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- PDB-39ai: Crystal structure of the CFTR inhibitory factor Cif with the R163... -

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Basic information

Entry
Database: PDB / ID: 39ai
TitleCrystal structure of the CFTR inhibitory factor Cif with the R163C mutation labelled with a fluorine probe
ComponentsCFTR inhibitory factor
KeywordsHYDROLASE / Epoxide hydrolase / Virulennce factor
Function / homologysoluble epoxide hydrolase / Alpha/beta hydrolase family / epoxide hydrolase activity / Alpha/beta hydrolase fold-1 / host cell / Alpha/Beta hydrolase fold / extracellular region / 1,1,1-tris(fluoranyl)propane-2,2-diol / CFTR inhibitory factor
Function and homology information
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNie, Z. / Madden, D.R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113132 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM165328 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30DK117469 United States
CitationJournal: To Be Published
Title: Crystal structure of the CFTR inhibitory factor Cif with the R163C mutation labelled with a fluorine probe
Authors: Nie, Z. / Madden, D.R.
History
DepositionSep 25, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CFTR inhibitory factor
B: CFTR inhibitory factor
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,84813
Polymers133,1274
Non-polymers7219
Water23,3831298
1
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9848
Polymers66,5642
Non-polymers4206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-41 kcal/mol
Surface area21160 Å2
MethodPISA
2
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8645
Polymers66,5642
Non-polymers3003
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-39 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.534, 83.895, 89.654
Angle α, β, γ (deg.)90.000, 100.703, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11D-822-

HOH

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Components

#1: Protein
CFTR inhibitory factor / Cif / Cystic fibrosis transmembrane conductance regulator inhibitory factor / Epoxide hydrolase ...Cif / Cystic fibrosis transmembrane conductance regulator inhibitory factor / Epoxide hydrolase virulence factor / Toxin Cif


Mass: 33281.777 Da / Num. of mol.: 4 / Mutation: R163C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Gene: cif, PA14_26090 / Plasmid: pET16b
Details (production host): N-terminal decahistidine-SUMO fusion
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0H2ZD27, soluble epoxide hydrolase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-W6Z / 1,1,1-tris(fluoranyl)propane-2,2-diol


Mass: 130.066 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5F3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1298 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 16% (w/v) PEG 8000, 200 mM calcium chloride, 100 mM sodium acetate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2026
Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.65→44.05 Å / Num. obs: 147168 / % possible obs: 99.88 % / Redundancy: 4.4 % / Biso Wilson estimate: 18.37 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1159 / Rpim(I) all: 0.06316 / Rrim(I) all: 0.1324 / Net I/σ(I): 7.75
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.8561 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 14644 / CC1/2: 0.564 / CC star: 0.849 / Rpim(I) all: 0.4648 / Rrim(I) all: 0.9782 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→44.05 Å / SU ML: 0.2139 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.489
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1895 7350 5 %
Rwork0.1666 139788 -
obs0.1678 147138 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.28 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9384 0 37 1298 10719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006610062
X-RAY DIFFRACTIONf_angle_d0.894313735
X-RAY DIFFRACTIONf_chiral_restr0.05541405
X-RAY DIFFRACTIONf_plane_restr0.00891822
X-RAY DIFFRACTIONf_dihedral_angle_d13.50143682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.690.33177350.30754165X-RAY DIFFRACTION99.94
1.73-1.750.2987350.2494175X-RAY DIFFRACTION99.98
1.8-1.830.24877350.21194187X-RAY DIFFRACTION99.98
1.89-1.920.23637350.19354184X-RAY DIFFRACTION99.98
1.99-2.030.22567350.20374132X-RAY DIFFRACTION99.96
2.13-2.180.21587350.1644159X-RAY DIFFRACTION99.84
2.31-2.380.18237350.15434160X-RAY DIFFRACTION99.9
2.56-2.680.19457350.16374168X-RAY DIFFRACTION99.96
3-3.230.18797350.16444188X-RAY DIFFRACTION99.51
4.07-5.120.12787350.11554226X-RAY DIFFRACTION99.82

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