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- PDB-5bw0: The crystal structure of minor pseudopilin binary complex of XcpV... -

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Basic information

Entry
Database: PDB / ID: 5bw0
TitleThe crystal structure of minor pseudopilin binary complex of XcpV and XcpW from the Type 2 secretion system of Pseudomonas aeruginosa
Components
  • Type II secretion system protein IType II secretion system
  • Type II secretion system protein JType II secretion system
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / plasma membrane
Similarity search - Function
Type II secretion system protein GspI, C-terminal / Type II secretion system protein GspI / Type II secretion system (T2SS), protein I / Type II secretion system protein GspJ / Type II secretion system (T2SS), protein J / GSPII I/J protein-like / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site ...Type II secretion system protein GspI, C-terminal / Type II secretion system protein GspI / Type II secretion system (T2SS), protein I / Type II secretion system protein GspJ / Type II secretion system (T2SS), protein J / GSPII I/J protein-like / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II secretion system protein I / Type II secretion system protein J
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, Y. / Faucher, F. / Poole, K. / Jia, Z.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Citation
Journal: PLoS Pathog. / Year: 2018
Title: Structure-guided disruption of the pseudopilus tip complex inhibits the Type II secretion in Pseudomonas aeruginosa.
Authors: Zhang, Y. / Faucher, F. / Zhang, W. / Wang, S. / Neville, N. / Poole, K. / Zheng, J. / Jia, Z.
#1: Journal: To Be Published
Title: Inhibition of Pseudomonas aeruginosa Type II secretion by structure-based peptides
Authors: Zhang, Y. / Faucher, F. / Poole, K. / Jia, Z.
History
DepositionJun 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list ...pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type II secretion system protein J
B: Type II secretion system protein I
C: Type II secretion system protein J
D: Type II secretion system protein I
E: Type II secretion system protein J
F: Type II secretion system protein I
G: Type II secretion system protein J
H: Type II secretion system protein I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,89412
Polymers126,5108
Non-polymers3844
Water9,404522
1
A: Type II secretion system protein J
B: Type II secretion system protein I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9165
Polymers31,6272
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-34 kcal/mol
Surface area13440 Å2
MethodPISA
2
C: Type II secretion system protein J
D: Type II secretion system protein I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7243
Polymers31,6272
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-8 kcal/mol
Surface area14440 Å2
MethodPISA
3
E: Type II secretion system protein J
F: Type II secretion system protein I


Theoretical massNumber of molelcules
Total (without water)31,6272
Polymers31,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-9 kcal/mol
Surface area13870 Å2
MethodPISA
4
G: Type II secretion system protein J
H: Type II secretion system protein I


Theoretical massNumber of molelcules
Total (without water)31,6272
Polymers31,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-16 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.110, 200.950, 66.450
Angle α, β, γ (deg.)90.00, 95.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Type II secretion system protein J / Type II secretion system / T2SS protein J / General secretion pathway protein J / PilD-dependent protein PddD


Mass: 20891.469 Da / Num. of mol.: 4 / Fragment: residues 28-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: xcpW, pddD, PA3098 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00517
#2: Protein
Type II secretion system protein I / Type II secretion system / T2SS protein I / General secretion pathway protein I / PilD-dependent protein PddC


Mass: 10736.025 Da / Num. of mol.: 4 / Fragment: residues 33-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: xcpV, pddC, PA3099 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00516
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10-15% PEG 3350, 0.1M Tris, pH 7.0, 0.5M caesium chloride . Protein solution: 25mM HEPES, pH 7.0, 150mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2→19.7 Å / Num. obs: 68807 / % possible obs: 97.9 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.73

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RET

2ret


Resolution: 2→19.7 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 3440 5 %
Rwork0.2062 --
obs0.2089 68807 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8020 0 20 522 8562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088172
X-RAY DIFFRACTIONf_angle_d1.09811015
X-RAY DIFFRACTIONf_dihedral_angle_d15.5423111
X-RAY DIFFRACTIONf_chiral_restr0.0431164
X-RAY DIFFRACTIONf_plane_restr0.0041447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02740.2421380.20792644X-RAY DIFFRACTION100
2.0274-2.05630.27631390.21492638X-RAY DIFFRACTION100
2.0563-2.0870.29221410.22582670X-RAY DIFFRACTION100
2.087-2.11960.2721420.22252705X-RAY DIFFRACTION100
2.1196-2.15430.27721360.222609X-RAY DIFFRACTION100
2.1543-2.19140.27421400.22872675X-RAY DIFFRACTION100
2.1914-2.23120.33841140.28882147X-RAY DIFFRACTION79
2.2312-2.2740.571140.45642160X-RAY DIFFRACTION83
2.274-2.32040.37611270.29582407X-RAY DIFFRACTION90
2.3204-2.37070.30911430.22152711X-RAY DIFFRACTION100
2.3707-2.42580.26151360.21562606X-RAY DIFFRACTION100
2.4258-2.48630.26581430.21952701X-RAY DIFFRACTION100
2.4863-2.55340.26041390.21282657X-RAY DIFFRACTION100
2.5534-2.62840.2651390.20662637X-RAY DIFFRACTION100
2.6284-2.7130.29281410.20562676X-RAY DIFFRACTION100
2.713-2.80970.23971410.21722669X-RAY DIFFRACTION100
2.8097-2.92190.23241410.21292669X-RAY DIFFRACTION100
2.9219-3.05440.23971400.20862673X-RAY DIFFRACTION100
3.0544-3.21480.25411410.20912671X-RAY DIFFRACTION100
3.2148-3.41530.25471400.19412667X-RAY DIFFRACTION100
3.4153-3.67740.21991430.19032701X-RAY DIFFRACTION100
3.6774-4.04460.23551390.17292646X-RAY DIFFRACTION100
4.0446-4.62330.22311400.1612666X-RAY DIFFRACTION100
4.6233-5.80020.22581420.17312694X-RAY DIFFRACTION100
5.8002-19.73870.24361410.20482668X-RAY DIFFRACTION99

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