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- PDB-9y9w: Vibrio cholerae protein FrhA peptid-binding domain and adjacent s... -

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Basic information

Entry
Database: PDB / ID: 9y9w
TitleVibrio cholerae protein FrhA peptid-binding domain and adjacent split domain (S1127-F1439) in complex with peptide AGWTD X-ray crystallography structure
Components
  • Ala-Gly-Trp-Thr-Asp (AGWTD)
  • Cadherin domain protein
KeywordsMETAL BINDING PROTEIN / Calcium / Adhesin / RTX / peptide-binding domain / split domain / Inhibitor
Function / homology
Function and homology information


cell communication / homophilic cell-cell adhesion / calcium ion binding / plasma membrane
Similarity search - Function
RapA2, cadherin-like domain / Bacterial cadherin-like domain / Type I secretion C-terminal target domain, VC_A0849 subclass / Bacterial Ig domain / : / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / CalX-like domain superfamily / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. ...RapA2, cadherin-like domain / Bacterial cadherin-like domain / Type I secretion C-terminal target domain, VC_A0849 subclass / Bacterial Ig domain / : / Na-Ca exchanger/integrin-beta4 / Calx-beta 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 / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Cadherin domain protein
Similarity search - Component
Biological speciesVibrio cholerae O395 (bacteria)
Vibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, M. / Guo, S. / Kinrade, B. / Davies, P.
Funding support Canada, 4items
OrganizationGrant numberCountry
Fonds de Recherche du Quebec - Sante (FRQS)359456 Canada
Fonds de Recherche du Quebec - Sante (FRQS)376506 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2024-04631 Canada
Canadian Institutes of Health Research (CIHR)FRN 148422 Canada
Citation
Journal: Febs Lett. / Year: 2025
Title: Peptide-based ligand antagonists block a Vibrio cholerae adhesin.
Authors: Wang, M. / Du, G. / Yongo-Luwawa, C. / Lu, A. / Kinrade, B. / Munro, K. / Klose, K.E. / Lubell, W.D. / Davies, P. / Guo, S.
#1: Journal: bioRxiv / Year: 2025
Title: Peptide-based ligand antagonists block a Vibrio cholerae adhesin
Authors: Wang, M. / Du, G. / Charity, Y. / Yongo-Luwawa, C. / Kinrade, B. / Munro, K.A. / Klose, K.E. / Lubell, W.D. / Davies, P.L. / Guo, S.
History
DepositionSep 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cadherin domain protein
B: Cadherin domain protein
E: Cadherin domain protein
G: Cadherin domain protein
I: Cadherin domain protein
K: Cadherin domain protein
M: Ala-Gly-Trp-Thr-Asp (AGWTD)
N: Ala-Gly-Trp-Thr-Asp (AGWTD)
O: Ala-Gly-Trp-Thr-Asp (AGWTD)
P: Ala-Gly-Trp-Thr-Asp (AGWTD)
Q: Ala-Gly-Trp-Thr-Asp (AGWTD)
R: Ala-Gly-Trp-Thr-Asp (AGWTD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,50355
Polymers231,53812
Non-polymers1,96543
Water24,2841348
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, ITC verified 1:1 protein:peptide ratio.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.273, 118.726, 118.706
Angle α, β, γ (deg.)60.03, 85.62, 76.70
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

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Protein / Protein/peptide , 2 types, 12 molecules ABEGIKMNOPQR

#1: Protein
Cadherin domain protein


Mass: 38041.129 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Vibrio cholerae protein FrhA peptid-binding domain and adjacent split domain (S1127-F1439). An N-terminal His tag expressed by pET28 was cleaved.
Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Gene: VC0395_A1227 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3AMP4
#2: Protein/peptide
Ala-Gly-Trp-Thr-Asp (AGWTD)


Mass: 548.546 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: This is a synthetic peptide designed to inhibit the V. cholerae adhesin FrhA.
Source: (synth.) Vibrio cholerae (bacteria)

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Non-polymers , 4 types, 1391 molecules

#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
Formula: Ca
Details: Vibrio cholerae protein FrhA peptid-binding domain and adjacent split domain (S1127-F1439). An N-terminal His tag expressed by pET28 was cleaved.
Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Gene: VC0395_A1227 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
Details: This sequence is designed to bind to Vibrio cholerae protein FrhA
Source: (synth.) Vibrio cholerae (bacteria)
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1348 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 9
Details: 0.16 M calcium acetate, 0.08 M sodium cacodylate, and 24.4% (w/v) PEG 8000. Ethylene glycol was used as a cryoprotectant.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.984 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.2→102.74 Å / Num. obs: 182986 / % possible obs: 98.56 % / Redundancy: 7 % / Biso Wilson estimate: 25.8 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.196 / Rrim(I) all: 0.212 / Net I/σ(I): 1.41
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 1.061 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 6929 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
xia23.21.1data reduction
DIALS3.21data scaling
PHENIX1.21.2-5419phasing
Coot0.9.8.95model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→102.72 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 1567 1.44 %5218
Rwork0.227 ---
obs0.227 108730 98.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→102.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13757 0 70 1348 15175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01214331
X-RAY DIFFRACTIONf_angle_d1.27519573
X-RAY DIFFRACTIONf_dihedral_angle_d14.5294866
X-RAY DIFFRACTIONf_chiral_restr0.0652275
X-RAY DIFFRACTIONf_plane_restr0.0162601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.29971560.29719723X-RAY DIFFRACTION98
2.48-2.570.26431460.27319657X-RAY DIFFRACTION98
2.57-2.670.27791340.26659698X-RAY DIFFRACTION98
2.67-2.790.26231550.2639661X-RAY DIFFRACTION98
2.79-2.940.26091400.24749772X-RAY DIFFRACTION99
2.94-3.120.2421290.23029705X-RAY DIFFRACTION99
3.12-3.360.19671460.21549729X-RAY DIFFRACTION99
3.36-3.70.22061550.20979772X-RAY DIFFRACTION99
3.7-4.240.24041410.20859783X-RAY DIFFRACTION99
4.24-5.340.18691260.19659821X-RAY DIFFRACTION99
5.34-102.720.22581390.22959842X-RAY DIFFRACTION100

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