PDB-3p9a: An atomic view of the nonameric small terminase subunit of Bacter...

ID or keywords:

Entry

Database: PDB / ID: 3p9a

Title

An atomic view of the nonameric small terminase subunit of Bacteriophage P22

Components

DNA-packaging protein gp3

Keywords

DNA BINDING PROTEIN / Terminase small subunit /

DNA Packaging / bacteriophage P22

Function / homology

Function and homology information

viral terminase, small subunit / viral terminase complex /

DNA binding / identical protein binding
Similarity search - Function

Biological species

Enterobacteria phage P22 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.755 Å

Authors

Bhardwaj, A. / Roy, A. / Cingolani, G.

Citation

Journal: Structure / Year: 2012
Title: Small terminase couples viral DNA binding to genome-packaging ATPase activity.
Authors: Roy, A. / Bhardwaj, A. / Datta, P. / Lander, G.C. / Cingolani, G.

History

Deposition	Oct 17, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 9, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 25, 2012	Group: Database references
Revision 1.2	Aug 29, 2012	Group: Database references
Revision 1.3	Feb 21, 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	3p9a.cif.gz	521.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3p9a.ent.gz	433.2 KB	Display	PDB format
PDBx/mmJSON format	3p9a.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/p9/3p9a ftp://data.pdbj.org/pub/pdb/validation_reports/p9/3p9a	HTTPS FTP

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Related structure data

Similar structure data	6maf-d 4rhe-d 6njj-d 6boj-d 4gn1-d 7jm6-d 5x2f-d 5huo-1 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: DNA-packaging protein gp3

B: DNA-packaging protein gp3

C: DNA-packaging protein gp3

D: DNA-packaging protein gp3

E: DNA-packaging protein gp3

F: DNA-packaging protein gp3

G: DNA-packaging protein gp3

H: DNA-packaging protein gp3

I: DNA-packaging protein gp3

168 kDa, 9 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)	76.480, 100.900, 89.847
Angle α, β, γ (deg.)	90.00, 93.73, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	DNA-packaging protein gp3 / Terminase small subunit Mass: 18675.049 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Details: Bacteriophage P22 / Source: (gene. exp.) Enterobacteria phage P22 (virus) / Gene: 3 / Plasmid: pMAL-2ce / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P04893
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1397 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

DNA-packaging protein gp3 / Terminase small subunit

Mass: 18675.049 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Details: Bacteriophage P22 / Source: (gene. exp.)

Enterobacteria phage P22 (virus) / Gene: 3 / Plasmid: pMAL-2ce / Production host:

Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P04893

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 1397 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.24 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, 0.2 M Potassium Thiocyanate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	NSLS	X6A	1	0.98
SYNCHROTRON	CHESS	F1	2	0.98

Detector

Type: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 10, 2010

Radiation

Monochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 1.75→30 Å / Num. obs: 126076 / % possible obs: 93.5 % / B_iso Wilson estimate: 23.9 Å² / R_sym value: 0.071 / Net I/σ(I): 28.2

Reflection shell

Resolution: 1.75→1.85 Å / Redundancy: 3.3 % / R_sym value: 0.674 / % possible all: 62.5

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
SOLVE		phasing
PHENIX	(phenix.refine: 1.6.3_473)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.755→14.997 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 24.23 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2165	3606	1.59 %	Random
R_work	0.1773	-	-	-
obs	0.178	126076	84.83 %	-
all	-	126076	-	-

Solvent computation

Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 56.509 Å² / k_sol: 0.398 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.8147 Å²	-0 Å²	6.2465 Å²
2-	-	-8.7148 Å²	-0 Å²
3-	-	-	2.9001 Å²

Refinement step

Cycle: LAST / Resolution: 1.755→14.997 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9761	0	0	1397	11158

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	9987
X-RAY DIFFRACTION	f_angle_d	0.918	13556
X-RAY DIFFRACTION	f_dihedral_angle_d	13.348	3656
X-RAY DIFFRACTION	f_chiral_restr	0.066	1460
X-RAY DIFFRACTION	f_plane_restr	0.004	1757

