PDB-4zni: Thermus Phage P74-26 Large Terminase ATPase domain (I 2 3 space group)

ID or keywords:

Entry

Database: PDB / ID: 4zni

Title

Thermus Phage P74-26 Large Terminase ATPase domain (I 2 3 space group)

Components

Phage terminase large subunit

Keywords

VIRAL PROTEIN / DNA Translocation

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 / Resolution: 2.097 Å

Authors

Hilbert, B.J. / Hayes, J.A. / Stone, N.P. / Duffy, C.M. / Sankaran, B. / Kelch, B.A.

Funding support

United States, 2items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure and mechanism of the ATPase that powers viral genome packaging.
Authors: Hilbert, B.J. / Hayes, J.A. / Stone, N.P. / Duffy, C.M. / Sankaran, B. / Kelch, B.A.

History

Deposition	May 4, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 8, 2015	Provider: repository / Type: Initial release
Revision 1.1	Aug 5, 2015	Group: Database references
Revision 1.2	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4zni.cif.gz	123.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4zni.ent.gz	98.6 KB	Display	PDB format
PDBx/mmJSON format	4zni.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/zn/4zni ftp://data.pdbj.org/pub/pdb/validation_reports/zn/4zni	HTTPS FTP

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Related structure data

Related structure data	4znjC 4znkC 4znlC C: citing same article (ref.)
Similar structure data	4znj-d 1yud-3 4ht4-d 4znk-d 3dh3-2 2fl3-d 2fkc-2 1yud-4 1yud-1 2q2a-4 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: Phage terminase large subunit

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	129.578, 129.578, 129.578
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	197
Space group name H-M	I23

#1: Protein	Phage terminase large subunit Mass: 31580.732 Da / Num. of mol.: 1 / Fragment: residues 1-256 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus phage P7426 (virus) / Gene: P74p84 / Plasmid: pet24a / Production host: Escherichia coli (E. coli) / Strain (production host): BLR DE3 / References: UniProt: A7XXR1
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.87 Å³/Da / Density % sol: 57.15 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.7 M ammonium sulfate and 0.1 M tri-sodium citrate pH 5.0

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Data collection

Diffraction	Mean temperature: 100 K
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: 2.097→45.813 Å / Num. obs: 21390 / % possible obs: 100 % / Redundancy: 13.9 % / R_merge(I) obs: 0.087 / Net I/σ(I): 15.8
Reflection shell	Resolution: 2.097→2.171 Å / Redundancy: 13.9 % / R_merge(I) obs: 1.275 / Mean I/σ(I) obs: 2.48 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.097→45.813 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2132	1767	8.26 %
R_work	0.1726	-	-
obs	0.1761	21390	99.99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.097→45.813 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2051	0	35	101	2187

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2178
X-RAY DIFFRACTION	f_angle_d	1.132	2961
X-RAY DIFFRACTION	f_dihedral_angle_d	13.883	797
X-RAY DIFFRACTION	f_chiral_restr	0.045	297
X-RAY DIFFRACTION	f_plane_restr	0.005	384

