PDB-3txq: Crystal Structure of phage 44RR small terminase gp16

ID or keywords:

Entry

Database: PDB / ID: 3txq

Title

Crystal Structure of phage 44RR small terminase gp16

Components

Terminase DNA packaging enzyme small subunit

Keywords

VIRAL PROTEIN / helix / small terminase

Function / homology

Bacteriophage T4, Gp16, DNA-packaging / Terminase DNA packaging enzyme / ESAT-6-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / identical protein binding / Terminase DNA packaging enzyme small subunit

Function and homology information

Biological species

Aeromonas phage 44RR2.8t (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Sun, S. / Xiang, Y. / Rossmann, M.G.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure and function of the small terminase component of the DNA packaging machine in T4-like bacteriophages.
Authors: Sun, S. / Gao, S. / Kondabagil, K. / Xiang, Y. / Rossmann, M.G. / Rao, V.B.

History

Deposition	Sep 23, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 28, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jan 25, 2012	Group: Database references
Revision 1.2	Feb 22, 2012	Group: Database references
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3txq.cif.gz	366.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3txq.ent.gz	309.8 KB	Display	PDB format
PDBx/mmJSON format	3txq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3txq_validation.pdf.gz	476.5 KB	Display	wwPDB validaton report
Full document	3txq_full_validation.pdf.gz	483.3 KB	Display
Data in XML	3txq_validation.xml.gz	29.4 KB	Display
Data in CIF	3txq_validation.cif.gz	42.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tx/3txq ftp://data.pdbj.org/pub/pdb/validation_reports/tx/3txq	HTTPS FTP

-
Related structure data

Related structure data	3txsC 3zqoS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4d7s-2 5i72-1 3txs-1 4d7s-1 6gso-d 4kl1-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Terminase DNA packaging enzyme small subunit

B: Terminase DNA packaging enzyme small subunit

C: Terminase DNA packaging enzyme small subunit

D: Terminase DNA packaging enzyme small subunit

E: Terminase DNA packaging enzyme small subunit

F: Terminase DNA packaging enzyme small subunit

G: Terminase DNA packaging enzyme small subunit

H: Terminase DNA packaging enzyme small subunit

I: Terminase DNA packaging enzyme small subunit

J: Terminase DNA packaging enzyme small subunit

K: Terminase DNA packaging enzyme small subunit

112 kDa, 11 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)	83.013, 106.292, 136.671
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 5 / Auth seq-ID: 26 - 112 / Label seq-ID: 1 - 87

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H
9	I	I
10	J	J
11	K	K

#1: Protein	Terminase DNA packaging enzyme small subunit Mass: 10161.699 Da / Num. of mol.: 11 / Fragment: UNP Residues 26-112 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas phage 44RR2.8t (virus) / Gene: 16, gene 16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6U9F0
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Terminase DNA packaging enzyme small subunit

Mass: 10161.699 Da / Num. of mol.: 11 / Fragment: UNP Residues 26-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Aeromonas phage 44RR2.8t (virus) / Gene: 16, gene 16 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6U9F0

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54.4 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG3350, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 6, 2010 / Details: mirrors
Radiation	Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.8→83.92 Å / Num. all: 30487 / Num. obs: 30459 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / B_iso Wilson estimate: 77.1 Å² / R_merge(I) obs: 0.078 / R_sym value: 0.078 / Net I/σ(I): 19.9
Reflection shell	Resolution: 2.8→2.9 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.389 / Mean I/σ(I) obs: 4.8 / Num. unique all: 2979 / R_sym value: 0.389 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZQO

3zqo

Resolution: 2.8→83.92 Å / Cor.coef. F_o:F_c: 0.925 / Cor.coef. F_o:F_c free: 0.874 / SU B: 35.819 / SU ML: 0.359 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29783	1540	5.1 %	RANDOM
R_work	0.23925	-	-	-
all	0.24223	28925	-	-
obs	0.24223	28893	99.89 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 61.069 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.44 Å²	0 Å²	0 Å²
2-	-	-1.28 Å²	0 Å²
3-	-	-	2.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→83.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7755	0	0	24	7779

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.022	7865
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.808	1.972	10571
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.961	5	946
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.945	25.405	407
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.652	15	1573
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.192	15	55
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	1166
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	5874
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.172	0.2	3534
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.287	0.2	5291
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.086	0.2	204
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	0.186	0.2	23
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.384	0.2	1
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	0.22	1.5	4962
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.36	2	7766
X-RAY DIFFRACTION	r_scbond_it	0.561	3	3208
X-RAY DIFFRACTION	r_scangle_it	0.968	4.5	2805
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	348	medium positional	0.23	0.5
2	B	348	medium positional	0.23	0.5
3	C	348	medium positional	0.3	0.5
4	D	348	medium positional	0.29	0.5
5	E	348	medium positional	0.27	0.5
6	F	348	medium positional	0.27	0.5
7	G	348	medium positional	0.19	0.5
8	H	348	medium positional	0.23	0.5
9	I	348	medium positional	0.23	0.5
10	J	348	medium positional	0.23	0.5
11	K	348	medium positional	0.2	0.5
1	A	357	loose positional	0.45	5
2	B	357	loose positional	0.49	5
3	C	357	loose positional	0.66	5
4	D	357	loose positional	0.51	5
5	E	357	loose positional	0.59	5
6	F	357	loose positional	0.48	5
7	G	357	loose positional	0.47	5
8	H	357	loose positional	0.43	5
9	I	357	loose positional	0.44	5
10	J	357	loose positional	0.49	5
11	K	357	loose positional	0.63	5
1	A	348	medium thermal	0.15	2
2	B	348	medium thermal	0.16	2
3	C	348	medium thermal	0.16	2
4	D	348	medium thermal	0.12	2
5	E	348	medium thermal	0.12	2
6	F	348	medium thermal	0.14	2
7	G	348	medium thermal	0.13	2
8	H	348	medium thermal	0.17	2
9	I	348	medium thermal	0.16	2
10	J	348	medium thermal	0.14	2
11	K	348	medium thermal	0.17	2
1	A	357	loose thermal	0.64	10
2	B	357	loose thermal	0.63	10
3	C	357	loose thermal	0.62	10
4	D	357	loose thermal	0.62	10
5	E	357	loose thermal	0.56	10
6	F	357	loose thermal	0.65	10
7	G	357	loose thermal	0.63	10
8	H	357	loose thermal	0.72	10
9	I	357	loose thermal	0.77	10
10	J	357	loose thermal	0.81	10
11	K	357	loose thermal	0.64	10

