PDB-6p7b: Crystal structure of Fowlpox virus resolvase and substrate Hollid...

ID or keywords:

Entry

Database: PDB / ID: 6p7b

Title

Crystal structure of Fowlpox virus resolvase and substrate Holliday junction DNA complex

Components

(DNA (29-MER)) x 2
Holliday junction resolvaseCrossover junction endodeoxyribonuclease

Keywords

HYDROLASE/DNA / resolvase-DNA complex / HYDROLASE-DNA complex /

TRANSCRIPTION

Function / homology

Function and homology information

crossover junction DNA endonuclease activity / hydrolase activity, acting on ester bonds / four-way junction DNA binding / DNA recombination /

Hydrolases; Acting on ester bonds /

DNA repair / magnesium ion binding
Similarity search - Function

Biological species

Fowlpox virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 3.317 Å

Authors

Li, N. / Shi, K. / Rao, T. / Banerjee, S. / Aihara, H.

Funding support

United States, 1items

Citation

Journal: Sci Rep / Year: 2020
Title: Structural insights into the promiscuous DNA binding and broad substrate selectivity of fowlpox virus resolvase.
Authors: Li, N. / Shi, K. / Rao, T. / Banerjee, S. / Aihara, H.

History

Deposition	Jun 5, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6p7b.cif.gz	331.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6p7b.ent.gz	271.4 KB	Display	PDB format
PDBx/mmJSON format	6p7b.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p7/6p7b ftp://data.pdbj.org/pub/pdb/validation_reports/p7/6p7b	HTTPS FTP

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Related structure data

Related structure data	6p7aC C: citing same article (ref.)
Similar structure data	4l62-2 6ztf-d 6jwy-d 7kja-d 2f1m-2 6e9w-d 4ncl-d 2rhk-2 3htx-2 1bp7-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
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: Holliday junction resolvase

B: Holliday junction resolvase

C: Holliday junction resolvase

D: Holliday junction resolvase

E: DNA (29-MER)

F: DNA (29-MER)

87.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	143.510, 143.510, 56.545
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	75
Space group name H-M	P4

#1: Protein	Holliday junction resolvase / Crossover junction endodeoxyribonuclease Mass: 17372.885 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fowlpox virus / Gene: FPV187 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A385H9X4, UniProt: Q9J546*PLUS
#2: DNA chain	DNA (29-MER) Mass: 8971.765 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Fowlpox virus
#3: DNA chain	DNA (29-MER) Mass: 8829.697 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Fowlpox virus

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.34 Å³/Da / Density % sol: 63.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M sodium cacodylate, pH6.6, 0.15M sodium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 3.3→39.803 Å / Num. obs: 17192 / % possible obs: 98.3 % / Redundancy: 3.6 % / CC_1/2: 1 / R_merge(I) obs: 0.0539 / Net I/σ(I): 8.2
Reflection shell	Resolution: 3.3→3.4 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.947 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6167 / CC_1/2: 0.68 / % possible all: 97.02

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Processing

Software

Name	Version	Classification
PHENIX	(dev_3366: ???)	refinement
XDS		data reduction
XDS		data scaling
SHELXDE		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 3.317→39.803 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.36

	R_factor	Num. reflection	% reflection
R_free	0.2677	805	4.7 %
R_work	0.2102	-	-
obs	0.2133	17139	98.36 %

Solvent computation

Shrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å

Refinement step

Cycle: LAST / Resolution: 3.317→39.803 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4857	1144	0	0	6001

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6237
X-RAY DIFFRACTION	f_angle_d	0.656	8656
X-RAY DIFFRACTION	f_dihedral_angle_d	18.414	3564
X-RAY DIFFRACTION	f_chiral_restr	0.047	960
X-RAY DIFFRACTION	f_plane_restr	0.01	919

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.3173-3.525	0.453	125	0.3436	2681	X-RAY DIFFRACTION	98
3.525-3.797	0.3876	149	0.3113	2645	X-RAY DIFFRACTION	98
3.797-4.1787	0.368	154	0.2686	2703	X-RAY DIFFRACTION	99
4.1787-4.7825	0.246	99	0.203	2765	X-RAY DIFFRACTION	98
4.7825-6.0221	0.2725	135	0.2256	2744	X-RAY DIFFRACTION	99
6.0221-39.8054	0.232	143	0.1723	2796	X-RAY DIFFRACTION	98

