PDB-6zgn: Crystal structure of VirB8-like OrfG central domain of Streptococ...

ID or keywords:

Entry

Database: PDB / ID: 6zgn

Title

Crystal structure of VirB8-like OrfG central domain of Streptococcus thermophilus ICESt3; a putative assembly factor of a gram positive conjugative Type IV secretion system.

Components

Putative transfer protein

Keywords

TRANSPORT PROTEIN / NTF2-like / VIRB8-like /

type IV secretion system /

gram positive

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 /

SAD / Resolution: 1.75 Å

Authors

Cappele, J. / Mohamad-Ali, A. / Leblond-Bourget, N. / Payot-Lacroix, S. / Mathiot, S. / Didierjean, C. / Favier, F. / Douzi, B.

Citation

Journal: Front Mol Biosci / Year: 2021
Title: Structural and Biochemical Analysis of OrfG: The VirB8-like Component of the Conjugative Type IV Secretion System of ICE St3 From Streptococcus thermophilus .
Authors: Cappele, J. / Mohamad Ali, A. / Leblond-Bourget, N. / Mathiot, S. / Dhalleine, T. / Payot, S. / Savko, M. / Didierjean, C. / Favier, F. / Douzi, B.

History

Deposition	Jun 19, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 28, 2021	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6zgn.cif.gz	52.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6zgn.ent.gz	39.4 KB	Display	PDB format
PDBx/mmJSON format	6zgn.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/zg/6zgn ftp://data.pdbj.org/pub/pdb/validation_reports/zg/6zgn	HTTPS FTP

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Related structure data

Similar structure data	2wqj-5 5dkd-2 6mwy-3 1fsl-2 5dkd-1 1hqz-9 2knd-d 2jjz-2 5wrd-1 6zs4-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
Related items in Molecule of the Month	#211 - Jul 2017 Pilus Machine similarity (1)

Deposited unit

A: Putative transfer protein

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, ~97% Monomeric form; ~3% Hexameric form

Unit cell

Length a, b, c (Å)	50.162, 50.162, 120.883
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-302- HOH
2	1	A-376- HOH
3	1	A-381- HOH

#1: Protein	Putative transfer protein Mass: 16337.188 Da / Num. of mol.: 1 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
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.2 Å³/Da / Density % sol: 61.62 % / Description: Bipyramid
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Ammonium sulfate; 2M Tris pH 8.5; 100 mM / PH range: 8 - 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.75→46.331 Å / Num. obs: 16372 / % possible obs: 100 % / Redundancy: 25.1 % / B_iso Wilson estimate: 29.93 Å² / CC_1/2: 1 / R_merge(I) obs: 0.027 / R_pim(I) all: 0.006 / R_rim(I) all: 0.028 / Χ²: 0.97 / Net I/σ(I): 67.5
Reflection shell	Resolution: 1.75→1.78 Å / Redundancy: 23.8 % / R_merge(I) obs: 0.499 / Num. unique obs: 869 / CC_1/2: 0.975 / R_pim(I) all: 0.105 / R_rim(I) all: 0.511 / Χ²: 1.08 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1-3660	refinement
XDS	20190315	data reduction
Aimless	0.7.4	data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.75→46.331 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.945 / Cross valid method: FREE R-VALUE / ESU R: 0.1 / ESU R Free: 0.091
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2081	835	5.12 %	Random
R_work	0.1996	15474	-	-
all	0.2	-	-	-
obs	-	16309	99.951 %	-

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: 35.347 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.701 Å²	-0 Å²	-0 Å²
2-	-	0.701 Å²	0 Å²
3-	-	-	-1.402 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→46.331 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	842	0	0	81	923

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	870
X-RAY DIFFRACTION	r_bond_other_d	0.021	0.017	824
X-RAY DIFFRACTION	r_angle_refined_deg	1.635	1.657	1180
X-RAY DIFFRACTION	r_angle_other_deg	1.784	1.596	1875
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.107	5	100
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.206	25	46
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.399	15	146
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	40.476	15	1
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	104
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	980
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	204
X-RAY DIFFRACTION	r_nbd_refined	0.226	0.2	144
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	712
X-RAY DIFFRACTION	r_nbtor_refined	0.204	0.2	420
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.1	0.2	512
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.191	0.2	56
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.176	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.387	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.175	0.2	30
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.2	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	3.555	3.001	403
X-RAY DIFFRACTION	r_mcbond_other	3.596	2.996	402
X-RAY DIFFRACTION	r_mcangle_it	4.522	4.446	499
X-RAY DIFFRACTION	r_mcangle_other	4.545	4.455	500
X-RAY DIFFRACTION	r_scbond_it	5.281	3.386	467
X-RAY DIFFRACTION	r_scbond_other	5.303	3.387	467
X-RAY DIFFRACTION	r_scangle_it	7.368	4.884	680
X-RAY DIFFRACTION	r_scangle_other	7.368	4.885	680
X-RAY DIFFRACTION	r_lrange_it	8.635	34.049	981
X-RAY DIFFRACTION	r_lrange_other	8.636	33.543	964

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
1.75-1.795	0.427	59	0.294	1116	0.3	1175	0.846	0.878	100	0.254
1.795-1.845	0.262	61	0.241	1086	0.242	1147	0.937	0.924	100	0.211
1.845-1.898	0.169	38	0.22	1073	0.218	1111	0.947	0.939	100	0.189
1.898-1.956	0.232	70	0.195	1001	0.198	1071	0.942	0.946	100	0.169
1.956-2.02	0.236	61	0.187	1000	0.19	1061	0.95	0.954	100	0.161
2.02-2.091	0.173	49	0.182	996	0.181	1045	0.961	0.96	100	0.163
2.091-2.17	0.195	43	0.173	919	0.174	962	0.956	0.959	100	0.16
2.17-2.258	0.217	55	0.188	903	0.189	958	0.947	0.954	100	0.177
2.258-2.358	0.224	44	0.194	877	0.196	921	0.943	0.952	100	0.183
2.358-2.473	0.186	48	0.177	822	0.177	870	0.956	0.957	100	0.169
2.473-2.606	0.237	46	0.196	800	0.198	846	0.946	0.95	100	0.19
2.606-2.764	0.201	37	0.208	758	0.207	795	0.958	0.954	100	0.206
2.764-2.954	0.154	34	0.211	738	0.208	772	0.968	0.953	100	0.211
2.954-3.19	0.25	43	0.197	651	0.2	694	0.936	0.949	100	0.2
3.19-3.493	0.178	19	0.195	637	0.195	656	0.954	0.956	100	0.208
3.493-3.902	0.175	40	0.183	568	0.183	608	0.966	0.964	100	0.2
3.902-4.5	0.184	24	0.161	517	0.161	542	0.947	0.972	99.8155	0.185
4.5-5.499	0.167	26	0.185	437	0.184	464	0.971	0.97	99.7845	0.217
5.499-7.722	0.254	26	0.285	351	0.283	377	0.956	0.947	100	0.323
7.722-46.331	0.288	12	0.28	224	0.28	241	0.944	0.942	97.9253	0.368

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