PDB-7ks4: Thermus Phage P74-26 Large Terminase ATPase domain with partially...

ID or keywords:

Entry

Database: PDB / ID: 7ks4

Title

Thermus Phage P74-26 Large Terminase ATPase domain with partially bound ADP

Components

Phage terminase large subunit

Keywords

VIRAL PROTEIN / Phage Large Terminase / ASCE ATPase

Function / homology

Function and homology information

viral terminase, large subunit / viral DNA genome packaging / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function

Biological species

Thermus phage P7426 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD /

molecular replacement / Resolution: 1.887 Å

Authors

Hilbert, B.J. / Kelch, B.A.

Funding support

United States, 2items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Viral packaging ATPases utilize a glutamate switch to couple ATPase activity and DNA translocation.
Authors: Pajak, J. / Atz, R. / Hilbert, B.J. / Morais, M.C. / Kelch, B.A. / Jardine, P.J. / Arya, G.

History

Deposition	Nov 20, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 5, 2021	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ks4.cif.gz	127.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7ks4.ent.gz	99.3 KB	Display	PDB format
PDBx/mmJSON format	7ks4.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/ks/7ks4 ftp://data.pdbj.org/pub/pdb/validation_reports/ks/7ks4	HTTPS FTP

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Related structure data

Similar structure data	4znl-3 4znj-d 4znl-1 4fxw-2 3hzf-d 5hca-3 3gbj-1 4wyq-1 2nbw-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

B: Phage terminase large subunit

hetero molecules

32.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	129.515, 129.515, 129.515
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	197
Space group name H-M	I23

#1: Protein	Phage terminase large subunit Mass: 31580.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus phage P7426 (virus) / Gene: P74p84 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR-DE3 / References: UniProt: A7XXR1
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.87 Å³/Da / Density % sol: 57.09 % / Description: Cube
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100 mM Sodium Acetate:HCl pH 5.0, 0.5M ammonium sulfate.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9774 Å / Relative weight: 1
Reflection	Resolution: 1.88→45.79 Å / Num. obs: 29147 / % possible obs: 100 % / Redundancy: 14.5 % / B_iso Wilson estimate: 36.57 Å² / R_merge(I) obs: 0.063 / Net I/σ(I): 21.5
Reflection shell	Resolution: 1.88→1.96 Å / Redundancy: 14 % / R_merge(I) obs: 1 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2900 / % possible all: 100

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
PHENIX	1.10_2155	refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 1.887→45.79 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.79 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2211	2400	8.23 %
R_work	0.1993	26747	-
obs	0.2011	29147	99.93 %

Solvent computation

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

Displacement parameters

B_iso max: 114.39 Å² / B_iso mean: 45.7883 Å² / B_iso min: 23.3 Å²

Refinement step

Cycle: final / Resolution: 1.887→45.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2056	0	63	129	2248
B_iso mean	-	-	69.78	44.59	-
Num. residues	-	-	-	-	252

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2208
X-RAY DIFFRACTION	f_angle_d	0.933	3007
X-RAY DIFFRACTION	f_chiral_restr	0.046	303
X-RAY DIFFRACTION	f_plane_restr	0.004	384
X-RAY DIFFRACTION	f_dihedral_angle_d	15.281	1285

