8F6V | pdb_00008f6v

Crystal Structure of Nanobody VHH108 Bound to Its Antigen PA14 Cif

  • Classification: IMMUNE SYSTEM
  • Organism(s): Vicugna pacos, Pseudomonas aeruginosa PA14
  • Expression System: Escherichia coli BL21, Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-11-17 Released: 2024-03-13 
  • Deposition Author(s): Simard, A.R., Madden, D.R.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cystic Fibrosis Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Crystal Structure of Nanobody VHH113 Bound to Its Antigen PA14 Cif

Simard, A.R., Madden, D.R.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody VHH108A,
C [auth B]		132Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CFTR inhibitory factorB [auth D],
D [auth C]		301Pseudomonas aeruginosa PA14Mutation(s): 0 
Gene Names: PA2394
UniProt
Find proteins for A0A0M3KL26 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore A0A0M3KL26 
Go to UniProtKB:  A0A0M3KL26
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KL26
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.995α = 90
b = 98.995β = 90
c = 196.987γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01-AI091699
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesP30-DK117469
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20-GM113132
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesT32AI007519
Cystic Fibrosis FoundationUnited StatesSTANTO19R0

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary