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- PDB-7pkw: Crystal structure of VIRB8-like OrfG central and C-terminal domai... -

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Basic information

Entry
Database: PDB / ID: 7pkw
TitleCrystal structure of VIRB8-like OrfG central and C-terminal domains of Streptococcus thermophilus ICESt3 (Gram positive conjugative type IV secretion system).
ComponentsPutative transfer protein
KeywordsTRANSPORT PROTEIN / VirB8-like protein / Type IV secretion system / T4SS
Function / homologyNuclear Transport Factor 2; Chain: A, - #540 / Conjugative transposon protein TcpC / TcpC, C-terminal / Conjugative transposon protein TcpC / Nuclear Transport Factor 2; Chain: A, / Roll / membrane / Alpha Beta / Putative transfer protein
Function and homology information
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.835 Å
AuthorsFavier, F. / Didierjean, C. / Cappele, J. / Douzi, B. / Leblond-Bourget, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
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, ...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, C. / Favier, F. / Leblond-Bourget, N. / Douzi, B.
#1: 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
Authors: Cappele, J. / Mohamad Ali, A. / Leblond-Bourget, N. / Mathiot, S. / Dhalleine, T. / Payot, S. / Savko, M. / Didierjean, C. / Favier, F. / Douzi, B.
History
DepositionAug 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 12, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1644
Polymers30,8841
Non-polymers2803
Water3,855214
1
A: Putative transfer protein
hetero molecules

A: Putative transfer protein
hetero molecules

A: Putative transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,49312
Polymers92,6533
Non-polymers8419
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z+1/2,-x+3/2,-y+11
crystal symmetry operation12_664-y+3/2,-z+1,x-1/21
Buried area13870 Å2
ΔGint-77 kcal/mol
Surface area36900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.920, 124.920, 124.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4
Components on special symmetry positions
IDModelComponents
11A-714-

HOH

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Components

#1: Protein Putative transfer protein


Mass: 30884.207 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulfate, 1.26 M; cacodylate buffer pH 6.5, 100 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.835→50 Å / Num. obs: 29698 / % possible obs: 99.8 % / Redundancy: 77.4 % / CC1/2: 1 / Rrim(I) all: 0.093 / Net I/σ(I): 48.17
Reflection shellResolution: 1.835→1.95 Å / Redundancy: 77 % / Mean I/σ(I) obs: 4.62 / Num. unique obs: 4676 / CC1/2: 0.9448 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
XDS20190315data reduction
Aimless0.7.4data scaling
MOLREP7.0.078phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6zgn, 3ub1

6zgn

3ub1


Resolution: 1.835→44.17 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.21469 1485 5 %random
Rwork0.18322 ---
obs0.18477 28213 99.89 %-
Displacement parametersBiso mean: 31.54 Å2
Refinement stepCycle: LAST / Resolution: 1.835→44.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 17 214 2198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01562177
X-RAY DIFFRACTIONf_angle_d1.71232962
X-RAY DIFFRACTIONf_chiral_restr0.0942313
X-RAY DIFFRACTIONf_plane_restr0.011388
X-RAY DIFFRACTIONf_dihedral_angle_d16.2748801
LS refinement shellResolution: 1.835→1.883 Å
RfactorNum. reflection% reflection
Rfree0.337 105 5 %
Rwork0.339 2020 -
obs--98.61 %

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