PDB-8qgr: Stopper protein of phage 812 in closed conformation

ID or keywords:

Entry

Database: PDB / ID: 8qgr

Title

Stopper protein of phage 812 in closed conformation

Components

Capsid protein

Keywords

VIRUS / phage / neck / connector

Function / homology

metal ion binding / Capsid protein

Function and homology information

Biological species

Staphylococcus phage 812 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Cienikova, Z. / Popelarova, B. / Plevka, P.

Funding support

Czech Republic, 1items

Citation

Journal: To Be Published
Title: Genome anchoring, retention, and release by neck proteins of Herelleviridae phage 812
Authors: Cienikova, Z. / Novacek, J. / Siborova, M. / Popelarova, B. / Fuzik, T. / Benesik, M. / Bardy, P. / Plevka, P.

History

Deposition	Sep 5, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 11, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8qgr.cif.gz	66.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8qgr.ent.gz	44.6 KB	Display	PDB format
PDBx/mmJSON format	8qgr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8qgr_validation.pdf.gz	423.5 KB	Display	wwPDB validaton report
Full document	8qgr_full_validation.pdf.gz	424.3 KB	Display
Data in XML	8qgr_validation.xml.gz	13 KB	Display
Data in CIF	8qgr_validation.cif.gz	17.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qg/8qgr ftp://data.pdbj.org/pub/pdb/validation_reports/qg/8qgr	HTTPS FTP

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Related structure data

Related structure data	18048C 18065C 18213C 18369C 18372C 18385C 18395C 18412C 18445C 18462C 18489C 18516C 18912C 18919C 18949C 8q01C 8q1iC 8q7dC 8qekC 8qemC 8qjeC 8qkhC 8r5gC 8r69C C: citing same article (ref.)
Similar structure data	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: Capsid protein

hetero molecules

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

1

B: Capsid protein

hetero molecules

x 6

defined by author&software
Evidence: electron microscopy, The protein is a component of phage viral particle where it assembles into a hexameric ring
203 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	93.366, 93.366, 122.531
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	177
Space group name H-M	P622

#1: Protein	Capsid protein / Stopper protein Mass: 33757.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus phage 812 (virus) / Strain: K1-420 Gene: 812_097, 812_099, 812a_099, 812F1_099, K1/420_099, K1_099 Plasmid: pET22T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1YTN7
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.95 Å³/Da / Density % sol: 58.28 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.6 M NaCl, 8% PEG 6000, 20% glycerol, 3% dextran sulphate sodium

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2017
Radiation	Monochromator: Si(111) single-crystal channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97857 Å / Relative weight: 1
Reflection	Resolution: 2.2→37.2 Å / Num. obs: 16664 / % possible obs: 99.9 % / Redundancy: 11.7 % / R_merge(I) obs: 0.13 / Net I/σ(I): 23.26
Reflection shell	Resolution: 2.2→2.28 Å / R_merge(I) obs: 0.689 / Mean I/σ(I) obs: 4.21 / Num. unique obs: 1627 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0411	refinement
XDS	2016-11-01	data reduction
Aimless		data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→37.159 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.939 / WR_factor R_free: 0.193 / WR_factor R_work: 0.172 / SU B: 5.096 / SU ML: 0.127 / Average fsc free: 0.9603 / Average fsc work: 0.9703 / Cross valid method: FREE R-VALUE / ESU R: 0.226 / ESU R Free: 0.18
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2192	1632	9.802 %
R_work	0.19	15017	-
all	0.193	-	-
obs	-	16649	99.844 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 31.435 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.375 Å²	-0.687 Å²	-0 Å²
2-	-	-1.375 Å²	0 Å²
3-	-	-	4.46 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→37.159 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1815	0	1	146	1962

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	1852
X-RAY DIFFRACTION	r_bond_other_d	0	0.016	1788
X-RAY DIFFRACTION	r_angle_refined_deg	1.223	1.665	2504
X-RAY DIFFRACTION	r_angle_other_deg	0.393	1.576	4127
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.954	5	218
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	3.017	5	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.68	10	347
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	2.014	10	4
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	11.971	10	92
X-RAY DIFFRACTION	r_chiral_restr	0.056	0.2	281
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2113
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	399
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	332
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.217	0.2	1729
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	922
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	948
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.199	0.2	120
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.153	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.168	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.178	0.2	82
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.142	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	2.129	3.105	881
X-RAY DIFFRACTION	r_mcbond_other	2.128	3.105	881
X-RAY DIFFRACTION	r_mcangle_it	3.431	5.535	1096
X-RAY DIFFRACTION	r_mcangle_other	3.43	5.537	1097
X-RAY DIFFRACTION	r_scbond_it	2.798	3.572	971
X-RAY DIFFRACTION	r_scbond_other	2.796	3.573	972
X-RAY DIFFRACTION	r_scangle_it	4.721	6.372	1408
X-RAY DIFFRACTION	r_scangle_other	4.719	6.372	1409
X-RAY DIFFRACTION	r_lrange_it	6.621	33.204	2091
X-RAY DIFFRACTION	r_lrange_other	6.546	32.736	2065

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.2-2.257	0.269	119	0.226	1075	0.23	1197	0.95	0.95	99.7494	0.181
2.257-2.319	0.233	127	0.203	1027	0.207	1155	0.958	0.961	99.9134	0.168
2.319-2.386	0.24	116	0.206	1034	0.209	1150	0.947	0.965	100	0.173
2.386-2.459	0.248	114	0.194	993	0.2	1107	0.956	0.968	100	0.156
2.459-2.539	0.228	97	0.2	972	0.202	1069	0.963	0.972	100	0.167
2.539-2.628	0.27	106	0.196	923	0.203	1029	0.953	0.968	100	0.163
2.628-2.726	0.283	105	0.208	906	0.215	1011	0.95	0.967	100	0.17
2.726-2.837	0.272	94	0.216	878	0.221	972	0.95	0.965	100	0.181
2.837-2.962	0.315	76	0.229	853	0.235	929	0.934	0.96	100	0.188
2.962-3.106	0.236	77	0.22	827	0.222	904	0.944	0.96	100	0.182
3.106-3.273	0.207	85	0.21	765	0.209	851	0.967	0.971	99.8825	0.187
3.273-3.469	0.209	72	0.189	739	0.191	811	0.978	0.98	100	0.176
3.469-3.707	0.238	76	0.186	698	0.191	774	0.967	0.982	100	0.181
3.707-4	0.196	79	0.179	647	0.181	726	0.973	0.981	100	0.17
4-4.377	0.203	64	0.14	615	0.146	680	0.978	0.988	99.8529	0.14
4.377-4.885	0.159	56	0.147	552	0.148	610	0.985	0.987	99.6721	0.146
4.885-5.625	0.195	61	0.173	487	0.176	551	0.98	0.985	99.4555	0.17
5.625-6.85	0.185	48	0.2	432	0.198	483	0.98	0.982	99.3789	0.194
6.85-9.527	0.153	34	0.175	359	0.173	393	0.985	0.983	100	0.177
9.527-37.159	0.188	26	0.208	235	0.206	263	0.979	0.975	99.2395	0.22

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