8E1C | pdb_00008e1c

Crystal Structure of Nanobody VHH222 Specific for PA14 Cif

PDB DOI: https://doi.org/10.2210/pdb8E1C/pdb

Classification: IMMUNE SYSTEM
Organism(s): Vicugna pacos
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2022-08-10 Released: 2023-10-04
Deposition Author(s): Simard, A.R., Taher, N.M., Balsam, S.S., 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: 1.90 Å
R-Value Free:
0.224 (Depositor), 0.224 (DCC)
R-Value Work:
0.212 (Depositor), 0.212 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Nanobody VHH222 Specific for PA14 Cif

Simard, A.R., Madden, D.R.

To be published.

Macromolecule Content

Total Structure Weight: 13.53 kDa
Atom Count: 939
Modeled Residue Count: 117
Deposited Residue Count: 126
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody VHH222	A	126	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.224 (Depositor), 0.224 (DCC)
R-Value Work: 0.212 (Depositor), 0.212 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.006	α = 90
b = 58.006	β = 90
c = 75.935	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI091699
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	P30-DK117469
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20-GM113132
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32AI007519
Cystic Fibrosis Foundation	United States	STANTO19R0

Revision History (Full details and data files)

Version 1.0: 2023-10-04
Type: Initial release
Version 1.1: 2024-10-16
Changes: Structure summary
Version 1.2: 2025-09-17
Changes: Structure summary
Version 1.3: 2026-03-04
Changes: Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.