycle: final / Resolution: 4.2→49.617 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11717	0	0	0	11717
Num. residues	-	-	-	-	1779

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11849
X-RAY DIFFRACTION	f_angle_d	1.573	16240
X-RAY DIFFRACTION	f_chiral_restr	0.047	2009
X-RAY DIFFRACTION	f_plane_restr	0.016	2141
X-RAY DIFFRACTION	f_dihedral_angle_d	10.701	3494

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	6883	X-RAY DIFFRACTION	7.016	TORSIONAL
1	2	B	6883	X-RAY DIFFRACTION	7.016	TORSIONAL
1	3	C	6883	X-RAY DIFFRACTION	7.016	TORSIONAL
1	4	D	6883	X-RAY DIFFRACTION	7.016	TORSIONAL
1	5	E	6883	X-RAY DIFFRACTION	7.016	TORSIONAL
1	6	F	6883	X-RAY DIFFRACTION	7.016	TORSIONAL
1	7	G	6883	X-RAY DIFFRACTION	7.016	TORSIONAL
1	8	H	6883	X-RAY DIFFRACTION	7.016	TORSIONAL
1	9	I	6883	X-RAY DIFFRACTION	7.016	TORSIONAL
1	10	J	6883	X-RAY DIFFRACTION	7.016	TORSIONAL
1	11	K	6883	X-RAY DIFFRACTION	7.016	TORSIONAL
1	12	L	6883	X-RAY DIFFRACTION	7.016	TORSIONAL
1	13	M	6883	X-RAY DIFFRACTION	7.016	TORSIONAL
1	14	N	6883	X-RAY DIFFRACTION	7.016	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
4.2003-4.3684	0.3816	22	0.3616	413	435	10
4.3684-4.567	0.3419	37	0.3118	705	742	17
4.567-4.8076	0.3647	59	0.3029	1135	1194	28
4.8076-5.1086	0.3391	94	0.3128	1768	1862	43
5.1086-5.5025	0.3703	170	0.3526	3236	3406	79
5.5025-6.0554	0.3971	217	0.3881	4130	4347	100
6.0554-6.9296	0.3694	219	0.3586	4145	4364	100
6.9296-8.7228	0.2714	221	0.2394	4203	4424	100
8.7228-49.6208	0.2568	232	0.2044	4389	4621	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.7992	-3.1755	1.9625	4.6462	-3.2136	2.5862	0.4463	0.1281	-1.3352	-0.6697	0.1499	0.426	0.5913	-0.0115	-0.6685	1.5401	-0.7577	0.4428	2.0931	-0.979	2.5902	-31.7714	-63.7229	19.749
2	2.82	-0.3672	1.2568	-0.0158	-0.07	2.8674	1.8038	0.179	-2.2155	0.7231	0.4553	-0.4468	1.791	-1.0058	-0.043	3.3934	-0.7147	0.1402	1.2749	0.0159	1.6383	-30.4696	-62.3476	38.4178
3	2.5083	0.0018	1.7437	1.6529	0.0318	2.0349	-0.448	0.2481	-0.1951	-0.216	0.4159	0.0045	0.6612	-0.5121	-0.3814	3.4509	-0.7746	0.3024	1.731	0.1166	0.9185	-35.3929	-57.7447	26.6277
4	0.5761	0.1964	-1.0703	1.9358	-1.6091	3.4354	-0.3165	0.5818	0.1014	-0.3413	0.095	0.167	0.4339	-0.3063	-0.6165	0.9888	-0.663	0.1574	1.9212	0.5794	0.5766	-24.4399	-43.8024	14.239
5	2.9544	-1.1913	-0.1465	3.3903	0.029	1.2088	-0.2132	0.893	0.794	0.2043	0.3434	-1.1179	0.8832	-0.1564	0.6788	2.5801	-0.7022	-0.032	1.3821	-0.1845	0.8561	-22.9155	-52.4334	26.6019
6	1.3718	0.5143	0.174	1.4273	-0.9571	2.0701	0.0265	-0.4974	1.0117	1.0306	-0.4629	0.0916	1.0701	-0.7083	-0.028	2.3688	-0.3005	-0.0899	1.6804	-0.0891	0.82	-23.6452	-43.9324	28.2423