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	9.7943	3.0033	1.4001	8.7913	1.3785	2.0746	0.6221	-0.2509	-0.7337	0.3513	-0.2859	-0.0418	0.2639	-0.2889	-0.2781	1.0334	0.1349	-0.1043	1.071	0.0213	0.994	65.0187	6.2576	13.6191
2	9.1407	0.6262	-0.4415	5.3982	4.3826	6.1553	0.6695	0.0303	0.1387	0.1128	0.0133	0.1824	-0.5069	-0.2341	-0.6448	0.9627	0.2235	0.1478	0.9576	0.0138	1.1009	62.3127	15.5807	14.0534
3	7.3125	-1.5799	1.3885	3.3979	0.2694	4.243	-0.5328	1.9631	-0.3031	-0.6019	0.7993	0.9824	0.7247	0.4161	-0.2898	1.2218	0.2357	-0.0523	1.1107	-0.1296	0.8833	57.9711	13.867	7.3072
4	1.0615	1.804	1.7788	4.4551	4.7046	7.0228	-1.6094	-0.311	-0.2982	0.1756	-0.9885	2.2885	-3.5179	2.2652	2.9711	1.5767	0.0519	-0.1574	2.499	-0.2855	2.522	47.5019	-0.7357	13.7025
5	9.0197	-1.7156	1.4558	4.1223	-1.3956	7.7784	0.1512	-0.574	-0.9388	-0.7486	0.3478	1.1249	1.0909	-0.4523	-0.5686	0.8181	-0.0268	-0.15	1.0188	-0.0113	1.5058	57.7895	-2.4171	10.3889
6	4.5566	5.15	-0.1181	7.0022	1.6211	3.0606	1.0031	1.0039	-1.7044	-3.0485	-1.5072	1.8666	0.5351	1.4803	0.4381	1.8739	0.4206	0.0411	1.2045	-0.0938	1.363	41.5332	47.5322	61.519
7	8.5716	3.8115	-3.236	8.7807	3.8704	5.2866	0.7881	-0.4405	1.8406	-0.0364	-0.6323	-0.5634	-1.3744	0.102	0.4255	1.4464	0.4994	0.0515	1.4373	0.1236	1.9843	41.1542	52.5125	64.5539
8	4.296	3.9263	2.8644	3.7882	2.8619	2.2452	0.9951	0.2868	-0.0166	-1.192	0.1079	-3.1614	-1.275	0.4376	-0.242	1.8925	0.1814	-0.1335	1.4081	0.0694	1.5349	36.7122	53.1133	62.9365
9	7.6617	-1.677	3.3009	2.543	-0.3514	5.531	1.2357	1.7645	-3.0272	-1.5686	-0.267	4.4896	1.3897	0.3377	1.0554	1.9201	1.0998	-0.2912	2.2646	-0.4774	3.073	35.9999	34.3452	54.0103
10	4.0664	4.7964	-1.8319	7.831	0.0382	2.9992	-0.0736	-0.2279	-2.6102	-0.1764	-1.0994	2.2712	-1.7873	-1.9304	1.1636	1.5829	0.2977	0.1552	1.3569	-0.4718	1.7951	32.316	41.3848	63.828
11	7.3125	0.2033	-7.776	3.7434	1.4566	9.0867	-1.4785	2.4155	0.0507	-1.7462	-0.4282	0.3302	-0.4623	-2.777	1.3838	2.1734	0.9181	-0.2622	1.7045	-0.405	1.4977	28.0307	50.5933	60.2296
12	5.7611	-1.3373	3.1593	4.1114	-3.2669	4.9154	4.2888	-2.0573	-0.8064	-1.7507	-3.6614	1.5979	-2.1828	-1.2274	-0.9266	2.4926	0.6063	0.1426	2.9701	-0.609	2.0021	46.2006	40.4694	46.204
13	7.5925	-5.9381	6.2016	7.875	-5.5402	5.2074	2.1083	4.7221	-0.5978	-1.82	-1.7396	-0.6472	-4.1678	2.7816	-1.0863	4.6036	0.169	1.1885	3.0894	0.0471	2.6344	52.7015	49.1792	49.2879
14	9.2489	-3.9095	7.0597	4.3731	-2.2426	7.3555	1.8502	0.3342	0.1215	-0.5888	0.0305	-0.0073	-1.8217	1.5187	0.7147	1.8769	-0.3285	0.6469	1.9257	1.0892	3.8504	54.4461	60.1518	57.2204
15	9.408	6.4646	-6.1727	5.5407	-3.0439	5.3582	1.4806	-2.8406	1.3599	-1.0615	-2.0706	-0.2515	0.9109	1.8626	-0.0656	1.4117	0.4164	0.3122	1.9151	0.0257	3.3735	56.0914	47.5185	60.5188
16	9.4234	5.3292	9.172	7.2872	3.3678	9.6854	-2.6121	0.7363	-0.6523	-1.7876	1.7077	0.0355	-0.357	-1.1585	-0.7112	1.9613	0.325	0.9161	2.1803	0.3849	1.2181	41.2501	53.9272	51.7023
17	5.7277	4.4003	-2.165	3.7398	-0.9207	2.3706	2.1759	0.2153	1.5098	1.7662	-1.1597	2.5094	-0.1266	0.1879	-0.7225	1.2045	0.0025	0.1743	1.1383	-0.3704	2.3732	67.7019	38.5935	16.3874
18	3.7537	0.1324	-4.2301	9.3212	4.6492	7.2481	-0.3503	0.895	3.1353	0.4969	0.6334	-1.1824	-0.7466	1.7837	-0.4185	1.3482	0.0502	-0.3515	1.3274	-0.292	2.3501	74.951	41.8078	15.1952
