39AI | pdb_000039ai

Crystal structure of the CFTR inhibitory factor Cif with the R163C mutation labelled with a fluorine probe

PDB DOI: https://doi.org/10.2210/pdb39AI/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa UCBPP-PA14
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2026-09-25 Released: 2026-10-07
Deposition Author(s): Nie, Z., Madden, D.R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.190 (Depositor), 0.190 (DCC)
R-Value Work:
0.167 (Depositor), 0.167 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the CFTR inhibitory factor Cif with the R163C mutation labelled with a fluorine probe

Nie, Z., Madden, D.R.

To be published.

Macromolecule Content

Total Structure Weight: 133.85 kDa
Atom Count: 11,031
Modeled Residue Count: 1,179
Deposited Residue Count: 1,180
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CFTR inhibitory factor	A, B, C, D	295	Pseudomonas aeruginosa UCBPP-PA14	Mutation(s): 1 Gene Names: cif, PA14_26090 EC: 3.3.2.10
UniProt
Find proteins for A0A0H2ZD27 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore A0A0H2ZD27 Go to UniProtKB: A0A0H2ZD27
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2ZD27
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W6Z (Subject of Investigation/LOI) Query on W6Z Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D]	F [auth A], J [auth B], L [auth C], M [auth D]	1,1,1-tris(fluoranyl)propane-2,2-diol C₃ H₅ F₃ O₂ BQAKXJSYMYZORI-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C]	E [auth A], G [auth A], H [auth A], I [auth B], K [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.190 (Depositor), 0.190 (DCC)
R-Value Work: 0.167 (Depositor), 0.167 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.534	α = 90
b = 83.895	β = 100.703
c = 89.654	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-07

Deposition Author(s):

Nie, Z.

Madden, D.R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM113132
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM165328
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	P30DK117469