7	2.5298	-1.3675	0.8311	3.9462	-2.7494	3.4283	-0.3926	0.4432	0.9519	0.1156	-0.1354	-0.2386	-0.407	0.614	-0.0084	1.845	-0.5356	-0.4713	1.0227	0.7474	1.1	-29.8652	-23.2589	20.3337
8	2.464	-0.6309	0.5435	2.8897	-0.213	5.2548	-0.6091	0.2896	0.2092	0.0103	1.3102	-0.194	0.8895	-0.3546	1.1364	1.7418	-0.578	0.0003	1.2964	-0.2026	0.3456	-21.6196	-34.0538	26.3284
9	1.0365	0.5581	1.3119	2.5406	0.6241	1.6565	-0.5434	-0.3238	0.3469	-0.1761	0.7067	-0.7003	-0.3928	0.6102	-0.1925	1.2591	-0.3401	-0.555	1.4188	-0.2894	0.6436	4.7749	-27.629	51.2548
10	2.5481	-1.488	-4.353	1.1886	2.5388	7.4311	-0.4622	-0.5061	0.0084	1.0616	-0.4497	0.6999	-0.4883	-0.05	0.1339	1.9155	0.0101	-0.4094	1.263	0.1508	0.8172	-8.6676	-26.5583	51.7978
11	2.6963	0.6718	0.6681	1.1526	0.4083	1.3708	0.5026	0.4228	-0.2517	-0.4302	-0.0362	0.2854	-0.1756	-0.3875	0.6649	2.7315	0.0127	-0.4374	1.5987	0.3807	0.5816	-30.7965	-30.1053	27.2392
12	1.7055	3.2736	0.7781	8.4881	2.7439	5.5992	0.5629	-0.5917	0.7864	-0.7043	-0.0984	-0.0819	-0.5542	0.1404	0.5877	1.6129	0.5808	0.0196	1.8787	-0.7093	0.9329	-43.7575	-14.695	35.2848
13	4.528	1.1671	5.2997	4.144	0.9033	6.9101	0.4109	-0.2727	-0.2953	-0.2585	0.3253	0.5985	-0.0767	-0.3164	-0.0441	1.2643	-0.2075	-0.0463	1.3814	-0.0849	0.6075	-29.8763	-20.6319	35.5765
14	2.8066	-1.233	1.6826	0.5411	-0.7407	1.0065	0.1439	-0.5419	0.768	0.3893	0.0462	-0.4324	-0.6652	1.6985	0.6673	1.6801	-0.1991	-0.8273	2.0397	-0.6286	1.4595	-6.7025	-15.7448	65.1267
15	1.4736	-0.2681	-0.4987	0.9892	0.0849	0.1565	-0.1321	-0.1107	-0.3895	-0.7066	0.7628	0.3385	0.4782	-0.2025	0.3122	2.099	0.5784	-0.517	2.2925	0.2458	0.215	-35.7632	-22.6527	41.7127
16	0.3624	0.4457	-0.7943	3.5501	1.1629	3.3966	-0.4431	-0.2817	0.6206	0.4225	-0.0839	0.8511	0.612	-0.4788	0.4607	1.5789	-0.2165	-0.0054	1.4264	-0.1405	0.5561	-44.8156	-20.7404	50.3767
17	0.7763	0.8473	-0.6361	3.1612	-0.8594	0.553	-0.1691	0.5129	0.4895	-0.1089	-0.455	0.1265	0.4311	0.0052	0.2027	1.0854	0.1835	-0.1822	2.8712	0.064	1.0441	-42.498	-26.7217	55.0795
18	1.7906	1.0213	-0.578	1.3955	-0.176	1.3544	-0.2535	-0.2008	-0.4014	0.2251	-0.3323	-0.1337	0.5055	0.0279	-0.5826	1.715	-1.333	0.5138	2.3055	0.0914	0.6053	-56.6673	-42.5065	63.3891
19	7.7463	-4.884	1.0644	5.2652	-0.3646	0.1897	-0.1855	2.9302	-2.8038	-0.0397	-0.7903	2.6006	0.5686	-0.8407	0.914	1.0616	-0.888	0.1467	2.9095	-0.0507	2.9769	-66.4455	-46.2418	46.8442
20	1.1171	-0.3149	0.8488	2.5852	0.4622	2.2015	-1.5051	0.0825	-0.2194	-0.4964	-0.3968	0.0496	-0.2996	-0.9544	1.232	1.0669	-0.1337	0.1672	2.1041	-0.1065	1.1073	-42.0856	-31.6415	67.902
21	2.5357	1.2144	3.2212	2.3044	1.7123	6.2064	-0.5734	-0.2523	-0.2637	-1.0897	-0.3192	0.3975	0.2913	-0.4906	-0.2281	1.7817	-0.95	0.1176	2.5012	-0.0805	1.116	-49.646	-41.3859	56.7019
