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- PDB-38we: Crystal structure of the CFTR inhibitory factor Cif with the F164... -

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Basic information

Entry
Database: PDB / ID: 38we
TitleCrystal structure of the CFTR inhibitory factor Cif with the F164A mutation
ComponentsCFTR inhibitory factor
KeywordsHYDROLASE / Epoxide hydrolase / Virulence 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 / CFTR inhibitory factor
Function and homology information
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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)P20-GM113132 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-GM165328 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30-DK117469 United States
CitationJournal: To Be Published
Title: Crystal structure of the CFTR inhibitory factor Cif with the F164A mutation
Authors: Nie, Z. / Madden, D.R.
History
DepositionSep 21, 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)133,27910
Polymers133,0394
Non-polymers2406
Water23,9781331
1
A: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6405
Polymers66,5192
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-41 kcal/mol
Surface area21030 Å2
MethodPISA
2
B: CFTR inhibitory factor
C: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6405
Polymers66,5192
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-49 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.607, 84.159, 89.306
Angle α, β, γ (deg.)90.000, 100.535, 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
11B-853-

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: 33259.734 Da / Num. of mol.: 4 / Mutation: F164A
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 BL21(DE3) (bacteria) / References: UniProt: A0A0H2ZD27, soluble epoxide hydrolase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1331 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 47.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 17% (w/v) PEG 8000, 175 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-1 / Wavelength: 0.92019 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 14, 2025 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92019 Å / Relative weight: 1
ReflectionResolution: 1.66→43.72 Å / Num. obs: 144615 / % possible obs: 99.89 % / Redundancy: 4.4 % / Biso Wilson estimate: 19.35 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.0911 / Rpim(I) all: 0.0483 / Rrim(I) all: 0.1035 / Net I/σ(I): 8.73
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.6669 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 14442 / CC1/2: 0.685 / CC star: 0.902 / Rpim(I) all: 0.357 / Rrim(I) all: 0.7592 / % possible all: 99.93

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→43.72 Å / SU ML: 0.2357 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.3263
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1956 7220 4.99 %
Rwork0.1692 137375 -
obs0.1704 144595 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.59 Å2
Refinement stepCycle: LAST / Resolution: 1.66→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9392 0 6 1332 10730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710152
X-RAY DIFFRACTIONf_angle_d0.921613843
X-RAY DIFFRACTIONf_chiral_restr0.05691410
X-RAY DIFFRACTIONf_plane_restr0.00921852
X-RAY DIFFRACTIONf_dihedral_angle_d13.48813740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.690.38173610.34716861X-RAY DIFFRACTION99.9
1.69-1.720.36013610.32336859X-RAY DIFFRACTION99.96
1.72-1.750.31533610.27936860X-RAY DIFFRACTION99.94
1.75-1.790.30623610.24676811X-RAY DIFFRACTION99.96
1.79-1.830.26033610.22786842X-RAY DIFFRACTION99.97
1.83-1.870.24863610.20776827X-RAY DIFFRACTION99.9
1.87-1.920.22423610.19476877X-RAY DIFFRACTION99.94
1.92-1.970.19773610.18466821X-RAY DIFFRACTION99.96
1.97-2.030.22563610.19466828X-RAY DIFFRACTION99.99
2.03-2.090.21683610.19296870X-RAY DIFFRACTION99.94
2.09-2.170.23673610.19716838X-RAY DIFFRACTION99.92
2.17-2.250.18243610.16426846X-RAY DIFFRACTION99.94
2.25-2.360.19163610.15936911X-RAY DIFFRACTION99.96
2.36-2.480.19693610.16026872X-RAY DIFFRACTION99.96
2.48-2.630.19053610.15956855X-RAY DIFFRACTION99.82
2.63-2.840.18083610.15726863X-RAY DIFFRACTION99.9
2.84-3.120.17993610.16096893X-RAY DIFFRACTION99.67
3.12-3.580.15453610.14866874X-RAY DIFFRACTION99.82
3.58-4.50.15243610.12876935X-RAY DIFFRACTION99.75
4.5-43.720.16993610.14337032X-RAY DIFFRACTION99.72

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