LS refinement shell

Resolution: 2.8→2.873 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.35	110	-
R_work	0.308	2114	-
obs	-	-	99.96 %

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	1.5665	0.1382	0.1123	4.1174	1.6374	2.9359	0.0634	-0.0378	-0.208	0.1714	-0.0467	-0.4737	0.155	0.2155	-0.0166	-0.2999	0.0305	-0.0943	-0.2364	0.008	0.0334	88.7922	19.1103	30.4974
2	4.5486	0.9196	0.6023	2.1735	0.0103	0.9852	0.2088	-0.0827	-0.3076	-0.2396	-0.2206	-0.0229	0.0442	-0.0538	0.0118	-0.2744	-0.0118	0.0092	-0.1737	-0.0842	-0.2973	62.4264	32.8792	11.1514
3	1.6133	-1.2723	-0.1125	3.6743	0.1213	1.3659	0.0112	-0.0528	-0.2507	0.5903	-0.0559	-0.2339	0.0177	0.0004	0.0447	-0.1118	0.0036	-0.2054	-0.2127	0.029	-0.0771	86.8369	19.8984	43.6691
4	1.0657	0.0158	-0.219	2.7113	-0.3242	2.7686	0.286	-0.4086	-0.0364	0.3816	-0.3324	0.3253	0.0773	-0.2443	0.0463	-0.0334	-0.1404	0.1583	0.0801	-0.0803	-0.1385	48.9195	39.4423	43.4233
5	1.8481	-2.3687	0.0554	4.9332	0.8971	0.5246	0.0354	-0.1627	-0.3194	0.8639	0.0367	0.2889	0.0406	-0.0379	-0.072	0.2612	-0.0468	-0.0728	-0.1565	0.138	-0.1822	78.883	23.709	53.772
6	2.0194	-1.9847	0.4552	5.662	-2.1973	2.002	0.0812	-0.2335	-0.2492	0.2642	-0.0697	0.054	0.5632	-0.1794	-0.0115	0.3409	-0.0999	0.0606	-0.0392	0.0802	-0.2258	67.5619	29.3494	57.4116
7	1.6866	-0.1106	-0.1935	4.2531	-3.0385	4.0062	-0.0015	-0.3454	-0.2911	0.3654	-0.0794	0.2185	0.4038	-0.3519	0.0809	0.1642	-0.1798	0.1337	0.0319	0.0342	-0.1709	56.4856	35.2706	53.4941
8	4.1387	0.7534	1.9587	2.7152	0.6993	2.1736	0.1544	0.183	-0.0982	-0.111	-0.1432	-0.0186	0.1657	0.1299	-0.0111	-0.3038	-0.0103	0.081	-0.2264	-0.0863	-0.1614	74.1864	26.8111	11.229
9	5.0079	1.4544	-0.8166	2.5109	-0.4318	0.9724	0.174	0.1994	-0.2809	-0.0524	-0.046	0.2122	-0.1336	-0.3041	-0.128	-0.3283	-0.0009	-0.0255	-0.1421	-0.0857	-0.2815	52.4893	38.0557	18.1696
10	5.34	1.8128	-1.775	1.6936	0.0072	2.4158	0.2802	-0.2441	0.0058	0.3627	-0.2016	0.3553	-0.1542	-0.3334	-0.0785	-0.302	-0.0214	0.0787	-0.1349	-0.0961	-0.106	47.4	40.6339	30.2937
11	1.4289	0.3196	0.7863	2.3905	1.0338	3.2396	0.0667	-0.0035	-0.173	-0.1496	-0.0688	-0.4454	0.2745	-0.0315	0.002	-0.2976	0.04	0.0672	-0.2331	-0.0307	0.0281	84.0449	21.7091	18.3746

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	34 - 112
2	X-RAY DIFFRACTION	2	B	34 - 112
3	X-RAY DIFFRACTION	3	C	34 - 112
4	X-RAY DIFFRACTION	4	D	34 - 112
5	X-RAY DIFFRACTION	5	E	34 - 112
6	X-RAY DIFFRACTION	6	F	34 - 112
7	X-RAY DIFFRACTION	7	G	34 - 112
8	X-RAY DIFFRACTION	8	H	34 - 112
9	X-RAY DIFFRACTION	9	I	34 - 112
10	X-RAY DIFFRACTION	10	J	34 - 112
11	X-RAY DIFFRACTION	11	K	34 - 112

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi