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- PDB-6utu: Crystal structure of minor pseudopilin ternary complex of XcpVWX ... -

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Basic information

Entry
Database: PDB / ID: 6utu
TitleCrystal structure of minor pseudopilin ternary complex of XcpVWX from the Type 2 secretion system of Pseudomonas aeruginosa in the P3 space group
Components
  • Type II secretion system protein IType II secretion system
  • Type II secretion system protein JType II secretion system
  • Type II secretion system protein KType II secretion system
KeywordsPROTEIN TRANSPORT / pseudopilus / minor pseduopilin
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
General secretion pathway protein K / GspK, central domain superfamily / Type II secretion system (T2SS), protein K / 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 / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif ...General secretion pathway protein K / GspK, central domain superfamily / Type II secretion system (T2SS), protein K / 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 / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Type II secretion system protein I / Type II secretion system protein J / Type II secretion system protein K
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsZhang, Y. / Wang, S. / Jia, Z.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)38855 Canada
CitationJournal: Int J Mol Sci / Year: 2020
Title: In Situ Proteolysis Condition-Induced Crystallization of the XcpVWX Complex in Different Lattices.
Authors: Zhang, Y. / Wang, S. / Jia, Z.
History
DepositionOct 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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
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 I
B: Type II secretion system protein J
C: Type II secretion system protein K
D: Type II secretion system protein I
E: Type II secretion system protein J
F: Type II secretion system protein K
G: Type II secretion system protein I
H: Type II secretion system protein J
I: Type II secretion system protein K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,54618
Polymers190,1859
Non-polymers3619
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16860 Å2
ΔGint-93 kcal/mol
Surface area62490 Å2
Unit cell
Length a, b, c (Å)158.100, 158.100, 64.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Space group name HallP3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z

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Components

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


Mass: 10534.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: xcpV, pddC, PA3099 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00516
#2: Protein Type II secretion system protein J / Type II secretion system / T2SS protein J / General secretion pathway protein J / PilD-dependent protein PddD


Mass: 22247.691 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: xcpW, pddD, PA3098 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00517
#3: Protein Type II secretion system protein K / Type II secretion system / T2SS protein K / General secretion pathway protein K


Mass: 30612.576 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: xcpX, PA3097 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00518
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 19 %-22 % PEG 2000 MME, 0.1 M Tris, pH 8.0-9.0, 0.2 M trimethylamine N-oxide (TMAO)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.83→19.91 Å / Num. obs: 42465 / % possible obs: 99.2 % / Redundancy: 10 % / Biso Wilson estimate: 79.02 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.77
Reflection shellResolution: 2.83→3 Å / Num. unique obs: 6545 / CC1/2: 0.646

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
PHENIXmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VTM

5vtm


Resolution: 2.85→19.91 Å / SU ML: 0.4998 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 31.2807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2941 2108 5 %
Rwork0.2143 40044 -
obs0.2183 42152 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.29 Å2
Refinement stepCycle: LAST / Resolution: 2.85→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10549 0 9 2 10560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910731
X-RAY DIFFRACTIONf_angle_d1.102114598
X-RAY DIFFRACTIONf_chiral_restr0.0541656
X-RAY DIFFRACTIONf_plane_restr0.00611921
X-RAY DIFFRACTIONf_dihedral_angle_d18.47581530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.920.37941410.28432687X-RAY DIFFRACTION100
2.92-2.990.39521410.27212668X-RAY DIFFRACTION100
2.99-3.070.34011390.2592653X-RAY DIFFRACTION100
3.07-3.160.36631430.25262701X-RAY DIFFRACTION100
3.16-3.260.32361400.25122670X-RAY DIFFRACTION100
3.26-3.380.35231390.24652645X-RAY DIFFRACTION100
3.38-3.510.33671400.21842648X-RAY DIFFRACTION100
3.51-3.670.28721400.21832663X-RAY DIFFRACTION100
3.67-3.860.30541410.21862683X-RAY DIFFRACTION100
3.86-4.10.31551410.21492673X-RAY DIFFRACTION100
4.1-4.420.28171390.19872654X-RAY DIFFRACTION100
4.42-4.850.26381420.1922689X-RAY DIFFRACTION100
4.85-5.540.26221400.20982656X-RAY DIFFRACTION100
5.54-6.930.28281400.22132674X-RAY DIFFRACTION100
6.94-19.910.26041420.18872680X-RAY DIFFRACTION99.96

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