PDB-3zqm: Crystal structure of the small terminase oligomerization core dom...

ID or keywords:

Entry

Database: PDB / ID: 3zqm

Title

Crystal structure of the small terminase oligomerization core domain from a SPP1-like bacteriophage (crystal form 1)

Components

TERMINASE SMALL SUBUNIT

Keywords

DNA BINDING PROTEIN / DNA-BINDING PROTEIN / MOLECULAR MOTOR / DNA PACKAGING

Function / homology

Function and homology information

chromosome organization / DNA binding / identical protein binding
Similarity search - Function

Biological species

BACILLUS PHAGE SF6 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.85 Å

Authors

Buttner, C.R. / Chechik, M. / Ortiz-Lombardia, M. / Smits, C. / Chechik, V. / Jeschke, G. / Dykeman, E. / Benini, S. / Alonso, J.C. / Antson, A.A.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural Basis for DNA Recognition and Loading Into a Viral Packaging Motor.
Authors: Buttner, C.R. / Chechik, M. / Ortiz-Lombardia, M. / Smits, C. / Ebong, I.O. / Chechik, V. / Jeschke, G. / Dykeman, E. / Benini, S. / Robinson, C.V. / Alonso, J.C. / Antson, A.A.

History

Deposition	Jun 10, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 28, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jan 18, 2012	Group: Other
Revision 1.2	Feb 15, 2012	Group: Other
Revision 1.3	Oct 23, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3zqm.cif.gz	235.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3zqm.ent.gz	195.8 KB	Display	PDB format
PDBx/mmJSON format	3zqm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3zqm_validation.pdf.gz	480.5 KB	Display	wwPDB validaton report
Full document	3zqm_full_validation.pdf.gz	481.4 KB	Display
Data in XML	3zqm_validation.xml.gz	28.2 KB	Display
Data in CIF	3zqm_validation.cif.gz	40.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zq/3zqm ftp://data.pdbj.org/pub/pdb/validation_reports/zq/3zqm	HTTPS FTP

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Related structure data

Related structure data	3zqnC 3zqoC 3zqpC 3zqqC 2cmp C: citing same article (ref.)
Similar structure data	6lm1-d 5hxk-1 5b6z-1 5h2p-1 3a57-1 2f4n-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: TERMINASE SMALL SUBUNIT

B: TERMINASE SMALL SUBUNIT

C: TERMINASE SMALL SUBUNIT

D: TERMINASE SMALL SUBUNIT

E: TERMINASE SMALL SUBUNIT

F: TERMINASE SMALL SUBUNIT

G: TERMINASE SMALL SUBUNIT

H: TERMINASE SMALL SUBUNIT

I: TERMINASE SMALL SUBUNIT

J: TERMINASE SMALL SUBUNIT

80.7 kDa, 10 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)	64.954, 60.009, 81.442
Angle α, β, γ (deg.)	90.00, 100.43, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	TERMINASE SMALL SUBUNIT / SF6 SMALL TERMINASE G1P / G1P Mass: 8067.110 Da / Num. of mol.: 10 / Fragment: OLIGOMERIZATION CORE DOMAIN, RESIDUES 53-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS PHAGE SF6 (virus) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q1EJR8, UniProt: P68928*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 58 % / Description: NONE
Crystal grow	Details: 0.1 M MALONATE/IMIDAZOLE/BORIC ACID BUFFER SYSTEM PH 7.0, 25 % PEG 1500

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.971557
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.971557 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. obs: 52842 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4 % / B_iso Wilson estimate: 28.5 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 18
Reflection shell	Resolution: 1.85→1.92 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.36 / Mean I/σ(I) obs: 4.3 / % possible all: 86

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0116	refinement
DENZO		data reduction
SCALEPACK		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.85→80.06 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.944 / SU B: 5.286 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21351	2644	5.1 %	RANDOM
R_work	0.17175	-	-	-
obs	0.17389	49111	97.92 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 31.483 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.18 Å²	0 Å²	0.09 Å²
2-	-	-0.7 Å²	0 Å²
3-	-	-	0.9 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→80.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4367	0	0	421	4788