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 (%)
2.0965-2.1532	0.3105	133	0.253	1524	X-RAY DIFFRACTION	100
2.1532-2.2166	0.2877	137	0.2297	1471	X-RAY DIFFRACTION	100
2.2166-2.2881	0.288	133	0.197	1498	X-RAY DIFFRACTION	100
2.2881-2.3699	0.2312	139	0.1959	1498	X-RAY DIFFRACTION	100
2.3699-2.4648	0.2183	131	0.1859	1485	X-RAY DIFFRACTION	100
2.4648-2.5769	0.2814	137	0.1967	1495	X-RAY DIFFRACTION	100
2.5769-2.7128	0.2435	137	0.1995	1510	X-RAY DIFFRACTION	100
2.7128-2.8827	0.2442	134	0.1892	1504	X-RAY DIFFRACTION	100
2.8827-3.1052	0.2058	137	0.1958	1512	X-RAY DIFFRACTION	100
3.1052-3.4176	0.2386	138	0.1851	1501	X-RAY DIFFRACTION	100
3.4176-3.912	0.2148	139	0.159	1512	X-RAY DIFFRACTION	100
3.912-4.9277	0.1633	133	0.1387	1528	X-RAY DIFFRACTION	100
4.9277-45.8237	0.2009	139	0.1662	1585	X-RAY DIFFRACTION	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	1.4032	0.195	0.0232	0.3308	0.1211	0.0464	0.3834	-0.3836	1.1743	0.555	-0.6764	0.266	0.2101	1.2791	-0.0216	0.5628	-0.017	-0.0494	0.7517	-0.0613	0.4052	-215.4734	145.8855	93.0083
2	0.1433	-0.1597	-0.2934	1.9525	0.4328	0.5893	-0.1872	-0.0619	-0.2599	0.5963	0.1922	0.5072	-0.5919	-0.0491	-0.0009	0.4319	0.0352	-0.0405	0.4469	0.0802	0.5569	-221.883	138.6977	92.2853
3	0.232	-0.0218	-0.2692	0.0753	0.0795	0.2675	-0.4818	0.383	0.3632	-0.1656	0.448	0.216	-0.5258	-0.2566	0.0003	0.3901	-0.0215	-0.0685	0.4979	0.0978	0.4649	-217.2857	127.5706	97.6114
4	0.7791	0.0853	-0.8463	0.5016	-0.6486	1.5216	-0.2809	0.1145	0.2889	0.8139	0.8184	-1.1757	-0.0608	-1.2074	0.1077	0.5208	-0.1797	-0.2591	0.7306	0.151	0.676	-225.4068	125.0662	88.1947
5	0.3334	-0.2037	0.0179	0.3278	-0.1042	-0.0355	0.0188	-0.1618	-0.3234	-0.5639	-0.1029	-0.4598	0.0174	0.1606	-0	0.4079	-0.0016	-0.0403	0.4369	0.0672	0.4303	-213.2867	138.0682	86.9167
6	0.0332	-0.0087	0.195	0.0968	-0.178	0.3139	-0.2544	0.0488	0.0891	-0.2784	0.1158	-0.2384	0.1493	0.5376	0.0003	0.4608	0.045	0.0303	0.5592	0.013	0.5157	-205.2855	132.1747	87.5456
7	0.5479	0.5334	0.1933	0.6407	-0.3967	1.2115	-0.2104	0.116	-0.2685	-0.9651	0.2206	0.0347	0.2485	-0.078	-0.0004	0.5795	-0.0158	-0.0376	0.4861	-0.0081	0.4884	-213.0377	134.8889	78.6743
8	0.4466	-0.3389	-0.623	1.8244	0.3176	0.7139	-0.431	-0.0957	-0.0469	-2.2656	0.4312	0.1256	0.1482	0.7841	0.0372	0.8659	0.0563	0.137	0.4482	-0.0206	0.4643	-204.084	133.5893	74.123
9	0.344	1.2195	0.6052	0.6228	0.1389	-0.2886	-0.4236	0.2043	-0.3499	-0.6838	0.2916	-0.9914	0.1228	0.5541	0.0055	0.5739	0.0335	0.1619	0.5498	0.0361	0.49	-201.2125	138.9671	79.2542
10	2.5744	-0.1044	0.6192	0.8243	-0.644	1.4075	-0.9114	-0.0439	0.4923	0.0961	0.1489	-0.1933	-0.1544	1.9467	-1.1759	0.2663	0.0792	0.0755	0.8617	0.2013	0.5382	-200.2619	128.3459	88.8253
11	0.0308	-0.043	-0.047	0.0756	-0.008	0.0499	0.4904	0.0997	-0.559	-0.2685	-0.5912	-0.3071	0.2576	-0.1917	-0.0002	0.4745	0.0007	-0.0618	0.4672	0.0144	0.62	-214.1701	120.3079	90.7282
12	0.1003	-0.2619	0.5071	0.4229	-0.6249	1.0874	-0.4636	-0.0491	0.4876	-0.7056	-0.372	-1.2386	0.0818	1.0962	-0.7907	0.3312	0.0264	0.0016	0.5354	0.231	0.8396	-202.2656	123.7292	96.0816
13	0.0546	-0.1776	0.1803	0.3749	-0.3834	0.1597	-0.1556	-0.2187	-0.7443	-0.0639	-0.0511	-0.7488	0.0706	0.3157	-0.0084	0.3606	-0.0135	-0.0666	0.4398	0.0829	0.4746	-212.8095	127.8846	95.3647
14	0.3345	-0.4147	0.149	0.7336	-0.4685	0.2516	-0.1109	-0.1584	-0.3106	0.1628	0.1977	0.1859	-0.0157	0.2953	-0.0002	0.3585	0.004	0.0017	0.4432	0.1268	0.4646	-217.5444	121.224	103.9246
15	0.1913	0.3439	-0.5512	0.3893	-0.6373	0.9248	0.3209	-0.2793	-0.0111	0.79	-0.035	0.1938	-0.4861	-0.099	0.0083	0.3999	-0.0018	-0.0178	0.5347	0.1359	0.4866	-218.6413	124.6933	108.7143
16	0.0287	-0.0926	-0.0928	0.4575	0.5924	0.4537	-0.2712	-0.1885	0.5779	-0.1901	-0.2446	0.0553	-0.2171	0.0237	-0	0.3854	0.0275	-0.0083	0.5587	0.1107	0.5864	-231.119	126.8685	94.1603
17	0.417	0.1027	0.3735	0.1391	0.06	0.1882	0.0057	-0.0238	0.0171	0.5503	0.155	0.8462	0.3515	-0.1296	0.001	0.4598	-0.044	-0.0091	0.6194	-0.077	0.5199	-238.2182	116.4362	89.9043
18	0.7869	-0.0701	0.5234	0.3492	-0.1327	0.3656	0.6307	0.7363	-0.7359	0.2634	-0.2351	0.5804	0.5685	0.2644	0.0029	0.5004	-0.0799	-0.1235	0.5384	0.0373	0.743	-229.9072	111.7701	93.8079
19	0.0302	0.0111	0.1249	0.0527	0.0341	0.676	-0.7396	0.2144	-0.8124	-0.1024	0.3953	0.0742	-0.6519	-0.5309	-0.0046	0.3605	-0.1022	-0.066	0.674	0.0503	0.6557	-226.538	116.9705	96.5174