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 (%)
1.7553-1.7784	0.3672	67	0.3318	3548	X-RAY DIFFRACTION	35
1.7784-1.8027	0.3796	85	0.3053	4529	X-RAY DIFFRACTION	45
1.8027-1.8284	0.3585	85	0.2921	5234	X-RAY DIFFRACTION	52
1.8284-1.8557	0.2683	80	0.2717	5705	X-RAY DIFFRACTION	56
1.8557-1.8846	0.3094	99	0.2636	6242	X-RAY DIFFRACTION	62
1.8846-1.9154	0.289	108	0.2554	7039	X-RAY DIFFRACTION	69
1.9154-1.9484	0.3124	120	0.2409	8042	X-RAY DIFFRACTION	79
1.9484-1.9838	0.2474	135	0.2182	8578	X-RAY DIFFRACTION	85
1.9838-2.0218	0.2744	143	0.2075	8941	X-RAY DIFFRACTION	89
2.0218-2.063	0.2362	169	0.1891	9209	X-RAY DIFFRACTION	91
2.063-2.1077	0.2339	133	0.1916	9366	X-RAY DIFFRACTION	92
2.1077-2.1566	0.22	167	0.1833	9328	X-RAY DIFFRACTION	93
2.1566-2.2104	0.2223	146	0.1847	9567	X-RAY DIFFRACTION	94
2.2104-2.27	0.2291	144	0.1834	9494	X-RAY DIFFRACTION	93
2.27-2.3365	0.2232	166	0.1673	9573	X-RAY DIFFRACTION	95
2.3365-2.4116	0.2156	156	0.1748	9680	X-RAY DIFFRACTION	96
2.4116-2.4975	0.2283	169	0.1824	9816	X-RAY DIFFRACTION	97
2.4975-2.597	0.2755	136	0.1837	9858	X-RAY DIFFRACTION	97
2.597-2.7145	0.2156	174	0.1809	9855	X-RAY DIFFRACTION	98
2.7145-2.8567	0.2302	159	0.1761	9886	X-RAY DIFFRACTION	98
2.8567-3.0343	0.2202	159	0.1704	9993	X-RAY DIFFRACTION	98
3.0343-3.2663	0.207	145	0.1697	10030	X-RAY DIFFRACTION	99
3.2663-3.5909	0.2031	173	0.1673	10038	X-RAY DIFFRACTION	99
3.5909-4.1012	0.1856	169	0.1498	9959	X-RAY DIFFRACTION	99
4.1012-5.1325	0.156	162	0.1384	9940	X-RAY DIFFRACTION	98
5.1325-14.9978	0.2005	157	0.1773	9848	X-RAY DIFFRACTION	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	0.8282	-0.2704	-1.1673	1.4176	1.3002	2.2771	0.3021	0.2287	0.0844	0.1208	-0.2544	0.1655	-0.1475	-0.3667	-0.0268	0.1994	0.0623	0.0241	0.2356	-0.0382	0.2416	5.9823	105.151	36.4192
2	0.7015	0.8712	0.894	1.2787	1.096	1.0553	0.2734	-0.2047	-0.0214	0.6762	-0.0347	-0.2603	0.3083	-0.0412	-0.2671	0.3919	-0.039	-0.0653	0.2429	-0.0149	0.1747	18.4761	86.5325	47.2307
3	1.3517	-0.7673	-1.4325	2.345	1.9714	2.4343	0.4194	0.4079	0.1023	-0.4121	-0.6267	0.0801	-0.3526	-0.731	0.1798	0.2059	0.1165	0.0166	0.3862	-0.077	0.2018	6.7987	101.7891	28.4761
4	0.463	-0.4118	-0.6823	0.7757	0.6359	1.2096	0.1124	0.0887	-0.0056	-0.16	-0.0815	0.0205	-0.0863	-0.2083	-0.0071	0.1559	0.0079	0.0046	0.1657	-0.0037	0.1249	19.0503	89.7295	17.7919
5	0.0611	-0.2325	0.1269	3.0375	-0.091	1.6063	0.0413	0.0448	-0.0043	0.7326	-0.2361	0.5247	-0.0019	-0.205	0.1372	0.2893	-0.0529	0.0769	0.1758	-0.0637	0.2099	-0.5415	80.1721	44.8965
6	0.4245	-0.1244	-0.3487	2.4484	0.1294	0.7543	0.0957	0.1056	-0.1407	-0.0069	-0.0991	0.4492	0.0036	-0.1456	0.0751	0.2014	-0.0218	0.0106	0.2353	-0.0364	0.2176	-3.8343	80.1033	36.938
7	3.1722	-0.1284	-1.7921	0.7526	-0.8493	2.15	-0.4148	-0.009	0.7983	-0.2977	0.4988	-0.1323	-0.5815	0.0405	-0.0329	1.6358	0.2544	-0.4215	0.7266	-0.1619	0.762	-15.8042	94.1917	27.8066
8	0.7738	-0.06	-0.8789	0.1783	-0.239	2.0215	0.0198	0.1251	0.0304	-0.105	-0.0676	0.0687	-0.3923	-0.1756	0.0521	0.1704	0.0016	-0.022	0.1597	-0.0268	0.134	8.0839	85.2048	22.7713
