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

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Basic information

Entry
Database: PDB / ID: 9ybq
TitleVibrio cholerae protein FrhA peptid-binding domain and adjacent split domain (S1127-F1439) in complex with peptide AGYTD X-ray crystallography structure
Components
  • ALA-GLY-TYR-THR-ASP
  • 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
Cadherin domain protein
Similarity search - Component
Biological speciesVibrio cholerae O395 (bacteria)
Vibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 17, 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

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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-TYR-THR-ASP
N: ALA-GLY-TYR-THR-ASP
O: ALA-GLY-TYR-THR-ASP
P: ALA-GLY-TYR-THR-ASP
Q: ALA-GLY-TYR-THR-ASP
R: ALA-GLY-TYR-THR-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,84348
Polymers231,40012
Non-polymers1,44336
Water30,8421712
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)61.394, 118.717, 118.728
Angle α, β, γ (deg.)60.05, 76.45, 81.42
Int Tables number1
Space group name H-MP1

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Components

#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-TYR-THR-ASP


Mass: 525.510 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: This is a synthetic peptide designed to inhibit V. cholerae FrhA.
Source: (synth.) Vibrio cholerae (bacteria)
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1712 / 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: 3.15 Å3/Da / Density % sol: 60.92 %
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: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→59.64 Å / Num. obs: 140116 / % possible obs: 98.1 % / Redundancy: 3.4 % / CC1/2: 0.904 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.135 / Rrim(I) all: 0.252 / Net I/σ(I): 3.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 6838 / CC1/2: 0.159 / Rpim(I) all: 0.396 / Rrim(I) all: 0.718 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
xia23.21.1data reduction
DIALS3.21data scaling
PHENIX(1.21.2_5419: ???)phasing
Coot0.9.8.96model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→59.18 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 1361 1.42 %
Rwork0.2479 --
obs0.248 95982 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→59.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13910 0 36 1712 15658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01414243
X-RAY DIFFRACTIONf_angle_d1.70419458
X-RAY DIFFRACTIONf_dihedral_angle_d15.54845
X-RAY DIFFRACTIONf_chiral_restr0.0762269
X-RAY DIFFRACTIONf_plane_restr0.0262590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.3241260.32059584X-RAY DIFFRACTION97.86
2.59-2.690.27471400.30529403X-RAY DIFFRACTION98
2.69-2.820.33661490.29539478X-RAY DIFFRACTION98
2.82-2.960.26511570.28869402X-RAY DIFFRACTION98
2.96-3.150.26671360.269430X-RAY DIFFRACTION98
3.15-3.390.24051490.23439564X-RAY DIFFRACTION99
3.39-3.730.22081170.22099467X-RAY DIFFRACTION99
3.73-4.270.23351420.21369390X-RAY DIFFRACTION98
4.27-5.380.18191180.19149452X-RAY DIFFRACTION98
5.39-59.180.26561270.27279577X-RAY DIFFRACTION99

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