22	2.1161	-1.1111	-0.4431	2.3876	-0.2525	1.9073	-1.3047	0.6109	-0.6116	-0.3698	0.9805	-0.7284	1.362	-0.5733	0.1851	1.7948	-0.6145	0.1152	2.2064	0.569	1.329	-46.3031	-52.7294	63.7381
23	9.25	-0.6117	6.5006	2.8657	-1.349	7.3819	2.397	0.6201	-2.6866	-0.1595	0.7538	0.8309	2.7379	-1.6285	-2.6608	2.0191	-0.3847	-0.6348	2.6176	0.1778	1.3886	-28.1203	-45.8355	99.7989
24	0.4403	-1.0281	-0.1267	3.5671	1.8643	2.3535	-0.1897	0.4099	0.8226	0.4933	0.6465	-0.7751	-0.0751	-0.2278	-0.9274	1.9586	-0.9793	0.1955	2.5035	0.4204	1.8106	-42.7605	-54.8137	56.9946
25	2.0117	0.473	0.9893	2.5065	0.0058	1.6427	-0.5194	-0.3687	0.0733	-0.2668	0.6142	1.0755	1.2361	-1.3272	-0.1507	1.3979	-0.2575	0.3296	0.9544	0.1874	1.0388	-33.3642	-63.7057	125.3927
26	4.2681	2.9902	-2.5474	7.2476	-3.4895	4.6814	-1.0093	2.5178	0.127	-3.58	1.2766	1.6252	0.814	-1.4696	-0.5229	2.2702	-0.263	-0.371	2.6663	0.6684	0.9889	-41.3736	-37.7821	95.912
27	1.7776	0.2505	-1.2413	2.5587	-0.1297	0.8682	0.0029	0.1693	0.1256	-1.3595	-0.2273	-0.7985	0.41	-0.1096	0.6849	1.088	-0.6088	0.3867	1.4068	-0.0573	1.115	-28.9268	-57.7913	126.0373
28	1.2592	0.2873	0.3468	1.6001	-0.6218	1.2956	0.2878	-0.1238	0.1836	0.3644	0.6858	0.6338	0.4881	-0.5012	1.3286	1.1803	-1.1365	0.3546	0.8202	0.2347	0.8422	-28.1034	-47.2037	132.8992
29	3.558	-0.9917	-1.9496	4.7573	2.1955	6.9807	0.007	1.4052	0.7383	-1.952	-0.6801	0.2826	0.1922	-0.6139	-1.8335	1.5294	-0.0136	-0.6499	0.7546	0.4553	0.8011	-33.2473	-26.0714	106.481
30	0.4941	-0.2018	0.4428	0.7621	-0.3324	1.0886	-0.2189	-0.0082	-0.0776	-0.2798	-0.5693	-0.0637	0.1186	-0.0472	-1.1793	1.8639	-1.0106	0.2959	1.6218	0.5664	0.399	-19.8737	-48.6843	134.3867
31	2.4567	0.0647	1.4706	1.8714	-0.3355	1.142	-0.3292	0.206	0.5066	-0.038	-0.0173	-0.0585	-0.3145	0.02	-1.1544	1.5529	-1.3514	0.1975	1.7232	-0.42	0.759	-1.9726	-37.3116	136.3459
32	1.0174	0.9228	-0.545	1.7258	-0.4837	1.7356	0.9728	-0.3078	0.1571	0.5041	0.271	-0.4495	0.0785	-0.8643	8.5111	-0.0205	-0.434	0.5779	0.9664	0.4262	0.497	-15.6545	-36.7874	130.0838
33	1.9605	-0.2123	1.0964	0.1743	0.1128	1.0099	0.1524	0.2143	0.5337	-0.9381	0.0306	0.9339	0.6584	-0.1709	0.122	0.991	-0.2123	0.2349	0.6029	0.4732	0.7655	-25.1255	-11.7122	104.453
34	2.8462	0.1924	1.1758	3.2601	-1.5489	4.0866	0.1409	0.3053	0.1644	-0.4159	-0.477	-0.4076	1.3593	-0.4713	0.1588	1.0304	-0.5585	0.1882	1.4112	0.1356	0.5371	-8.3668	-39.0301	125.6957
35	3.2707	0.1261	-1.119	2.0131	0.0104	0.7912	0.1729	0.0815	0.2903	-0.2045	-0.0416	-1.0718	-0.0883	0.0565	0.8994	0.467	-0.6373	0.2741	1.972	0.2559	1.6981	12.942	-43.9417	121.1819
