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- PDB-4yx9: Crystal structure of the CFTR inhibitory factor Cif bound to tira... -

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Basic information

Entry
Database: PDB / ID: 4yx9
TitleCrystal structure of the CFTR inhibitory factor Cif bound to tiratricol
ComponentsCFTR inhibitory factor
KeywordsHydrolase/Hydrolase inhibitor / inhibitor / enzyme / Cif / CFTR / epoxide hydrolase / alpha beta hydrolase / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4HY / CFTR inhibitory factor / Putative hydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBahl, C.D. / Madden, D.R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI091699 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32-AI007519 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)T32-DK007301 United States
Cystic Fibrosis FoundationMADDEN08G0 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Inhibiting an Epoxide Hydrolase Virulence Factor from Pseudomonas aeruginosa Protects CFTR.
Authors: Bahl, C.D. / Hvorecny, K.L. / Bomberger, J.M. / Stanton, B.A. / Hammock, B.D. / Morisseau, C. / Madden, D.R.
History
DepositionMar 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Other
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)139,1478
Polymers136,6594
Non-polymers2,4884
Water21,0421168
1
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5734
Polymers68,3292
Non-polymers1,2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-23 kcal/mol
Surface area20330 Å2
MethodPISA
2
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5734
Polymers68,3292
Non-polymers1,2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-24 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.628, 84.016, 89.522
Angle α, β, γ (deg.)90.00, 100.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-725-

HOH

21A-743-

HOH

31C-754-

HOH

41C-779-

HOH

51D-804-

HOH

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Components

#1: Protein
CFTR inhibitory factor /


Mass: 34164.699 Da / Num. of mol.: 4 / Fragment: UNP residues 25-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: PA14_26090 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q02P97, UniProt: A0A0M3KL26*PLUS
#2: Chemical
ChemComp-4HY / [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID / Tiratricol


Mass: 621.932 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H9I3O4 / Comment: hormone*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1168 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15% [wt/vol] PEG 8000, 0.125M calcium chloride, 0.1M sodium acetate, 0.0002M [4-(4-hydroxy-3-iodophenoxy)-3,5-diiodophenyl]acetic acid, 0.2% [vol/vol] dimethyl sulfoxide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 25, 2012 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→42.23 Å / Num. obs: 124414 / % possible obs: 100 % / Redundancy: 4.2 % / Rsym value: 0.081 / Net I/σ(I): 12.4
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 1.75→42.226 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.24 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 6197 4.98 %thin shells
Rwork0.1637 ---
obs0.1653 124405 99.98 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.7 Å2 / ksol: 0.395 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4108 Å20 Å20.8641 Å2
2---1.0729 Å20 Å2
3---2.4836 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9352 0 84 1168 10604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079818
X-RAY DIFFRACTIONf_angle_d1.10513344
X-RAY DIFFRACTIONf_dihedral_angle_d13.0033588
X-RAY DIFFRACTIONf_chiral_restr0.0781366
X-RAY DIFFRACTIONf_plane_restr0.0061749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.26293090.21423740X-RAY DIFFRACTION100
1.7699-1.79071000000000.21164168X-RAY DIFFRACTION100
1.7907-1.81250.26413100.20183801X-RAY DIFFRACTION100
1.8125-1.83550.25193100.19083819X-RAY DIFFRACTION100
1.8355-1.85961000000000.1874142X-RAY DIFFRACTION100
1.8596-1.88510.21823090.18743814X-RAY DIFFRACTION100
1.8851-1.9120.23063100.17663801X-RAY DIFFRACTION100
1.912-1.94061000000000.16034164X-RAY DIFFRACTION100
1.9406-1.97090.21683100.16263809X-RAY DIFFRACTION100
1.9709-2.00320.18843100.16323831X-RAY DIFFRACTION100
2.0032-2.03781000000000.16084112X-RAY DIFFRACTION100
2.0378-2.07480.20443100.15683832X-RAY DIFFRACTION100
2.0748-2.11470.18853100.15353843X-RAY DIFFRACTION100
2.1147-2.15791000000000.15474150X-RAY DIFFRACTION100
2.1579-2.20480.19423100.15943818X-RAY DIFFRACTION100
2.2048-2.25610.19343100.15643809X-RAY DIFFRACTION100
2.2561-2.31251000000000.15634136X-RAY DIFFRACTION100
2.3125-2.3750.20013100.15553846X-RAY DIFFRACTION100
2.375-2.44490.20453100.15653823X-RAY DIFFRACTION100
2.4449-2.52381000000000.16144137X-RAY DIFFRACTION100
2.5238-2.6140.19983100.16123857X-RAY DIFFRACTION100
2.614-2.71860.18733100.15773846X-RAY DIFFRACTION100
2.7186-2.84241000000000.15744140X-RAY DIFFRACTION100
2.8424-2.99220.20413100.17063863X-RAY DIFFRACTION100
2.9922-3.17960.21193100.17083840X-RAY DIFFRACTION100
3.1796-3.4251000000000.1634173X-RAY DIFFRACTION100
3.425-3.76950.16773100.1523857X-RAY DIFFRACTION100
3.7695-4.31440.14043100.14443866X-RAY DIFFRACTION100
4.3144-5.43391000000000.13864213X-RAY DIFFRACTION100
5.4339-42.23860.19723090.2113958X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6984-0.00870.020.6804-0.00910.7525-0.0123-0.0828-0.04910.0656-0.0040.06230.0764-0.03820.01330.06490.00390.00770.06890.00930.0456-22.154812.241227.1497
21.1106-0.4083-0.03380.9177-0.0550.4605-0.0094-0.00250.1322-0.02480.00420.0073-0.0646-0.02270.00530.05820.007-0.01930.056-0.00250.068-31.106851.3415.6534
30.72690.09690.0820.9520.11930.8156-0.0138-0.04470.09420.0459-0.0038-0.0895-0.0740.04760.01660.05840.009-0.00810.05560.00070.06845.668244.737126.9632
40.9375-0.21410.07470.74950.10840.41530.0270.0264-0.0515-0.014-0.0159-0.07260.03860.0084-0.00720.06230.01440.01150.067-0.00150.0414.68125.668115.635
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:317)
2X-RAY DIFFRACTION2(chain B and resid 25:317)
3X-RAY DIFFRACTION3(chain C and resid 25:317)
4X-RAY DIFFRACTION4(chain D and resid 25:317)

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