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- PDB-8sx0: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 8sx0
TitleBordetella filamentous hemagglutinin (FhaB) C-terminal domain
ComponentsFilamentous hemagglutinin
KeywordsTOXIN
Function / homology
Function and homology information


Filamentous haemagglutinin repeat / Haemagglutinin repeat / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / ESPR domain / Extended Signal Peptide of Type V secretion system / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
PHOSPHATE ION / Filamentous hemagglutinin
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsCuthbert, B.J. / Goulding, C.W. / Hayes, C.S. / Costello, M.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain
Authors: Cuthbert, B.J. / Goulding, C.W. / Hayes, C.S. / Costello, M.S.
History
DepositionMay 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Filamentous hemagglutinin
B: Filamentous hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0008
Polymers25,5422
Non-polymers4576
Water2,252125
1
A: Filamentous hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0014
Polymers12,7711
Non-polymers2303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Filamentous hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9984
Polymers12,7711
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.060, 46.576, 75.987
Angle α, β, γ (deg.)90.000, 91.690, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Filamentous hemagglutinin


Mass: 12771.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: fhaB_1, NCTC10911_02131 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A381A265
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.6 Å3/Da / Density % sol: 22.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M phosphate citrate pH 5, 26.5% PEG 8000, 0.2 M NaCl
Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9795, 1.0
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2022
RadiationMonochromator: Double-crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
211
Reflection

Entry-ID: 8SX0 / CC1/2: 0.999 / Rpim(I) all: 0.038 / Χ2: 0.99 / Diffraction-ID: 1

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)Rmerge(I) obsRrim(I) allNet I/σ(I)
1.65-46.581926498.86.722.570.060.07115
1.58-46.522169398.24.70.0490.06214.6
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 962 / CC1/2: 0.704 / Rpim(I) all: 0.501 / Rrim(I) all: 0.952 / Χ2: 0.98 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→39.71 Å / SU ML: 0.1898 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2043 1925 10 %
Rwork0.179 17324 -
obs0.1815 19249 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.44 Å2
Refinement stepCycle: LAST / Resolution: 1.65→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 23 125 1667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881634
X-RAY DIFFRACTIONf_angle_d1.07972215
X-RAY DIFFRACTIONf_chiral_restr0.0564247
X-RAY DIFFRACTIONf_plane_restr0.0109290
X-RAY DIFFRACTIONf_dihedral_angle_d4.9385235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.29731370.2471210X-RAY DIFFRACTION99.26
1.69-1.740.2811370.22741231X-RAY DIFFRACTION98.35
1.74-1.790.25911440.23621246X-RAY DIFFRACTION98.93
1.79-1.850.28231350.22681201X-RAY DIFFRACTION98.09
1.85-1.910.23861330.21661236X-RAY DIFFRACTION97.02
1.91-1.990.21981340.18171210X-RAY DIFFRACTION98.46
1.99-2.080.21091330.18861260X-RAY DIFFRACTION98.79
2.08-2.190.23821410.17851222X-RAY DIFFRACTION99.27
2.19-2.330.21211410.16891237X-RAY DIFFRACTION98.57
2.33-2.510.18251340.17571226X-RAY DIFFRACTION98.55
2.51-2.760.20251380.16931245X-RAY DIFFRACTION99.5
2.76-3.160.21281410.18011245X-RAY DIFFRACTION99.21
3.16-3.980.16011410.15851271X-RAY DIFFRACTION98.74
3.98-39.710.19561360.17411284X-RAY DIFFRACTION98.82

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