36	1.8883	-0.5129	0.5133	6.4483	-1.8483	3.5465	0.233	-0.5692	-1.0018	-0.1624	-0.5884	-0.2358	-0.3595	0.8992	0.2459	0.7259	-0.2302	0.2537	1.0889	0.3274	0.8272	0.0947	-36.0096	120.7765
37	1.7103	2.2706	0.1882	4.1565	3.0162	6.8505	0.214	0.7182	-0.2625	-0.551	0.5117	0.2492	-0.6955	-1.6673	0.4108	0.7125	-0.0766	0.0161	0.9623	0.7021	2.0568	-9.7556	-16.6177	90.7874
38	1.7818	0.9417	-0.0498	1.3771	0.3971	1.6944	-0.022	-0.2386	-0.4024	-0.3596	0.2188	-0.5562	0.3507	-0.0737	0.3881	0.9327	0.102	0.1326	1.9963	0.5607	0.8239	2.4905	-42.7835	115.7251
39	2.9562	0.7068	-0.4742	1.6325	-0.0915	1.8858	0.0935	-0.6184	-0.6319	-0.0346	-0.3002	0.6823	-0.5482	-0.063	-0.7114	1.1833	0.5396	0.4345	1.8275	-0.2948	1.2289	12.6753	-59.4023	106.0076
40	1.371	0.315	-0.0834	2.5017	-0.1499	0.9504	-0.7952	0.0216	-0.2282	-0.174	0.3437	-0.0929	0.675	0.4323	-0.0308	1.206	0.1107	0.2078	1.2693	0.2748	0.6491	7.2832	-45.2218	106.6213
41	3.0006	0.2463	-0.0487	3.682	-1.8725	2.8367	-0.1805	0.3489	-0.974	-0.8155	0.2254	0.0751	0.8676	0.1408	-0.0066	1.8492	0.8444	0.1286	1.6233	0.0516	0.5403	2.3878	-50.1802	101.477
42	0.6475	-0.2394	-0.0237	2.4406	0.6058	0.1518	-0.1957	0.0082	0.1693	-0.7628	-0.3806	0.7524	-0.2182	-0.2746	-0.213	2.8916	-0.4665	0.803	0.6659	-0.718	1.9221	-2.4447	-72.4172	96.2371
43	3.4304	0.6954	-0.4527	1.4345	-0.5227	0.9091	-0.8023	0.4395	-0.2919	0.5072	0.4355	-0.2953	1.1075	-0.4741	-0.0538	2.1655	-0.2879	0.2561	0.5404	0.2433	1.2325	1.2284	-58.0554	95.449
44	0.8705	0.2194	0.2521	4.2497	-4.9133	5.7072	-0.3953	0.2057	0.3027	-1.6657	-0.4547	-0.0273	1.7062	0.2943	0.2036	2.3697	0.009	-0.1701	0.7474	0.1153	1.7665	-7.0953	-60.177	95.171
45	3.7724	-0.1136	0.4872	1.8407	0.0056	3.9661	0.4171	-0.1286	0.1236	-0.5791	-0.8302	1.4437	1.0868	0.4013	-0.382	1.2693	-0.112	-0.0146	0.7873	0.1121	1.5774	-16.8464	-69.3187	94.8089
46	1.9883	-7.6524	-8.4204	5.905	5.294	6.218	-0.6194	-1.1585	-4.55	0.253	0.4168	2.5622	1.4283	-0.2479	-0.1092	1.5951	0.4859	-0.1825	2.4985	0.6503	1.5388	-23.0837	-52.4792	58.6458
47	0.7144	-1.1088	1.3069	2.5628	-4.3217	7.9886	-1.5743	0.7042	1.3756	-0.1514	-0.6531	-0.6815	0.1886	-0.4664	0.4038	1.6874	-0.2947	0.0328	1.5512	0.5854	1.4033	-20.4722	-66.8593	101.7252

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 17 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 90 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 91 through 135 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 17 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 18 through 65 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 66 through 135 )	B
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 17 )	C
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 18 through 65 )	C