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.8872-1.9257	0.2927	139	0.2797	1561	100
1.9257-1.9676	0.2708	140	0.2594	1588	100
1.9676-2.0133	0.2485	137	0.2488	1533	100
2.0133-2.0637	0.3185	143	0.2459	1566	100
2.0637-2.1195	0.327	138	0.2373	1538	100
2.1195-2.1818	0.2559	143	0.2448	1594	100
2.1818-2.2523	0.2954	136	0.2281	1540	100
2.2523-2.3328	0.249	145	0.2214	1575	100
2.3328-2.4262	0.2316	136	0.2209	1565	100
2.4262-2.5366	0.2574	141	0.2194	1562	100
2.5366-2.6703	0.2792	143	0.2352	1571	100
2.6703-2.8376	0.2488	143	0.2144	1567	100
2.8376-3.0566	0.2233	141	0.2202	1578	100
3.0566-3.3641	0.2374	143	0.2058	1566	100
3.3641-3.8507	0.2	146	0.18	1586	100
3.8507-4.8506	0.1736	141	0.1531	1610	100
4.8506-45.79	0.1921	145	0.1871	1647	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	7.6162	3.6315	0.512	2.8175	1.3959	7.2886	-0.3022	-1.6416	0.9283	1.3886	0.2328	0.5733	0.9604	1.9017	0.0725	0.5283	0.1912	-0.0319	0.6652	-0.0255	0.4882	-87.1666	145.3729	221.3448
2	1.9935	1.2677	-0.0201	7.6334	-3.0686	6.2003	0.347	0.3187	-0.3304	-0.5072	0.5284	1.9464	-1.0569	-1.0083	-0.371	0.3902	0.053	-0.2489	0.3101	0.0189	0.426	-93.1442	142.7582	215.1996
3	5.6787	-1.1758	-2.9336	6.061	-1.3835	4.6783	-0.683	0.7253	0.5431	-0.0522	0.604	1.7107	0.1639	-0.7044	0.1647	0.3274	0.0174	0.0538	0.4534	0.2133	0.7463	-94.5393	135.5897	223.9441
4	6.089	-2.6483	0.1628	7.8215	-0.2268	7.037	-0.4258	0.4685	1.8917	0.9076	-0.0684	-0.6161	-0.8865	-0.2004	0.4839	0.4934	0.0136	-0.0787	0.3209	0.068	0.4572	-85.049	137.8168	230.0524
5	1.3927	0.9942	-0.411	2.7486	0.0354	1.6177	-0.0376	0.0894	0.3485	-0.0435	0.1492	0.5282	-0.1959	-0.2736	-0.0976	0.319	-0.0161	-0.0768	0.3575	0.1085	0.3906	-87.6258	127.4494	227.185
6	8.8314	-1.2855	-4.1649	3.2881	-2.9947	6.056	-1.0335	0.8571	-0.7071	-1.0733	-0.4705	-0.289	1.2498	-1.2653	-0.8164	0.2672	-0.1709	-0.4952	0.6703	0.5005	0.7079	-97.109	124.9058	218.1464
7	5.05	1.1769	-1.9957	7.0414	-2.4071	1.8785	-0.0926	-0.3022	-0.4358	-0.3075	0.0152	0.1956	0.117	-0.0875	0.0163	0.3105	0.0066	-0.0492	0.3446	0.0596	0.3304	-83.9442	136.9771	217.197
8	1.3836	2.1495	0.0801	7.7096	0.1127	0.5591	0.0933	-0.2521	-0.3367	-0.3965	-0.3156	-0.8089	0.1066	0.47	0.1812	0.3479	0.0349	0.0401	0.4085	0.0538	0.3821	-75.5314	130.372	216.5289
9	3.6493	-1.9823	3.9358	2.2269	-1.3297	5.114	0.246	1.0592	-0.945	-1.4895	-0.409	0.1799	1.5659	0.1423	0.1547	0.7006	-0.0071	-0.0449	0.4802	-0.0727	0.5104	-82.8915	121.6857	209.6675
10	0.5472	-1.8176	0.3737	6.8934	-2.6699	1.5147	-0.0317	0.1389	-0.0247	-0.9623	0.1146	0.7752	0.2554	-0.3046	-0.1418	0.4491	-0.0225	-0.1293	0.3823	0.0398	0.3654	-84.5831	137.5852	207.5438
11	2.7278	-1.6696	0.2574	8.4986	1.8537	2.5983	-0.1674	0.4012	-0.3585	-1.2463	0.1649	0.2693	0.2708	0.3558	0.0175	0.6401	-0.0238	0.0049	0.4444	-0.0461	0.336	-76.5494	139.7487	204.2538
12	1.8926	2.7497	0.1006	4.9181	-0.6716	1.3272	-0.3752	0.0303	-0.4005	-1.0142	0.0952	-0.9592	0.2619	0.4809	0.2317	0.4485	0.0323	0.1342	0.4079	0.0247	0.3689	-71.7163	140.0521	208.1602
13	4.3668	-3.2888	-1.5816	4.3249	1.151	2.3719	-0.5529	1.4044	1.4172	-0.7571	1.1938	-0.3352	0.5107	1.6932	-0.4267	0.5291	0.1163	0.0234	0.8382	0.1755	0.5389	-69.1777	122.2795	215.6224
14	0.5391	-0.7725	-0.4145	4.1774	-1.7521	2.5565	-0.1025	0.0372	-0.0796	-0.5799	-0.3158	-0.5376	0.2686	0.3772	0.3776	0.2697	0.0428	0.0257	0.3274	0.1005	0.4352	-77.3552	122.4716	223.3417
15	4.3561	1.362	0.339	5.1305	-0.6432	2.3013	0.0974	-0.0782	-0.4761	0.1924	-0.1975	-0.7616	-0.0616	0.2684	0.0278	0.2574	-0.0149	-0.0761	0.3517	0.0947	0.3753	-78.7301	129.2079	225.1929
16	1.3189	-0.7589	-0.3918	3.2956	-1.0104	3.2356	0.0434	-0.1121	-0.1515	0.2621	0.1543	0.2336	-0.135	-0.226	-0.2042	0.2733	0.0149	-0.0171	0.4065	0.1357	0.4178	-88.5655	122.4905	235.9717
17	3.6911	1.3969	2.0453	0.654	1.93	2.3304	-0.0845	0.4503	0.5199	-0.1638	-0.306	0.2089	0.0948	-0.0052	0.3481	0.3348	-0.0233	-0.0415	0.4905	0.0972	0.4837	-103.762	124.4558	222.4851
18	2.8669	-2.7851	0.152	3.3803	0.6665	1.8298	0.369	-0.4405	-0.0412	0.0684	-0.0999	0.1209	-0.1047	0.1836	-0.0509	0.3723	-0.0463	-0.0458	0.407	-0.0136	0.4407	-107.4227	112.108	217.8427
19	3.8351	-3.2518	-0.9657	5.2798	5.1022	9.0541	0.3931	0.5208	-1.465	0.4972	-0.3158	1.6981	1.2546	1.6015	-0.0887	0.4088	-0.0576	-0.1388	0.656	-0.021	0.6436	-100.5391	111.4965	223.7296
20	9.3802	-0.0468	-1.2463	3.8776	2.5732	2.4685	-0.7453	0.0166	-0.9488	-0.4151	0.4218	0.2239	0.5473	0.231	0.4346	0.3445	-0.1313	-0.0378	0.558	0.1431	0.5881	-95.6799	114.8337	226.5971

