PDB-8s7l: Crystal structure of a double mutant of VirB8-like OrfG central a...

ID or keywords:

Entry

Database: PDB / ID: 8s7l

Title

Crystal structure of a double mutant of VirB8-like OrfG central and C-terminal domains of Streptococcus thermophilus ICESt3 (Gram positive conjugative type IV secretion system).

Components

Putative transfer protein

Keywords

TRANSPORT PROTEIN / VirB8 / Gram-positive / T4SS

Function / homology

Conjugative transposon protein TcpC / TcpC, C-terminal / Conjugative transposon protein TcpC / membrane / Putative transfer protein

Function and homology information

Biological species

Streptococcus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Favier, F. / Didierjean, C. / Maffo-Woulefack, R. / Douzi, B. / Leblond-Bourget, N.

Funding support

1items

Citation

Journal: Sci Adv / Year: 2025
Title: Elucidating assembly and function of VirB8 cell wall subunits refines the DNA translocation model in Gram-positive T4SSs.
Authors: Maffo-Woulefack, R. / Ali, A.M. / Laroussi, H. / Cappele, J. / Romero-Saavedra, F. / Ramia, N. / Robert, E. / Mathiot, S. / Soler, N. / Roussel, Y. / Fronzes, R. / Huebner, J. / Didierjean, ...

History

Deposition	Mar 3, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 12, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8s7l.cif.gz	284.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8s7l.ent.gz	229.6 KB	Display	PDB format
PDBx/mmJSON format	8s7l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s7/8s7l ftp://data.pdbj.org/pub/pdb/validation_reports/s7/8s7l	HTTPS FTP

-
Related structure data

Related structure data	7pkwC C: citing same article (ref.)
Similar structure data	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: Putative transfer protein

B: Putative transfer protein

C: Putative transfer protein

92.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: cross-linking, trimer observed in the crystal structure of the wild-type, assembly confirmed by cross-linking (via cysteine residues) in vitro and in vivo.

Unit cell

Length a, b, c (Å)	152.743, 89.185, 98.424
Angle α, β, γ (deg.)	90, 112.314, 90
Int Tables number	5
Space group name H-M	C121

#1: Protein	Putative transfer protein Mass: 30948.336 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Plasmid: PLYSS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70CA4
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.35 Å³/Da / Density % sol: 63.3 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Droplet: 0.3 ul [protein (33mg/ml) in 50 mM Tris pH 8.0 + 100 mM NaCl] + 0.3 ul [reservoir] Reservoir: 50 ul [40% v/v PEG 300, 100 mM potassium phosphate citrate, pH 4.2]

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967697 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 11, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.967697 Å / Relative weight: 1
Reflection	Resolution: 2.6→91.054 Å / Num. obs: 37215 / % possible obs: 98.8 % / Redundancy: 3.1 % / B_iso Wilson estimate: 50.28 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.062 / R_pim(I) all: 0.061 / R_rim(I) all: 0.087 / Net I/σ(I): 10.6
Reflection shell	Resolution: 2.6→2.72 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.665 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4577 / CC_1/2: 0.682 / R_pim(I) all: 0.653 / R_rim(I) all: 0.933 / % possible all: 99.8

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
pointless	1.12.15	data scaling
MOLREP	11.9.02	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→91.054 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.921 / SU B: 11.501 / SU ML: 0.231 / Cross valid method: FREE R-VALUE / ESU R: 0.38 / ESU R Free: 0.278
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2563	1819	4.888 %
R_work	0.2017	35392	-
all	0.204	-	-
obs	-	37211	98.564 %

Solvent computation

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

Displacement parameters

B_iso mean: 86.279 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.736 Å²	-0 Å²	-1.259 Å²
2-	-	0.313 Å²	0 Å²
3-	-	-	2.585 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→91.054 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5912	0	0	0	5912

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	6054
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	5497
X-RAY DIFFRACTION	r_ext_dist_refined_b	0.001	0.01	13924
X-RAY DIFFRACTION	r_angle_refined_deg	2.562	1.838	8208
X-RAY DIFFRACTION	r_angle_other_deg	0.816	1.774	12692
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.758	5	714
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	16.183	5	9
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.808	10	1036
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.479	10	321
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	893
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	6981
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1425
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	998
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.209	0.2	4748
X-RAY DIFFRACTION	r_nbtor_refined	0.197	0.2	2866
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.095	0.2	3444
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	108
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.1	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.203	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.206	0.2	89
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.276	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	10.727	8.299	2871
X-RAY DIFFRACTION	r_mcbond_other	10.725	8.301	2872
X-RAY DIFFRACTION	r_mcangle_it	12.904	14.922	3580
X-RAY DIFFRACTION	r_mcangle_other	12.904	14.923	3581
X-RAY DIFFRACTION	r_scbond_it	12.387	8.921	3183
X-RAY DIFFRACTION	r_scbond_other	12.385	8.921	3184
X-RAY DIFFRACTION	r_scangle_it	15.375	16.025	4628
X-RAY DIFFRACTION	r_scangle_other	15.374	16.025	4629
X-RAY DIFFRACTION	r_lrange_it	15.484	122.032	16651
X-RAY DIFFRACTION	r_lrange_other	15.484	122.032	16652

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
2.6-2.668	0.371	148	0.343	2617	0.345	2769	0.91	0.925	99.8555	0.333
2.668-2.741	0.373	122	0.314	2565	0.317	2695	0.909	0.937	99.7032	0.299
2.741-2.82	0.349	143	0.292	2485	0.295	2636	0.93	0.949	99.6965	0.27
2.82-2.907	0.3	116	0.264	2422	0.266	2544	0.941	0.959	99.7642	0.246
2.907-3.002	0.34	123	0.266	2358	0.27	2492	0.919	0.958	99.5586	0.247
3.002-3.107	0.304	110	0.253	2262	0.256	2380	0.946	0.962	99.6639	0.234
3.107-3.224	0.326	113	0.251	2190	0.254	2311	0.939	0.963	99.6538	0.234
3.224-3.356	0.316	108	0.232	2091	0.235	2237	0.939	0.97	98.3013	0.217
3.356-3.505	0.277	101	0.218	2017	0.22	2163	0.946	0.974	97.9196	0.207
3.505-3.676	0.243	111	0.211	1866	0.212	2045	0.961	0.977	96.6748	0.202
3.676-3.874	0.24	93	0.188	1752	0.19	1942	0.962	0.979	95.0051	0.179
3.874-4.109	0.254	79	0.174	1650	0.177	1842	0.964	0.983	93.8654	0.171
4.109-4.392	0.23	79	0.157	1647	0.16	1741	0.97	0.985	99.1384	0.153
4.392-4.743	0.206	86	0.145	1528	0.148	1624	0.976	0.988	99.3842	0.146
4.743-5.194	0.172	78	0.143	1403	0.144	1500	0.979	0.989	98.7333	0.144
5.194-5.804	0.174	51	0.15	1276	0.151	1346	0.981	0.987	98.5884	0.15
5.804-6.698	0.253	56	0.169	1129	0.173	1199	0.964	0.984	98.8324	0.169
6.698-8.192	0.283	46	0.189	961	0.192	1025	0.956	0.978	98.2439	0.191
8.192-11.539	0.209	29	0.175	742	0.176	792	0.973	0.983	97.3485	0.181
11.539-91.054	0.26	27	0.319	430	0.315	469	0.931	0.91	97.4414	0.518

-
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