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and ((resseq 3:10))
2	X-RAY DIFFRACTION	2	chain A and ((resseq 11:31))
3	X-RAY DIFFRACTION	3	chain A and ((resseq 32:38))
4	X-RAY DIFFRACTION	4	chain A and ((resseq 39:43))
5	X-RAY DIFFRACTION	5	chain A and ((resseq 44:57))
6	X-RAY DIFFRACTION	6	chain A and ((resseq 58:68))
7	X-RAY DIFFRACTION	7	chain A and ((resseq 69:93))
8	X-RAY DIFFRACTION	8	chain A and ((resseq 94:104))
9	X-RAY DIFFRACTION	9	chain A and ((resseq 105:136))
10	X-RAY DIFFRACTION	10	chain A and ((resseq 137:146))
11	X-RAY DIFFRACTION	11	chain A and ((resseq 147:153))
12	X-RAY DIFFRACTION	12	chain A and ((resseq 154:170))
13	X-RAY DIFFRACTION	13	chain A and ((resseq 171:180))
14	X-RAY DIFFRACTION	14	chain A and ((resseq 181:198))
15	X-RAY DIFFRACTION	15	chain A and ((resseq 199:215))
16	X-RAY DIFFRACTION	16	chain A and ((resseq 216:228))
17	X-RAY DIFFRACTION	17	chain A and ((resseq 229:238))
18	X-RAY DIFFRACTION	18	chain A and ((resseq 239:246))
19	X-RAY DIFFRACTION	19	chain A and ((resseq 247:253))

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