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- PDB-9das: Crystal structure of vWFA domain from large adhesion protein of A... -

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Basic information

Entry
Database: PDB / ID: 9das
TitleCrystal structure of vWFA domain from large adhesion protein of Aeromonas hydrophila
ComponentsFlagellin hook IN motif family
KeywordsCELL ADHESION / RTX adhesin / Gram-negative bacteria / Biofilm / Putative ligand-binding domain
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
VCBS repeat / Type I secretion C-terminal target domain, VC_A0849 subclass / RapA2, cadherin-like domain / Bacterial cadherin-like domain / Bacterial Ig-like domain 13 / : / Bacterial Ig-like domain / Bacterial Ig domain / CalX-like domain superfamily / Hemolysin-type calcium-binding conserved site ...VCBS repeat / Type I secretion C-terminal target domain, VC_A0849 subclass / RapA2, cadherin-like domain / Bacterial cadherin-like domain / Bacterial Ig-like domain 13 / : / Bacterial Ig-like domain / Bacterial Ig domain / CalX-like domain superfamily / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Flagellin hook IN motif family
Similarity search - Component
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsVance, T.D.R. / Ye, Q. / Davies, P.L.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FRN 148422 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-04810 Canada
CitationJournal: Mbio / Year: 2025
Title: Aeromonas hydrophila RTX adhesin has three ligand-binding domains that give the bacterium the potential to adhere to and aggregate a wide variety of cell types.
Authors: Ye, Q. / Eves, R. / Vance, T.D.R. / Hansen, T. / Sage, A.P. / Petkovic, A. / Bradley, B. / Escobedo, C. / Graham, L.A. / Allingham, J.S. / Davies, P.L.
History
DepositionAug 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellin hook IN motif family
B: Flagellin hook IN motif family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,60215
Polymers63,0292
Non-polymers57313
Water4,720262
1
A: Flagellin hook IN motif family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7557
Polymers31,5141
Non-polymers2406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellin hook IN motif family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8478
Polymers31,5141
Non-polymers3337
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.235, 156.288, 57.496
Angle α, β, γ (deg.)90.00, 99.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-4806-

CA

21B-4996-

HOH

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Components

#1: Protein Flagellin hook IN motif family


Mass: 31514.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: AHA_3491 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0KNW4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 295 K / Method: microbatch / Details: 20% PEG3350, 0.2M CaCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2Si(111)
Radiation wavelength
IDWavelength (Å)Relative weight
11.033181
21
ReflectionResolution: 1.4→45.95 Å / Num. obs: 119428 / % possible obs: 98.6 % / Redundancy: 7.6 % / Biso Wilson estimate: 15.063 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.029 / Rrim(I) all: 0.08 / Χ2: 1.01 / Net I/σ(I): 17.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5790 / CC1/2: 0.446 / Rpim(I) all: 0.746 / Χ2: 0.99 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: 000)refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.4→45.97 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 5948 5.01 %
Rwork0.1912 --
obs0.192 118765 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4026 0 18 262 4306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064094
X-RAY DIFFRACTIONf_angle_d0.8085565
X-RAY DIFFRACTIONf_dihedral_angle_d12.1211405
X-RAY DIFFRACTIONf_chiral_restr0.077646
X-RAY DIFFRACTIONf_plane_restr0.006734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.38092140.37333599X-RAY DIFFRACTION95
1.42-1.440.36811630.35183713X-RAY DIFFRACTION96
1.44-1.450.35861960.32493735X-RAY DIFFRACTION98
1.45-1.470.33612080.3023641X-RAY DIFFRACTION97
1.47-1.490.29131920.28733735X-RAY DIFFRACTION98
1.49-1.510.28972080.26283690X-RAY DIFFRACTION97
1.51-1.530.2691890.25073699X-RAY DIFFRACTION98
1.53-1.560.25922030.23343724X-RAY DIFFRACTION97
1.56-1.580.23831960.23013721X-RAY DIFFRACTION98
1.58-1.610.25531780.22933718X-RAY DIFFRACTION97
1.61-1.630.23091780.22333801X-RAY DIFFRACTION98
1.63-1.660.2341910.22453749X-RAY DIFFRACTION98
1.66-1.70.25182070.22583740X-RAY DIFFRACTION98
1.7-1.730.24551940.21593732X-RAY DIFFRACTION99
1.73-1.770.23162120.20283729X-RAY DIFFRACTION98
1.77-1.810.23881590.19913819X-RAY DIFFRACTION98
1.81-1.850.19281960.18673765X-RAY DIFFRACTION99
1.85-1.90.20691830.18713832X-RAY DIFFRACTION99
1.9-1.960.21221930.18573759X-RAY DIFFRACTION99
1.96-2.020.20952320.19113735X-RAY DIFFRACTION99
2.02-2.10.20612070.18453818X-RAY DIFFRACTION99
2.1-2.180.22421900.19063777X-RAY DIFFRACTION99
2.18-2.280.19811940.18163820X-RAY DIFFRACTION99
2.28-2.40.18542110.18193812X-RAY DIFFRACTION99
2.4-2.550.18422020.18183793X-RAY DIFFRACTION100
2.55-2.750.20022180.18953811X-RAY DIFFRACTION100
2.75-3.020.20752240.18843818X-RAY DIFFRACTION100
3.02-3.460.20162160.17643797X-RAY DIFFRACTION100
3.46-4.360.17311970.16143841X-RAY DIFFRACTION100
4.36-4.60.16571970.16493894X-RAY DIFFRACTION100

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