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	4395
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3075
X-RAY DIFFRACTION	r_angle_refined_deg	1.581	2.005	5862
X-RAY DIFFRACTION	r_angle_other_deg	0.919	3	7658
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.458	5	564
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.452	26.471	170
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.178	15	984
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.55	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	713
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	4707
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	681
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.85→1.898 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.247	160	-
R_work	0.211	3026	-
obs	-	-	83.53 %

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	5.9572	-0.9806	-4.3725	0.8377	1.9424	5.4271	-0.0022	0.0278	0.0072	-0.0422	0.1725	-0.0902	-0.108	0.2851	-0.1704	0.1993	-0.0241	-0.0892	0.3298	0.0255	0.3503	34.232	60.511	73.614
2	0.6719	-0.5726	0.5931	1.2966	-0.7485	1.265	-0.1588	-0.0752	0.1003	0.0012	0.0447	-0.2857	-0.179	-0.0663	0.1141	0.3099	-0.0099	-0.0495	0.2177	0.0115	0.3179	18.213	74.804	66.836
3	2.3085	-2.7168	1.8898	3.7806	-1.3185	3.0473	0.0588	-0.0159	0.0279	-0.0725	-0.1242	-0.0681	0.165	-0.1894	0.0654	0.2762	-0.0039	-0.0298	0.2796	-0.0018	0.3001	18.447	58.258	77.759
4	4.4688	-1.8148	-2.0629	0.7546	0.648	3.0451	-0.3231	-0.5483	0.2272	0.1823	0.2257	-0.118	-0.3834	0.0987	0.0975	0.3233	0.0263	-0.1328	0.2723	-0.0329	0.2715	20.285	61.838	87.279
5	0.4607	-0.4192	-0.2132	1.4256	-1.13	1.8387	-0.1121	-0.0732	0.1732	0.1328	0.1596	-0.1019	-0.0774	-0.0521	-0.0474	0.3249	0.0139	-0.1028	0.2205	0.0065	0.3062	8.45	75.482	73.16
6	3.6496	-3.1793	4.0282	5.3403	-3.0032	4.5493	0.1064	-0.1258	0.0968	-0.1008	-0.1715	-0.2436	0.1566	-0.2066	0.065	0.2983	0.0028	-0.0192	0.3027	-0.0086	0.2546	8.246	56.958	81.651
7	10.7129	1.2083	2.2961	0.4531	0.2322	0.504	0.1472	-0.8876	0.0974	0.1585	-0.1417	0.0943	-0.0154	-0.2193	-0.0055	0.3393	0.0049	0.009	0.3902	0.0049	0.1593	5.051	59.102	91.208
8	0.4862	0.1756	0.1867	2.2522	-1.607	1.3725	-0.2506	-0.099	0.1144	0.0042	0.1187	-0.0256	-0.1322	-0.2081	0.1319	0.2915	0.0322	-0.0464	0.2795	-0.0391	0.2977	-2.772	71.636	73.839
9	1.8494	-0.2437	1.7933	4.7479	-5.9447	8.7713	-0.1428	-0.1197	-0.0572	-0.2182	-0.0743	-0.2971	0.3235	-0.1923	0.2171	0.3598	-0.0563	-0.0125	0.3323	0.0204	0.225	-1.421	52.25	80.046
10	4.1627	1.6	5.4788	0.6298	2.1736	10.1515	0.0448	-0.4913	-0.0359	0.0223	-0.1273	-0.0121	0.0603	-0.7922	0.0824	0.2944	-0.0898	0.1003	0.4187	0.0263	0.1548	-9.671	51.4	85.065
11	0.1717	-0.2745	0.4608	3.1204	-1.3467	1.5899	-0.1166	-0.0765	0.0684	0.1185	0.0228	0.0502	-0.0737	-0.3129	0.0938	0.2827	0.0026	-0.0289	0.3189	-0.0171	0.2721	-11.528	66.89	68.454
12	0.2023	-0.4717	-0.18	4.1148	-2.9851	6.2192	-0.1015	0.1925	0.0728	0.1999	-0.1129	-0.2759	0.3612	-0.1719	0.2144	0.3381	-0.0718	0.0487	0.32	0.0075	0.218	-7.09	47.38	71.471
13	1.8203	-0.3054	-1.5656	0.6445	2.2455	8.0013	-0.1052	-0.0824	-0.0453	0.088	-0.1593	0.0879	0.2685	-0.3651	0.2646	0.3443	-0.2055	0.1875	0.2915	-0.0824	0.2056	-16.693	43.404	72.55