9	1.1158	0.4726	-0.6487	0.5422	0.1764	1.2449	-0.1694	-0.064	-0.0852	-0.1084	0.0643	0.1225	0.1886	-0.1041	0.1053	0.1935	-0.0222	0.045	0.1704	0.0383	0.2224	-9.5558	57.3703	40.4771
10	0.2916	-0.3943	0.1501	0.5578	-0.105	0.8396	-0.179	-0.2897	0.1761	0.2705	0.1052	-0.0785	0.1563	0.2434	0.049	0.217	0.0733	-0.0082	0.3356	0.0162	0.2313	16.8281	60.7002	47.9636
11	0.8265	0.2036	-0.0412	1.1897	-0.1392	1.772	-0.0943	0.0877	-0.0277	-0.1587	0.0485	0.1538	0.1217	-0.1625	0.0449	0.1577	-0.0029	0.0281	0.1437	0.0134	0.1754	-6.5846	61.2214	34.3082
12	0.0828	0.0902	-0.1889	0.7826	-0.6518	0.8298	0.0254	0.0563	0.0675	-0.0789	0.0111	0.0789	0.0099	0.0482	-0.0301	0.154	-0.0131	0.0053	0.1503	-0.0054	0.1431	5.7626	74.0335	23.8464
13	4.3597	-2.3614	-0.8052	3.9213	-0.2772	5.1083	0.3264	-0.4228	-0.6914	0.4309	-0.6118	0.6177	1.3878	0.8544	0.3919	0.8014	0.129	0.2165	0.2739	0.0874	0.2654	20.1801	38.8081	33.649
14	1.6988	0.0802	0.4701	0.4116	-0.4538	1.848	0.0353	0.02	-0.5276	0.0095	-0.0722	0.1583	0.9503	0.0341	-0.0572	0.4037	0.0226	0.0325	0.1411	0.0174	0.2027	13.858	44.9831	35.7295
15	1.7681	-0.6969	-0.202	0.7017	-0.1802	0.3275	0.0336	0.2366	-0.1679	-0.1806	-0.0916	0.0603	0.2972	-0.0648	0.158	0.881	-0.1496	0.0265	0.3387	-0.1151	0.5529	-3.4872	39.8811	21.4067
16	0.3647	-0.2003	-0.0274	1.053	-0.4357	1.0245	0.0005	0.0152	-0.0458	-0.1114	0.0433	0.2157	0.2077	-0.1318	-0.0446	0.1333	-0.0261	-0.0172	0.1662	0.0038	0.169	6.729	61.4002	23.0208
17	1.4912	1.4748	0.5441	1.5975	0.6654	0.5916	0.1168	-0.1039	-0.1949	0.3401	-0.154	-0.2058	0.1563	0.0953	0.0215	0.1914	0.0158	-0.07	0.1417	0.0358	0.1461	34.8477	42.8254	27.3667
18	1.0309	0.607	0.4228	0.8272	0.038	0.3078	-0.2071	0.2218	-0.0084	-0.0909	0.1966	-0.0743	-0.0648	-0.0291	0.0495	0.2622	-0.0096	0.0049	0.2141	-0.0293	0.2022	24.3667	32.1897	10.515
19	0.6521	-0.814	0.0405	0.8083	0.0353	0.4392	-0.0337	0.0427	-0.0447	-0.0506	0.0137	0.2333	0.061	-0.0513	0.0145	0.1356	0.0045	0.0023	0.1411	0.0066	0.1341	20.1662	48.3467	21.0606
20	0.3047	0.2628	0.3572	3.2825	-1.9266	2.1866	-0.0679	0.3353	0.0299	-0.3438	0.2539	0.8237	0.1514	-0.3103	-0.2465	0.1391	0.0097	-0.0804	0.2924	0.0508	0.2387	2.8211	76.0391	7.5542
21	3.5417	2.3658	0.5396	1.9358	-0.481	2.4174	-0.0864	0.9013	-1.1412	0.3509	-0.0709	-0.9427	-0.3237	0.0549	-0.0624	0.2759	0.1833	0.0504	0.6137	-0.0716	0.6253	56.9603	52.1021	11.2572
22	1.5884	0.3375	1.0653	2.0306	0.2817	1.0417	0.0595	0.2196	-0.1016	0.2519	0.0608	-0.5111	0.1965	0.4575	-0.0991	0.1124	0.0232	-0.034	0.2222	0.0116	0.2288	48.0421	56.5153	22.9257
23	7.4126	0.8593	-0.188	1.4755	-0.6201	1.3496	0.5609	2.2363	0.2542	-0.3965	0.2387	-0.1415	0.589	1.1754	-0.6517	0.4088	0.1641	-0.0426	0.9926	-0.2277	0.3227	45.003	44.0272	0.8147
24	1.6671	-0.0768	0.4459	0.2005	0.1337	0.3739	0.0155	0.0999	0.0112	-0.0276	-0.0363	-0.0128	0.0831	-0.0072	0.0096	0.1539	-0.0019	-0.015	0.1553	0.0112	0.1552	28.3601	55.7995	13.5791
25	0.9771	-0.7203	-0.7206	3.7225	0.5851	1.9011	-0.5122	-0.0343	0.5509	-0.2794	0.4955	-0.8189	-0.103	0.6952	-0.1324	0.2137	-0.0728	0.011	0.4195	0.047	0.3654	60.8642	80.6646	8.9745
