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

ID or keywords:

Entry

Database: PDB / ID: 4zwr

Title

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

Components

Recombination protein uvsY

Genetic recombination

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 /

SAD / Resolution: 3.3857 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4zwr.cif.gz	361.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4zwr.ent.gz	309.9 KB	Display	PDB format
PDBx/mmJSON format	4zwr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zw/4zwr ftp://data.pdbj.org/pub/pdb/validation_reports/zw/4zwr	HTTPS FTP

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Related structure data

Related structure data	4zwqC 4zwsC 4zwtC C: citing same article (ref.)
Similar structure data	4zwq-d 4zwt-1 2dw2-d 4zwt-2 5gsq-d 4c2g-1 6fmh-d 6w62-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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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

129 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	85.600, 123.830, 302.730
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain C and (resseq 0:136 )
2	1	chain B and (resseq 0:135 )
3	1	chain A and (resseq 1:65 or resseq 73:135 )
4	1	chain D and (resseq 0:134 )
5	1	chain E and (resseq 0:136 )
6	1	chain F and (resseq 0:136 )
1	2	chain C
2	2	chain B
3	2	chain A and (resseq 1:65 or resseq 73:135 )
4	2	chain D
5	2	chain E
6	2	chain F

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain C and (resseq 0:136 )	C	0 - 136
2	1	1	chain B and (resseq 0:135 )	B	0 - 135
3	1	1	chain A and (resseq 1:65 or resseq 73:135 )	A	1 - 65
3	2	1	chain A and (resseq 1:65 or resseq 73:135 )	A	73 - 135
4	1	1	chain D and (resseq 0:134 )	D	0 - 134
5	1	1	chain E and (resseq 0:136 )	E	0 - 136
6	1	1	chain F and (resseq 0:136 )	F	0 - 136
1	1	2	chain C	C	0 - 136
2	1	2	chain B	B	0 - 135
3	1	2	chain A and (resseq 1:65 or resseq 73:135 )	A	1 - 65
3	2	2	chain A and (resseq 1:65 or resseq 73:135 )	A	73 - 135
4	1	2	chain D	D	0 - 134
5	1	2	chain E	E	0 - 136
6	1	2	chain F	F	0 - 136

NCS ensembles :

ID
1
2

#1: Protein	Recombination protein uvsY / Genetic recombination Mass: 18364.889 Da / Num. of mol.: 7 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

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.13 Å³/Da / Density % sol: 60.68 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 1:1 Se-Met-labeled UvsY (12 mg/mL in 0.5 M sodium chloride, 15 mM HEPES, pH 8.2, 2 mM DTT) to 18% MPD, 225 mM sodium chloride, 0.1 M MES, pH 6.4, sample subjected to reductive alkylation ...Details: 1:1 Se-Met-labeled UvsY (12 mg/mL in 0.5 M sodium chloride, 15 mM HEPES, pH 8.2, 2 mM DTT) to 18% MPD, 225 mM sodium chloride, 0.1 M MES, pH 6.4, sample subjected to reductive alkylation with formaldehyde prior to crystallization

Crystal

Density Matthews: 3.13 Å³/Da / Density % sol: 60.68 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 1:1 Se-Met-labeled UvsY (12 mg/mL in 0.5 M sodium chloride, 15 mM HEPES, pH 8.2, 2 mM DTT) to 18% MPD, 225 mM sodium chloride, 0.1 M MES, pH 6.4, sample subjected to reductive alkylation ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.2 / Wavelength: 0.9793 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2010

Radiation

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

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 3.3857→20 Å / Num. obs: 14057 / % possible obs: 63.9 % / Redundancy: 6.6 % / B_iso Wilson estimate: 87.48 Å² / R_merge(I) obs: 0.151 / R_pim(I) all: 0.063 / R_rim(I) all: 0.163 / Χ²: 1.396 / Net I/av σ(I): 16.8 / Net I/σ(I): 6.9 / Num. measured all: 93454