19	3.8437	4.821	-0.5208	8.8376	2.6121	9.9324	-0.8614	0.3759	1.4559	-0.916	1.0492	1.2187	-1.9794	0.8917	-0.2264	1.4657	-0.1024	0.0241	1.2767	0.1023	1.4076	70.9627	33.434	11.7525
20	0.0054	-0.038	0.1817	0.0658	-0.478	3.0973	-0.6041	-2.027	-0.4209	0.8534	0.8637	1.1175	0.3457	0.0063	4.6051	-0.6544	1.2804	1.0705	1.4389	-0.3342	3.7037	56.2805	31.5195	23.0981
21	9.3305	-0.7251	1.2229	2.2336	1.7084	2.9008	-0.3098	-0.8899	-1.3403	0.4289	0.3277	1.4555	0.1092	-0.2581	0.0855	1.0663	0.1568	0.2221	1.0167	0.0022	1.5757	66.3971	26.6949	17.081
22	3.2237	-2.2214	-2.491	2.9371	3.022	3.0436	-1.4718	-1.7833	-1.6868	1.9277	0.4498	-0.1367	-0.2223	1.5088	0.7029	1.6158	0.0795	0.4034	1.7395	-0.2468	1.0013	74.7808	28.8211	21.4019
23	6.263	6.8823	-2.8302	9.8265	-7.2202	8.8235	0.9823	-0.8278	3.6001	3.3668	1.5569	-0.7645	-2.0311	0.5511	0.6855	3.4709	-0.124	0.4679	2.3102	-1.8557	2.9951	62.6259	49.0673	28.0135
24	8.5645	-4.0763	-4.8251	5.5187	-1.7092	7.1956	-0.813	2.2593	5.3665	-2.8678	2.0391	1.2635	0.5972	-0.8318	1.2593	3.4101	-0.9022	-1.6154	0.895	0.5879	3.5555	76.7506	55.3014	15.0926
25	7.6758	7.2733	-7.8814	7.8253	-6.6049	8.8947	3.1483	3.2765	3.1872	-3.4885	-0.7053	3.6647	-0.1309	0.9518	-2.6429	1.4032	0.7255	0.4551	3.3225	0.6375	3.6769	64.1465	52.7806	12.4643
26	8.9779	-7.3246	2.7391	9.0583	-6.2992	6.1531	-2.8245	-2.2151	0.8691	3.146	0.9694	3.1791	-2.4294	-1.4285	2.0856	3.5583	-0.2089	0.4962	1.7023	-0.8361	2.1088	73.0394	43.1661	25.3708
27	9.3195	-7.3332	-1.4657	5.9934	2.3485	5.9522	-0.6822	-0.8259	-1.0051	-2.0679	2.793	-1.2414	1.9542	-1.3425	-0.5885	1.8948	-1.1698	0.0456	1.5568	0.4117	2.2758	16.2337	30.8485	68.6728
28	4.8478	6.8053	-0.6478	2.01	-0.6377	0.1219	1.7832	0.9751	-0.737	1.9124	-1.8803	-2.1179	0.1238	1.1025	-1.1269	1.6653	-0.1883	-0.3401	3.8951	0.0323	5.7204	12.0405	32.5838	83.5335
29	9.0652	-5.1031	-2.2679	4.2169	-0.1744	4.789	0.3452	0.4094	-2.1452	0.1847	0.3865	2.5033	-0.0831	-3.3034	-0.7968	1.4265	0.3385	0.0311	2.4162	0.2883	2.1647	19.3211	36.2888	69.6611
30	9.2137	6.4182	3.1936	7.6756	-1.9004	6.3391	3.0103	3.0064	-1.0507	2.1118	-1.4313	-0.4107	-0.8841	-0.7281	-2.0719	3	0.4286	0.1366	2.7412	-0.4186	2.788	13.7871	15.8816	72.3447
31	0.3251	-2.0673	-1.364	2	8.7974	5.8042	0.4497	5.1394	1.0539	1.4251	-4.7603	2.8389	-0.2236	-2.381	3.4315	2.3098	0.292	-0.1765	4.9328	1.0257	2.7507	-0.2631	27.4895	77.8262
32	7.938	1.8549	6.7798	1.0582	3.0402	2.0039	-2.7694	-0.2261	1.4032	0.2786	1.375	-0.8161	2.0658	-4.5872	0.4024	3.002	-0.1452	-0.0297	3.9501	1.7139	2.8023	4.9986	25.042	65.0146
33	2.6673	1.632	2.2723	2.2633	2.0589	2.2801	3.0313	1.1228	-0.1436	1.812	2.1142	-0.3514	2.1463	-4.3352	-5.0203	2.1279	-1.0153	-0.4862	2.39	0.5257	2.9495	15.2034	25.4324	78.9083
34	9.138	2.4524	3.6916	1.0622	0.1139	2.4568	0.7582	-1.4952	0.4571	1.0478	-0.4738	0.1048	2.8088	0.3472	-0.4073	2.7382	0.796	0.076	3.2599	-0.1987	1.9095	39.7316	26.5157	29.6952
35	0.2105	-1.0858	1.1254	5.9237	-5.9569	6.0112	0.8703	1.116	4.3471	6.52	0.1208	-6.4593	-1.1892	1.9089	-0.2773	2.7374	0.1545	0.2017	2.9274	-0.0863	3.5505	64.0646	27.1924	35.9797
36	5.9619	1.9422	-5.0309	0.4409	-1.8849	4.3431	1.4845	-2.162	-0.347	0.2464	-0.2079	0.1107	-0.6406	1.079	-1.1753	2.7227	0.4665	0.1235	2.9488	0.1038	1.8246	51.8201	23.787	48.9708
37	5.939	-3.5797	5.0617	3.7655	-4.8388	6.2472	0.0233	0.5086	1.0509	-0.2165	-0.8492	0.4082	-1.0315	-1.5224	0.8186	2.276	0.5653	-0.0808	2.4593	-0.0415	1.5614	46.8045	25.0929	54.8465