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 66 through 79 )	C
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 80 through 90 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 91 through 134 )	C
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 1 through 17 )	D
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 18 through 65 )	D
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 66 through 79 )	D
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 80 through 135 )	D
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 1 through 65 )	E
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 66 through 135 )	E
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 1 through 14 )	F
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 15 through 20 )	F
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 21 through 90 )	F
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 91 through 135 )	F
22	X-RAY DIFFRACTION	22	chain 'G' and (resid 2 through 64 )	G
23	X-RAY DIFFRACTION	23	chain 'G' and (resid 65 through 88 )	G
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 89 through 135 )	G
25	X-RAY DIFFRACTION	25	chain 'H' and (resid 1 through 65 )	H
26	X-RAY DIFFRACTION	26	chain 'H' and (resid 66 through 79 )	H
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 80 through 135 )	H
28	X-RAY DIFFRACTION	28	chain 'I' and (resid 1 through 65 )	I
29	X-RAY DIFFRACTION	29	chain 'I' and (resid 66 through 90 )	I
30	X-RAY DIFFRACTION	30	chain 'I' and (resid 91 through 135 )	I
31	X-RAY DIFFRACTION	31	chain 'J' and (resid 1 through 17 )	J
32	X-RAY DIFFRACTION	32	chain 'J' and (resid 18 through 65 )	J
33	X-RAY DIFFRACTION	33	chain 'J' and (resid 66 through 79 )	J
34	X-RAY DIFFRACTION	34	chain 'J' and (resid 80 through 135 )	J
35	X-RAY DIFFRACTION	35	chain 'K' and (resid 1 through 17 )	K
36	X-RAY DIFFRACTION	36	chain 'K' and (resid 18 through 65 )	K
37	X-RAY DIFFRACTION	37	chain 'K' and (resid 66 through 81 )	K
38	X-RAY DIFFRACTION	38	chain 'K' and (resid 82 through 135 )	K
39	X-RAY DIFFRACTION	39	chain 'L' and (resid 1 through 17 )	L
40	X-RAY DIFFRACTION	40	chain 'L' and (resid 18 through 65 )	L
41	X-RAY DIFFRACTION	41	chain 'L' and (resid 66 through 135 )	L
42	X-RAY DIFFRACTION	42	chain 'M' and (resid 1 through 17 )	M
43	X-RAY DIFFRACTION	43	chain 'M' and (resid 18 through 65 )	M
44	X-RAY DIFFRACTION	44	chain 'M' and (resid 66 through 135 )	M
45	X-RAY DIFFRACTION	45	chain 'N' and (resid 1 through 63 )	N
46	X-RAY DIFFRACTION	46	chain 'N' and (resid 64 through 90 )	N
47	X-RAY DIFFRACTION	47	chain 'N' and (resid 91 through 135 )	N

-
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