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	CC_1/2	R_pim(I) all	Χ²	% possible all	R_rim(I) all
3.3857-3.52	6.6	0.938	1.76	159	0.785	0.393	0.613	7.4
3.52-3.66	6.8	0.707		359	0.885	0.291	0.657	16.7	0.766
3.66-3.83	6.8	0.705		682	0.867	0.29	0.727	31.2	0.763
3.83-4.03	6.9	0.648		1041	0.909	0.267	0.777	47.9	0.702
4.03-4.28	7	0.387		1339	0.969	0.157	0.973	61.6	0.418
4.28-4.6	6.9	0.295		1679	0.99	0.123	1.04	76.6	0.32
4.6-5.06	6.4	0.211		2029	0.991	0.089	1.271	92.5	0.23
5.06-5.78	6.4	0.227		2215	0.989	0.095	1.266	99.7	0.246
5.78-7.22	6.6	0.176		2241	0.984	0.073	1.633	100	0.191
7.22-20	6.6	0.11		2313	0.993	0.046	2.59	99.6	0.12

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
SHELX		phasing
PHASER		phasing
RESOLVE		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 3.3857→19.911 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.77 / Stereochemistry target values: ML
Details: THE X-RAY DIFFRACTION DATA EXHIBITED STRONG ANISOTROPY. REFINEMENT WAS PERFORMED AGAINST ELLIPTICALLY TRUNCATED DATA (RESOLUTION LIMITS OF 1/5.0, 1/3.8, AND 1/3.4 A IN A*, B*, C*, ...

	R_factor	Num. reflection	% reflection
R_free	0.2665	698	5 %
R_work	0.2391	13260	-
obs	0.2405	13958	61.31 %

Solvent computation

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

Displacement parameters

B_iso max: 291.64 Å² / B_iso mean: 95.6672 Å² / B_iso min: 32.56 Å²

Refinement step

Cycle: final / Resolution: 3.3857→19.911 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6850	0	0	0	6850
Num. residues	-	-	-	-	926

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.001	6946
X-RAY DIFFRACTION	f_angle_d	0.333	9379
X-RAY DIFFRACTION	f_chiral_restr	0.013	1079
X-RAY DIFFRACTION	f_plane_restr	0.001	1195
X-RAY DIFFRACTION	f_dihedral_angle_d	9.004	2405

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	C	1029	X-RAY DIFFRACTION	POSITIONAL	0.012
1	2	B	1029	X-RAY DIFFRACTION	POSITIONAL	0.012
1	3	A	968	X-RAY DIFFRACTION	POSITIONAL	0.016
1	4	D	1026	X-RAY DIFFRACTION	POSITIONAL	0.011
1	5	E	1018	X-RAY DIFFRACTION	POSITIONAL	0.012
1	6	F	965	X-RAY DIFFRACTION	POSITIONAL	0.013
2	1	C	1029	X-RAY DIFFRACTION	POSITIONAL	0.012
2	2	B	1029	X-RAY DIFFRACTION	POSITIONAL	0.012
2	3	A	968	X-RAY DIFFRACTION	POSITIONAL	0.016
2	4	D	1026	X-RAY DIFFRACTION	POSITIONAL	0.011
2	5	E	1018	X-RAY DIFFRACTION	POSITIONAL	0.012
2	6	F	965	X-RAY DIFFRACTION	POSITIONAL	0.013