38	2.7023	-0.065	-3.6193	1.5478	-0.437	5.0454	0.2352	1.7571	-0.2716	-1.9127	0.1702	-0.4623	3.6179	-1.4389	0.4829	6.0126	1.2884	-0.6295	4.9179	-0.0889	1.6452	26.9164	39.8313	45.8757
39	5.8374	5.2708	-7.3781	4.7543	-6.6706	9.3634	-2.5441	5.345	0.8949	-1.4865	-2.3688	-0.6198	0.1271	-6.3017	3.7308	2.1252	0.5742	-0.2082	3.4538	-0.438	2.281	27.1193	33.2034	48.9924
40	9.4822	6.2612	6.232	5.8452	5.5223	6.7231	-2.1853	-0.8567	1.563	-0.1476	2.4966	0.816	0.1852	4.331	0.0563	3.1577	0.3767	-0.1419	3.0053	0.2929	2.3473	38.584	27.0986	27.2544

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 49 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 50 through 79 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 80 through 97 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 98 through 112 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 113 through 149 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 13 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 14 through 50 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 51 through 60 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 61 through 66 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 67 through 79 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 80 through 89 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 90 through 100 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 101 through 112 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 113 through 124 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 125 through 132 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 133 through 148 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 1 through 13 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 14 through 40 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 41 through 60 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 61 through 67 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 68 through 80 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 81 through 89 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 90 through 112 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 113 through 124 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 125 through 132 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 133 through 148 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 2 through 13 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 14 through 25 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 26 through 89 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 90 through 112 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 113 through 124 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 125 through 132 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 133 through 147 )
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 1 through 10 )
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 11 through 15 )
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 16 through 29 )
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 1 through 10 )
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 11 through 15 )
39	X-RAY DIFFRACTION	39	chain 'F' and (resid 16 through 20 )
40	X-RAY DIFFRACTION	40	chain 'F' and (resid 21 through 29 )

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