26	1.6165	-0.5973	-0.4156	1.8142	0.1285	1.0553	-0.1715	-0.2369	0.0292	0.1937	0.025	-0.0938	0.0502	0.3139	0.1291	0.0897	-0.0023	-0.0573	0.1619	0.0031	0.1034	52.4296	75.2851	18.1114
27	0.2647	-0.7052	-0.6576	5.8802	0.6352	6.6583	-0.1715	-0.131	-0.2178	-0.1809	0.4024	0.3666	-0.0842	1.6146	-0.5563	0.3717	0.0825	0.0363	0.4994	-0.0031	0.2661	56.2528	68.0936	-7.1788
28	0.8677	0.5315	-0.1655	0.3694	0.0726	0.382	0.0221	0.0985	-0.0547	-0.0657	-0.0156	-0.0257	0.0348	0.0529	-0.0049	0.1664	0.0117	-0.0172	0.1701	-0.004	0.153	36.2804	65.6013	9.7274
29	1.8788	-0.4101	-0.6383	0.7496	1.2326	2.4251	0.0834	-0.2085	0.4403	-0.1131	0.0894	-0.2299	-0.2618	0.1689	-0.1671	0.2107	-0.0533	-0.0083	0.1972	-0.0194	0.2589	49.0338	97.5767	16.9765
30	1.0129	-0.6423	-0.8413	1.292	0.449	1.6206	-0.0827	-0.2663	0.1534	0.3083	0.0221	-0.1587	-0.0705	0.0616	0.0704	0.214	-0.0327	-0.0399	0.2258	-0.0608	0.1576	41.1312	91.6742	28.1229
31	1.7052	0.324	-0.5062	1.3183	1.1435	1.386	0.1075	0.2564	-0.0773	-0.5646	-0.0439	0.1089	-0.6375	0.1258	-0.0563	0.3402	-0.0092	0.046	0.1953	0.0067	0.1638	48.9042	94.4647	-0.1284
32	0.3164	0.3731	0.2381	0.5885	0.4642	0.2472	0.0333	0.0003	-0.0295	-0.0406	-0.0222	-0.0457	0.0353	-0.0229	-0.0182	0.162	-0.0033	-0.0299	0.1442	-0.004	0.1389	33.9884	76.0834	10.9699
33	1.1465	-0.0407	0.0061	0.3789	-0.6171	1.5062	0.3451	0.0233	0.0947	0.1053	-0.1841	0.5431	-0.4643	-0.1802	-0.1193	0.2247	-0.0067	0.0528	0.1522	-0.0535	0.3645	23.806	114.17	24.0915
34	0.7882	0.2563	-0.1161	0.7125	0.4746	0.7074	0.056	-0.1493	0.2158	0.1208	-0.1263	-0.0404	0.0379	0.006	0.0771	0.1959	-0.0396	0.0377	0.1604	-0.0772	0.2294	28.4538	101.3933	28.2904
35	9.301	3.5063	-1.2067	2.2481	-1.0221	2.3756	0.2769	0.8949	-0.8921	0.7376	-0.1637	-0.5514	-0.1245	0.0594	-0.2322	0.4757	0.0327	0.0044	0.2601	-0.0492	0.3192	29.3925	112.12	4.9178
36	0.3969	-0.0874	-0.2988	1.1154	0.5588	0.4398	0.0284	0.0315	0.0938	-0.1782	0.0029	0.068	-0.1059	-0.0379	-0.0236	0.1772	0.0106	-0.0222	0.1475	0.0088	0.1431	29.5949	88.1717	12.6536

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:36)
2	X-RAY DIFFRACTION	2	(chain A and resid 37:57)
3	X-RAY DIFFRACTION	3	(chain A and resid 58:94)
4	X-RAY DIFFRACTION	4	(chain A and resid 95:139)
5	X-RAY DIFFRACTION	5	(chain B and resid 8:57)
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8	X-RAY DIFFRACTION	8	(chain B and resid 92:139)
9	X-RAY DIFFRACTION	9	(chain C and resid 7:36)
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14	X-RAY DIFFRACTION	14	(chain D and resid 14:80)
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16	X-RAY DIFFRACTION	16	(chain D and resid 92:139)
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19	X-RAY DIFFRACTION	19	(chain E and resid 91:130)
20	X-RAY DIFFRACTION	20	(chain E and resid 131:139)
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35	X-RAY DIFFRACTION	35	(chain I and resid 87:91)
36	X-RAY DIFFRACTION	36	(chain I and resid 92:139)

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