14	0.0564	-0.1518	-0.223	3.9318	0.0772	1.0122	-0.0168	0.0467	-0.0247	-0.1076	-0.1511	0.1778	0.0044	-0.1493	0.1679	0.2413	0.0018	-0.0355	0.3088	-0.0328	0.2853	-13.852	60.798	58.52
15	0.3958	1.2808	-0.9659	6.845	-1.9163	3.0446	-0.0115	0.0043	0.0257	0.2786	-0.0494	-0.0777	0.2616	-0.0521	0.0609	0.3242	-0.0423	0.0244	0.3005	-0.0203	0.2611	-6.814	41.84	62.043
16	0.0388	0.1458	-0.0156	2.2011	2.115	2.9045	-0.0126	-0.0492	-0.0275	0.1316	-0.4121	0.2091	0.2096	-0.1877	0.4247	0.3346	-0.0883	0.03	0.3009	-0.0445	0.2615	-12.334	37.66	54.785
17	0.0366	0.0554	-0.0593	1.455	0.6179	0.7178	-0.007	-0.0493	-0.0551	-0.2838	-0.0935	0.1458	-0.1357	-0.0557	0.1005	0.3124	0.0544	-0.0256	0.2857	0.0037	0.2614	-10.319	60.207	48.747
18	1.3728	2.4431	-0.8273	7.9284	-2.9005	1.3009	0.042	-0.1118	-0.0968	0.0242	-0.128	-0.2091	0.0151	0.0889	0.086	0.2902	-0.0001	0.0102	0.2757	0.0261	0.2785	0.096	40.75	53.162
19	1.0443	0.7067	-0.4406	1.127	0.5209	1.2407	0.0809	0.1689	-0.1663	0.1682	-0.007	-0.2241	0.1561	-0.1647	-0.0739	0.2874	0.0321	0.0014	0.2687	-0.0326	0.3201	-1.585	35.628	44.097
20	1.0863	-0.3763	0.1749	1.5707	0.284	0.1207	-0.0684	-0.1309	-0.1475	-0.4034	0.1218	0.0146	-0.1464	0.0208	-0.0534	0.3731	0.0283	0.0254	0.2796	0.0455	0.2124	-1.485	59.481	42.109
21	3.9113	0.5995	-0.9909	10.4737	-0.1926	0.2988	-0.1684	-0.3746	-0.0797	0.1067	0.31	0.0956	0.0201	0.1527	-0.1416	0.1761	0.0653	0.0577	0.3221	-0.0476	0.3918	10.145	41.975	49.469
22	9.2186	6.5227	0.0245	8.6839	3.1729	2.4504	-0.3455	0.2977	-0.1193	-0.3573	0.618	-0.4219	-0.0712	0.2999	-0.2725	0.2103	0.1064	-0.026	0.3143	-0.0696	0.3568	15.748	38.646	41.74
23	0.7841	-0.7155	0.1111	3.057	0.4931	0.1652	-0.1935	0.0745	-0.0682	-0.4747	0.2793	-0.1806	-0.1965	0.099	-0.0858	0.3152	-0.0472	0.0999	0.3039	0.0612	0.2419	10.905	60.447	40.92
24	1.971	1.5031	0.5078	7.6035	1.0744	1.3951	0.1784	0.1126	-0.1469	0.1163	0.3898	0.0295	0.0426	0.3473	-0.5683	0.1335	0.0532	0.0326	0.3049	-0.0846	0.3848	19.919	46.128	52.094
25	2.0145	2.5571	1.17	4.558	4.4805	7.5196	-0.1136	0.2636	-0.1225	-0.0821	0.5575	-0.3096	0.0863	0.6671	-0.4439	0.0413	0.0949	-0.0119	0.466	-0.2465	0.3966	28.024	45.314	45.507
26	1.5647	-0.9578	0.6195	2.1475	0.1979	0.4917	-0.1343	0.1593	0.1176	-0.2777	0.2165	-0.216	-0.2163	0.2377	-0.0822	0.2355	-0.1332	0.0914	0.3188	0.0232	0.3131	19.565	65.767	46.381
27	2.9481	-2.9581	0.0835	10.5086	1.399	0.3013	-0.3814	0.373	-0.4245	0.3251	0.4757	0.219	-0.0466	0.1761	-0.0943	0.1808	0.0006	0.0943	0.3417	-0.0816	0.3745	25.591	51.52	59.675
28	2.9728	1.3205	1.8036	3.4206	2.9814	2.7734	-0.0396	0.3035	-0.2069	-0.179	0.3442	-0.3364	-0.1641	0.3307	-0.3045	0.092	-0.004	0.0393	0.3932	-0.0669	0.425	35.67	53.612	60.325
29	1.4694	-0.5699	1.4279	0.6012	-0.2242	1.7166	-0.1619	0.0047	0.1705	-0.0602	0.1289	-0.2291	-0.1807	0.168	0.033	0.2774	-0.0935	0.0201	0.2693	-0.0025	0.3292	22.141	70.984	56.721
30	2.8857	-2.7504	0.3215	3.2222	-1.6845	3.2556	0.0459	-0.0826	0.0351	-0.1103	0.1362	0.002	0.1958	-0.0402	-0.1821	0.1929	-0.0074	-0.0315	0.3012	-0.0326	0.3493	25.705	55.729	69.787

