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- PDB-9q5u: Crystal structure of Aeromonas salmonicida putative carbohydrate ... -

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Basic information

Entry
Database: PDB / ID: 9q5u
TitleCrystal structure of Aeromonas salmonicida putative carbohydrate binding module and split domain
ComponentsRTX protein
KeywordsCELL ADHESION / Adhesins / Aquaculture / Aeromonads / Biofilms / Glycan-binding / Calcium-containing
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
Type I secretion C-terminal target domain, VC_A0849 subclass / 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 ...Type I secretion C-terminal target domain, VC_A0849 subclass / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesAeromonas salmonicida subsp. salmonicida A449 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDykstra-MacPherson, T. / Ye, Q. / Davies, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-03845 Canada
CitationJournal: To Be Published
Title: Crystal structure of Aeromonas salmonicida putative carbohydrate binding module and split domain
Authors: Dykstra-MacPherson, T. / Ye, Q. / Davies, P.L.
History
DepositionAug 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RTX protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5186
Polymers34,3181
Non-polymers2005
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-44 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.279, 81.231, 56.133
Angle α, β, γ (deg.)90.000, 99.025, 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 RTX protein


Mass: 34317.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal His Tag. Crystallized in the presence of CaCl2.
Source: (gene. exp.) Aeromonas salmonicida subsp. salmonicida A449 (bacteria)
Strain: strain A449 / Gene: asx, ASA_0826 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4SJA3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.05 Å3/Da / Density % sol: 40.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 20% w/v PEG 6000, 0.2M Calcium chloride, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 2.2909 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 18, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.2909 Å / Relative weight: 1
ReflectionResolution: 2.5→45.791 Å / Num. obs: 9640 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 11.347 Å2 / CC1/2: 0.993 / R split: 0.079 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.072 / Rrim(I) all: 0.134 / Rsym value: 0.129 / Χ2: 1 / Net I/av σ(I): 3.29 / Net I/σ(I): 13.9
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1086 / CC1/2: 0.912 / R split: 0.285 / Rpim(I) all: 0.284 / Rrim(I) all: 0.521 / Rsym value: 0.473 / Χ2: 0.93 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.79 Å / SU ML: 0.4576 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.9177
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3156 491 5.12 %
Rwork0.2196 9094 -
obs0.2248 9585 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 5 53 2364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772347
X-RAY DIFFRACTIONf_angle_d1.08223181
X-RAY DIFFRACTIONf_chiral_restr0.0586359
X-RAY DIFFRACTIONf_plane_restr0.0072423
X-RAY DIFFRACTIONf_dihedral_angle_d16.4855823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.750.41761170.27172267X-RAY DIFFRACTION99.62
2.75-3.150.33781150.25552297X-RAY DIFFRACTION99.96
3.15-3.970.29351520.20532236X-RAY DIFFRACTION99.62
3.97-45.790.28251070.1882294X-RAY DIFFRACTION98.56

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