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- PDB-9cse: Crystal structure of Repeats-in-Toxin-like domain from Aeromonas ... -

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Basic information

Entry
Database: PDB / ID: 9cse
TitleCrystal structure of Repeats-in-Toxin-like domain from Aeromonas hydrophila
ComponentsLarge adhesion protein
KeywordsCELL ADHESION / RTX proteins / Adhesin / Gram-negative bacteria / 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: 1.95 Å
AuthorsYe, Q. / Vance, T.D.R. / 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
DepositionJul 23, 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: Large adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,13315
Polymers36,4621
Non-polymers67114
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.603, 103.327, 95.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Large adhesion protein / LAP


Mass: 36461.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: AHA_3491 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0KNW4
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.3 Å3/Da / Density % sol: 46.51 % / Description: Thin plate
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 8000, MES, Acetate calcium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.53484 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2018
RadiationMonochromator: Axilon double crystal/multi-layer monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.53484 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 24829 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 28.365 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.037 / Rrim(I) all: 0.132 / Χ2: 0.96 / Net I/σ(I): 15.9
Reflection shellResolution: 1.95→2 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.657 / Mean I/σ(I) obs: 2 / Num. unique obs: 1739 / CC1/2: 0.73 / Rpim(I) all: 0.675 / Χ2: 0.87 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→48.75 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.737 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 1197 4.8 %RANDOM
Rwork0.20322 ---
obs0.20587 23607 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.498 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0 Å2-0 Å2
2--0.88 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.95→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 29 226 2355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132145
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171925
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.6352906
X-RAY DIFFRACTIONr_angle_other_deg1.3761.5784476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9125290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91425.32692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79815321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.349155
X-RAY DIFFRACTIONr_chiral_restr0.0690.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022476
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2563.5561163
X-RAY DIFFRACTIONr_mcbond_other3.2513.5511162
X-RAY DIFFRACTIONr_mcangle_it4.675.3191451
X-RAY DIFFRACTIONr_mcangle_other4.6685.3251452
X-RAY DIFFRACTIONr_scbond_it3.7193.811982
X-RAY DIFFRACTIONr_scbond_other3.7173.813983
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.475.5871455
X-RAY DIFFRACTIONr_long_range_B_refined8.23544.4012372
X-RAY DIFFRACTIONr_long_range_B_other8.17344.0352327
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 78 -
Rwork0.287 1721 -
obs--99.94 %

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