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 4:10)	B	4 - 10
2	X-RAY DIFFRACTION	2	(chain B and resid 11:18)	B	11 - 18
3	X-RAY DIFFRACTION	3	(chain B and resid 19:26)	B	19 - 26
4	X-RAY DIFFRACTION	4	(chain B and resid 27:31)	B	27 - 31
5	X-RAY DIFFRACTION	5	(chain B and resid 32:38)	B	32 - 38
6	X-RAY DIFFRACTION	6	(chain B and resid 39:42)	B	39 - 42
7	X-RAY DIFFRACTION	7	(chain B and resid 43:58)	B	43 - 58
8	X-RAY DIFFRACTION	8	(chain B and resid 59:68)	B	59 - 68
9	X-RAY DIFFRACTION	9	(chain B and resid 69:75)	B	69 - 75
10	X-RAY DIFFRACTION	10	(chain B and resid 76:89)	B	76 - 89
11	X-RAY DIFFRACTION	11	(chain B and resid 90:101)	B	90 - 101
12	X-RAY DIFFRACTION	12	(chain B and resid 102:133)	B	102 - 133
13	X-RAY DIFFRACTION	13	(chain B and resid 134:143)	B	134 - 143
14	X-RAY DIFFRACTION	14	(chain B and resid 144:165)	B	144 - 165
15	X-RAY DIFFRACTION	15	(chain B and resid 166:180)	B	166 - 180
16	X-RAY DIFFRACTION	16	(chain B and resid 181:215)	B	181 - 215
17	X-RAY DIFFRACTION	17	(chain B and resid 216:233)	B	216 - 233
18	X-RAY DIFFRACTION	18	(chain B and resid 234:239)	B	234 - 239
19	X-RAY DIFFRACTION	19	(chain B and resid 240:245)	B	240 - 245
20	X-RAY DIFFRACTION	20	(chain B and resid 246:255)	B	246 - 255

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