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	62 - 79
2	X-RAY DIFFRACTION	2	A	80 - 107
3	X-RAY DIFFRACTION	3	A	108 - 120
4	X-RAY DIFFRACTION	4	B	65 - 80
5	X-RAY DIFFRACTION	5	B	81 - 107
6	X-RAY DIFFRACTION	6	B	108 - 120
7	X-RAY DIFFRACTION	7	C	64 - 80
8	X-RAY DIFFRACTION	8	C	81 - 108
9	X-RAY DIFFRACTION	9	C	109 - 120
10	X-RAY DIFFRACTION	10	D	65 - 80
11	X-RAY DIFFRACTION	11	D	81 - 107
12	X-RAY DIFFRACTION	12	D	108 - 120
13	X-RAY DIFFRACTION	13	E	64 - 80
14	X-RAY DIFFRACTION	14	E	81 - 108
15	X-RAY DIFFRACTION	15	E	109 - 120
16	X-RAY DIFFRACTION	16	F	65 - 84
17	X-RAY DIFFRACTION	17	F	85 - 107
18	X-RAY DIFFRACTION	18	F	108 - 120
19	X-RAY DIFFRACTION	19	G	63 - 84
20	X-RAY DIFFRACTION	20	G	85 - 107
21	X-RAY DIFFRACTION	21	G	108 - 120
22	X-RAY DIFFRACTION	22	H	66 - 80
23	X-RAY DIFFRACTION	23	H	81 - 107
24	X-RAY DIFFRACTION	24	H	108 - 120
25	X-RAY DIFFRACTION	25	I	63 - 80
26	X-RAY DIFFRACTION	26	I	81 - 107
27	X-RAY DIFFRACTION	27	I	108 - 120
28	X-RAY DIFFRACTION	28	J	65 - 80
29	X-RAY DIFFRACTION	29	J	81 - 108
30	X-RAY DIFFRACTION	30	J	109 - 120

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