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- PDB-5jyc: Crystal structure of the E153Q mutant of the CFTR inhibitory fact... -

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Basic information

Entry
Database: PDB / ID: 5jyc
TitleCrystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 14,15-EET hydrolysis intermediate
ComponentsCFTR inhibitory factor
KeywordsHYDROLASE / epoxide hydrolase / hydroxyalkyl-enzyme intermediate
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-EET / Putative hydrolase / CFTR inhibitory factor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHvorecny, K.L. / Madden, D.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Pseudomonas aeruginosa sabotages the generation of host proresolving lipid mediators.
Authors: Flitter, B.A. / Hvorecny, K.L. / Ono, E. / Eddens, T. / Yang, J. / Kwak, D.H. / Bahl, C.D. / Hampton, T.H. / Morisseau, C. / Hammock, B.D. / Liu, X. / Lee, J.S. / Kolls, J.K. / Levy, B.D. / ...Authors: Flitter, B.A. / Hvorecny, K.L. / Ono, E. / Eddens, T. / Yang, J. / Kwak, D.H. / Bahl, C.D. / Hampton, T.H. / Morisseau, C. / Hammock, B.D. / Liu, X. / Lee, J.S. / Kolls, J.K. / Levy, B.D. / Madden, D.R. / Bomberger, J.M.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Apr 13, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)138,0098
Polymers136,6554
Non-polymers1,3544
Water14,430801
1
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0044
Polymers68,3272
Non-polymers6772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-21 kcal/mol
Surface area20810 Å2
MethodPISA
2
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0044
Polymers68,3272
Non-polymers6772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-23 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.93, 83.602, 89.241
Angle α, β, γ (deg.)90.00, 100.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
CFTR inhibitory factor


Mass: 34163.715 Da / Num. of mol.: 4 / Mutation: E153Q
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: A0A0M3KL26, UniProt: A0A0H2ZD27*PLUS
#2: Chemical
ChemComp-EET / (5~{Z},11~{Z},14~{R},15~{R})-14,15-bis(oxidanyl)icosa-5,8,11-trienoic acid


Mass: 338.482 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C20H34O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 801 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsThe ligand EET as a substrate is an epoxide, which is converted into a diol via a two-step reaction ...The ligand EET as a substrate is an epoxide, which is converted into a diol via a two-step reaction which includes a covalent intermediate. The protein plus adduct (C15 atom of EET covalently linked to OD2 atom of ASP 129) is the result of the first step in the reaction.

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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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 8K, calcium chloride, sodium acetate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→35.41 Å / Num. obs: 82560 / % possible obs: 99.96 % / Redundancy: 6.24 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 14.27
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.16 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.44 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: 000)refinement
XDSDec 6th, 2010data reduction
XDSDec 6th, 2010data scaling
PHENIX(1.7_650: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 2→35.41 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.6
RfactorNum. reflection% reflection
Rfree0.191 4138 5.01 %
Rwork0.153 --
obs0.1549 82560 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→35.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9584 0 0 801 10385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069980
X-RAY DIFFRACTIONf_angle_d0.82913546
X-RAY DIFFRACTIONf_dihedral_angle_d16.1195904
X-RAY DIFFRACTIONf_chiral_restr0.0511384
X-RAY DIFFRACTIONf_plane_restr0.0061775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.24612070.18012533X-RAY DIFFRACTION100
2.0227-2.04651000000000.17212770X-RAY DIFFRACTION100
2.0465-2.07150.25232070.17152488X-RAY DIFFRACTION100
2.0715-2.09770.20672070.16832544X-RAY DIFFRACTION100
2.0977-2.12531000000000.16352726X-RAY DIFFRACTION100
2.1253-2.15440.20042070.15512543X-RAY DIFFRACTION100
2.1544-2.18520.22012070.1662554X-RAY DIFFRACTION100
2.1852-2.21781000000000.15682698X-RAY DIFFRACTION100
2.2178-2.25240.19562070.15412544X-RAY DIFFRACTION100
2.2524-2.28940.22632070.16732572X-RAY DIFFRACTION100
2.2894-2.32881000000000.1592705X-RAY DIFFRACTION100
2.3288-2.37120.22462070.15142524X-RAY DIFFRACTION100
2.3712-2.41680.20192070.16022563X-RAY DIFFRACTION100
2.4168-2.46611000000000.16442744X-RAY DIFFRACTION100
2.4661-2.51970.22892060.16352510X-RAY DIFFRACTION100
2.5197-2.57830.21062070.16072526X-RAY DIFFRACTION100
2.5783-2.64271000000000.16182780X-RAY DIFFRACTION100
2.6427-2.71420.21342070.1572535X-RAY DIFFRACTION100
2.7142-2.7940.21832070.16092553X-RAY DIFFRACTION100
2.794-2.88421000000000.15762744X-RAY DIFFRACTION100
2.8842-2.98720.20482060.17162558X-RAY DIFFRACTION100
2.9872-3.10670.22522070.16982525X-RAY DIFFRACTION100
3.1067-3.2481000000000.16142770X-RAY DIFFRACTION100
3.248-3.41910.16912070.15272543X-RAY DIFFRACTION100
3.4191-3.63320.15132070.14322550X-RAY DIFFRACTION100
3.6332-3.91331000000000.13992767X-RAY DIFFRACTION100
3.9133-4.30650.1612070.12732552X-RAY DIFFRACTION100
4.3065-4.92830.13632070.11512577X-RAY DIFFRACTION100
4.9283-6.20371000000000.14722778X-RAY DIFFRACTION100
6.2037-35.41510.16862070.15392646X-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)
10.6128-0.02290.03770.5674-0.05120.55220.00280.0586-0.0579-0.0379-0.0028-0.02160.09290.040500.0964-0.0026-0.00360.1063-0.01570.088721.969512.1975-27.482
20.69270.22670.01870.69070.12090.4889-0.0202-0.01880.11960.0270.0227-0.0316-0.08510.00290.0010.107-0.026-0.01830.0984-0.0030.146131.063351.755-15.6217
30.6533-0.0853-0.050.63620.00980.57510.01560.04560.1216-0.0539-0.01470.0504-0.0841-0.0158-0.00820.1004-0.0057-0.00130.09410.01010.1315-5.82244.9818-27.258
40.64710.1057-0.10590.5795-0.14780.3991-0.0039-0.0497-0.05860.0157-0.00670.07140.04390.00610.0080.1016-0.02730.00480.10840.00320.083-15.03295.4048-15.6676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 25:321 OR RESID 401:401 ) )A25 - 321
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 25:321 OR RESID 401:401 ) )A401
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 25:321 OR RESID 401:401 ) )B25 - 321
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 25:321 OR RESID 401:401 ) )B401
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 25:321 OR RESID 401:401 ) )C25 - 321
6X-RAY DIFFRACTION3( CHAIN C AND ( RESID 25:321 OR RESID 401:401 ) )C401
7X-RAY DIFFRACTION4( CHAIN D AND ( RESID 25:321 OR RESID 401:401 ) )D25 - 321
8X-RAY DIFFRACTION4( CHAIN D AND ( RESID 25:321 OR RESID 401:401 ) )D401

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