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- PDB-7o23: C-terminal head domain of the trimeric autotransporter adhesin Bp... -

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Basic information

Entry
Database: PDB / ID: 7o23
TitleC-terminal head domain of the trimeric autotransporter adhesin BpaC from Burkholderia pseudomallei fused to a GCN4 anchor
ComponentsAutotransporter adhesin BpaC,Autotransporter adhesin BpaC,General control transcription factor GCN4
KeywordsCELL ADHESION / left-handed parallel beta-roll / extracellular
Function / homology
Function and homology information


cell outer membrane / protein transport / cell adhesion / cell surface
Similarity search - Function
: / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / ESPR domain / Extended Signal Peptide of Type V secretion system / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Serralysin-like metalloprotease, C-terminal / Pilin-like
Similarity search - Domain/homology
Autotransporter adhesin BpaC
Similarity search - Component
Biological speciesBurkholderia pseudomallei 1026b (bacteria)
Saccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKiessling, A.R. / Goldman, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765042 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M023281/1 United Kingdom
CitationJournal: Mol.Microbiol. / Year: 2022
Title: The C-terminal head domain of Burkholderia pseudomallei BpaC has a striking hydrophilic core with an extensive solvent network.
Authors: Kiessling, A.R. / Harris, S.A. / Weimer, K.M. / Wells, G. / Goldman, A.
History
DepositionMar 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autotransporter adhesin BpaC,Autotransporter adhesin BpaC,General control transcription factor GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5014
Polymers31,2941
Non-polymers2073
Water5,008278
1
A: Autotransporter adhesin BpaC,Autotransporter adhesin BpaC,General control transcription factor GCN4
hetero molecules

A: Autotransporter adhesin BpaC,Autotransporter adhesin BpaC,General control transcription factor GCN4
hetero molecules

A: Autotransporter adhesin BpaC,Autotransporter adhesin BpaC,General control transcription factor GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,50312
Polymers93,8823
Non-polymers6229
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area20570 Å2
ΔGint-126 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.390, 57.390, 516.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-647-

HOH

21A-688-

HOH

31A-695-

HOH

41A-706-

HOH

51A-708-

HOH

61A-733-

HOH

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Components

#1: Protein Autotransporter adhesin BpaC,Autotransporter adhesin BpaC,General control transcription factor GCN4 / Type 5 secretion system autotransporter BpaC


Mass: 31293.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1026b (bacteria), (gene. exp.) Saccharomyces cerevisiae S288C (yeast)
Strain: 1026b, ATCC 204508 / S288c
Gene: bpaC, BP1026B_I1575, GCN4, AAS101, AAS3, ARG9, YEL009C
Plasmid: pET28a
Details (production host): KanR, T7 promoter, C-terminal His6 tag
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3HIJ5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 53 % / Description: Large hexagonal crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein solution at 130 mg/mL in 20 mM Tris-HCl pH 8, 150 mM NaCl. Hit in JCSG IV, E10: 100 nL protein solution + 100 nL reservoir solution 0.1 M HEPES pH 6.5, 0.8 M (NH4)2SO4 Cryoprotection: ...Details: Protein solution at 130 mg/mL in 20 mM Tris-HCl pH 8, 150 mM NaCl. Hit in JCSG IV, E10: 100 nL protein solution + 100 nL reservoir solution 0.1 M HEPES pH 6.5, 0.8 M (NH4)2SO4 Cryoprotection: add 400 nL of 0.15 M HEPES pH 6.5, 1.2 M (NH4)2SO4, 35% Glycerol
Temp details: Controlled

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.4→44.79 Å / Num. obs: 65740 / % possible obs: 99.53 % / Observed criterion σ(F): 6 / Redundancy: 8 % / Biso Wilson estimate: 12.07 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.168 / Net I/σ(I): 6.87
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.061 / Mean I/σ(I) obs: 1.39 / Num. unique obs: 6377 / CC1/2: 0.657 / % possible all: 99.28

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDS2019-04-17data reduction
pointless1.11.21data scaling
Aimless0.7.4data scaling
PHASER2.8.3phasing
BUCCANEERmodel building
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S6L

3s6l


Resolution: 1.4→44.79 Å / SU ML: 0.1998 / Cross valid method: FREE R-VALUE / σ(F): 1.71 / Phase error: 19.2899
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2171 3239 4.93 %
Rwork0.184 62431 -
obs-65740 99.48 %
Solvent computationShrinkage radii: 0.4 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 1.4→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 13 278 2322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612121
X-RAY DIFFRACTIONf_angle_d0.81652912
X-RAY DIFFRACTIONf_chiral_restr0.079363
X-RAY DIFFRACTIONf_plane_restr0.0043411
X-RAY DIFFRACTIONf_dihedral_angle_d5.6287363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.33251470.2852497X-RAY DIFFRACTION95.11
1.42-1.440.24931380.25782687X-RAY DIFFRACTION99.54
1.44-1.470.27151330.23852676X-RAY DIFFRACTION99.26
1.47-1.490.26781520.22772630X-RAY DIFFRACTION99.71
1.49-1.520.22331330.20532717X-RAY DIFFRACTION99.41
1.52-1.550.24061420.19572675X-RAY DIFFRACTION99.54
1.55-1.580.24321230.19332678X-RAY DIFFRACTION99.22
1.58-1.610.22271280.19792698X-RAY DIFFRACTION99.93
1.61-1.650.25781370.1922728X-RAY DIFFRACTION100
1.65-1.690.19851300.17662718X-RAY DIFFRACTION100
1.69-1.740.22211340.16732722X-RAY DIFFRACTION99.96
1.74-1.790.21871240.16032718X-RAY DIFFRACTION100
1.79-1.850.18361560.15042693X-RAY DIFFRACTION100
1.85-1.910.17791430.14482736X-RAY DIFFRACTION100
1.91-1.990.15831320.14292717X-RAY DIFFRACTION100
1.99-2.080.17921580.14522693X-RAY DIFFRACTION100
2.08-2.190.19251420.15292736X-RAY DIFFRACTION100
2.19-2.330.20311430.15692730X-RAY DIFFRACTION99.9
2.33-2.510.22141420.172768X-RAY DIFFRACTION99.76
2.51-2.760.18861250.17032790X-RAY DIFFRACTION99.93
2.76-3.160.20691610.18952755X-RAY DIFFRACTION99.62
3.16-3.980.24251460.19982776X-RAY DIFFRACTION98.45
3.98-44.790.30311670.29742893X-RAY DIFFRACTION96.5

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