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.3857-3.6456	0.3719	35	0.3629	371	406	9
3.6456-4.0098	0.4088	70	0.3254	1513	1583	35
4.0098-4.5839	0.2858	140	0.2426	2835	2975	66
4.5839-5.752	0.281	210	0.2497	4110	4320	95
5.752-19.9116	0.228	243	0.2136	4431	4674	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	0.1179	-0.1472	0.0351	0.6881	-0.3056	0.1395	0.1054	-0.5676	-0.4575	0.1289	0.3003	0.171	-0.2182	-0.5859	-0.0003	0.9158	-0.1577	0.0529	0.8155	0.1058	0.6377	-1.1324	65.5804	133.7272
2	0.4732	0.6088	-0.5498	0.852	-0.8162	0.9405	0.2482	0.4787	-0.7565	-0.3915	0.8501	1.0198	1.3069	-1.3368	0.1941	0.9733	-0.361	-0.1175	0.6938	0.2828	0.7764	-14.1448	65.2123	100.7164
3	0.6152	0.0017	-0.5618	0.2161	-0.1891	0.6846	-0.1422	0.0007	0.3453	0.3016	-0.2018	-0.0478	-0.2803	0.5026	-0.0023	1.0326	-0.0128	-0.0437	0.7341	0.0361	0.6108	6.7083	70.9212	136.3034
4	0.6685	0.3555	-0.5288	0.3058	-0.1861	0.4389	0.0322	-0.6695	0.5559	0.6129	-0.1491	0.4416	-0.3636	-0.8305	0.0055	0.8943	0.0905	0.1098	0.5884	-0.1594	0.5219	1.4381	83.1172	127.3602
5	1.5005	-1.443	-0.0381	3.9595	0.6796	5.1484	-0.1542	0.0408	0.0962	-0.3102	0.0074	0.6913	-0.6005	-0.6099	-0.8139	0.5247	0.2362	0.0258	-0.0151	0.2939	0.759	-11.7234	81.7627	95.7056
6	0.39	0.1579	-0.6456	0.1716	-0.3313	1.0662	0.2758	-0.3172	0.1389	0.3103	-0.4797	-0.3736	-0.0684	0.6926	-0.1114	0.9625	0.0039	-0.1517	0.4811	-0.0897	0.4904	11.1834	82.9596	129.2403
7	0.2148	-0.1132	0.0365	0.5642	-0.4834	0.4382	0.0349	-0.1869	0.2162	0.1749	-0.0263	-0.1113	-0.095	0.2237	1.3308	0.9286	-0.5608	-0.3804	0.7994	-0.5665	0.9904	24.6563	95.7631	120.925
8	0.5767	0.1886	-0.6281	1.3725	-0.304	2.9222	0.1166	-0.124	0.5198	-0.0413	-0.1606	-0.1922	-0.6715	0.496	-0.2996	0.6707	0.0292	0.0822	-0.0041	-0.1129	0.6017	7.1941	90.6729	105.9108
9	0.5151	-0.0452	0.5676	0.8844	-0.4225	2.9539	0.116	-0.1495	0.1904	0.2954	0.1109	-0.1861	-0.0143	0.6446	-0.666	0.7707	-0.3455	-0.4858	0.4032	-0.2381	0.7413	22.1057	86.2017	120.4112
10	0.7335	-0.0646	-0.2557	0.0013	0.0183	0.0865	-0.046	0.0188	-0.1041	0.0227	0.0249	-0.2041	-0.0116	0.2287	0.809	0.2043	-0.282	-0.2719	1.248	-0.0976	1.271	39.4828	84.8334	110.1101
11	0.7293	-0.0298	-0.9821	1.2222	0.5058	2.5514	0.0241	-0.4565	0.1471	0.2672	0.2352	-0.4606	-0.4011	0.8545	0.0442	0.7807	-0.5445	0.014	0.3597	0.0518	0.6354	25.4495	88.5911	105.5173
12	0.5206	-0.1222	0.0259	0.8765	0.5194	0.3243	0.0899	0.4774	0.4186	-0.6994	-0.4523	-0.7609	-0.378	0.1853	-0.1584	0.7984	-0.3978	0.0946	0.588	0.255	0.3708	12.3929	90.3106	72.5386
13	1.2806	0.3455	-0.0325	0.6679	0.5381	2.8731	-0.0266	-0.3	0.029	0.5241	0.0719	-0.4177	0.1321	0.976	0.1874	0.0401	-0.5111	0.0008	0.6781	0.1149	0.5803	28.4358	80.1025	104.8499
14	0.1064	0.0019	-0.0755	0.0613	0.0068	0.0544	0.0146	0.044	-0.0363	0.0299	0.0043	-0.0991	0.0304	0.0944	0.0877	0.1127	0.0927	-0.1974	1.6154	0.0419	0.8979	43.0684	64.4921	104.2104
15	0.6741	0.0858	0.1069	0.3994	0.0594	0.9126	0.1171	0.1666	-0.0229	0.0288	0.0004	-0.5099	-0.1464	0.6743	0.1649	0.0553	-0.0353	0.1607	1.1689	0.0193	0.731	31.5584	75.2281	89.5858
16	0.3434	0.6421	0.2184	1.2327	0.2869	0.2164	-0.3347	-0.4367	-0.3116	0.6453	-0.2854	-0.3694	0.8841	0.3665	-0.0229	0.9224	0.2933	0.0576	1.1207	0.0265	0.6823	31.0714	66.6068	99.1114
17	0.0577	0.0127	0.0043	0.1846	0.0105	0.0812	0.3859	-0.1246	0.3251	-0.0679	0.2726	-0.7013	-0.1167	0.4391	-0.0009	1.0897	0.4648	0.0735	0.8089	0.1035	0.9395	32.4062	45.8123	104.027
18	1.2853	-0.1501	-0.108	0.94	0.8074	1.5818	0.3021	0.19	-0.4011	-0.0808	-0.0144	-0.2276	0.5265	0.1693	0.2054	0.7968	0.6023	-0.0826	0.8879	-0.2044	0.6445	29.4583	57.1551	87.6673
19	1.4977	0.8604	0.615	1.0586	1.2811	1.8123	0.0788	-0.5167	0.2267	0.0036	-0.5154	0.3167	0.4581	0.0154	-0.5199	0.5918	0.5168	0.0161	0.6483	-0.1907	0.8509	24.3731	53.7097	98.0953
20	2.7118	1.5686	1.6852	2.3649	0.1397	4.5456	-0.2539	0.5084	-0.1609	-0.8493	0.386	0.0642	0.6336	-0.2047	0.413	1.323	-0.517	0.1917	0.6658	0.1866	0.7335	13.0361	39.1096	110.6504
21	0.3265	0.05	-0.3177	0.3905	-0.0771	0.3415	-0.1734	-0.3903	-0.5833	0.4305	0.082	0.0921	0.3532	-0.5013	0.0006	1.1121	0.0318	0.0363	0.7904	-0.1848	0.872	18.2207	45.4189	93.9794
22	0.5672	-0.5685	0.1906	0.5731	-0.2707	0.3049	0.324	-0.8971	0.0873	-0.0312	-0.0512	0.4325	0.2071	-0.4116	0.0505	1.0465	-0.5391	0.4315	1.0464	-0.4112	1.1514	12.5881	48.4592	106.9696

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 65 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 66 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 0 through 65 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 66 through 90 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 91 through 135 )	B
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 0 through 17 )	C
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 18 through 90 )	C
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 91 through 136 )	C
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 0 through 17 )	D
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 18 through 65 )	D
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 66 through 79 )	D
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 80 through 134 )	D
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 0 through 17 )	E
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 18 through 79 )	E
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 80 through 136 )	E
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 0 through 17 )	F
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 18 through 79 )	F
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 80 through 136 )	F
20	X-RAY DIFFRACTION	20	chain 'G' and (resid 1 through 20 )	G
21	X-RAY DIFFRACTION	21	chain 'G' and (resid 21 through 91 )	G
22	X-RAY DIFFRACTION	22	chain 'G' and (resid 92 through 133 )	G

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-Movie

-Structure viewers

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-This page

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-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

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-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

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Movie

-
Structure viewers

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Viewer log

-
This page

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This web site

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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

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Yorodumi