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

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Basic information

Entry
Database: PDB / ID: 5tne
TitleCrystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted cis-Stilbene Oxide 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
(1R,2R)-1,2-diphenylethane-1,2-diol / Putative hydrolase / CFTR inhibitory factor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHvorecny, K.L. / Madden, D.R.
Funding support United States, 5items
OrganizationGrant numberCountry
Cystic Fibrosis Foundation United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: Structure / Year: 2017
Title: Active-Site Flexibility and Substrate Specificity in a Bacterial Virulence Factor: Crystallographic Snapshots of an Epoxide Hydrolase.
Authors: Hvorecny, K.L. / Bahl, C.D. / Kitamura, S. / Lee, K.S.S. / Hammock, B.D. / Morisseau, C. / Madden, D.R.
History
DepositionOct 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Revision 1.4Nov 6, 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

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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)137,0836
Polymers136,6554
Non-polymers4292
Water20,0331112
1
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5423
Polymers68,3272
Non-polymers2141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-22 kcal/mol
Surface area21050 Å2
MethodPISA
2
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5423
Polymers68,3272
Non-polymers2141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-22 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.944, 83.690, 89.175
Angle α, β, γ (deg.)90.00, 100.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-627-

HOH

21D-684-

HOH

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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-7F6 / (1R,2R)-1,2-diphenylethane-1,2-diol / cis-stilbene epoxide, bound form


Mass: 214.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H14O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details7F6 is the bound form ( covalently linked via OD1 atom of ASP 129 of CIF) of cis-Stilbene epoxide

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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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: sodium acetate, pH5 calcium chloride PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→36.554 Å / Num. obs: 122215 / % possible obs: 99.8 % / Redundancy: 3.94 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.62
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.91 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 4.53 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSDec 6, 2010data reduction
XDSDec 6, 2010data scaling
PHENIX1.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 1.75→36.554 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18
RfactorNum. reflection% reflection
Rfree0.1835 6090 4.98 %
Rwork0.1504 --
obs0.1521 122201 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→36.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9472 0 30 1112 10614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069928
X-RAY DIFFRACTIONf_angle_d0.80713513
X-RAY DIFFRACTIONf_dihedral_angle_d14.4545855
X-RAY DIFFRACTIONf_chiral_restr0.0531391
X-RAY DIFFRACTIONf_plane_restr0.0061779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.24133040.19223799X-RAY DIFFRACTION100
1.7699-1.79071000000000.19313983X-RAY DIFFRACTION100
1.7907-1.81250.23853050.19143725X-RAY DIFFRACTION100
1.8125-1.83550.2583050.18763774X-RAY DIFFRACTION100
1.8355-1.85961000000000.18884084X-RAY DIFFRACTION100
1.8596-1.88510.23253040.17843731X-RAY DIFFRACTION100
1.8851-1.9120.20023050.16613786X-RAY DIFFRACTION100
1.912-1.94061000000000.15914031X-RAY DIFFRACTION100
1.9406-1.97090.20583050.16093718X-RAY DIFFRACTION100
1.9709-2.00320.19783040.15933775X-RAY DIFFRACTION100
2.0032-2.03781000000000.164110X-RAY DIFFRACTION100
2.0378-2.07480.18873050.15413735X-RAY DIFFRACTION100
2.0748-2.11470.20933050.14923722X-RAY DIFFRACTION100
2.1147-2.15791000000000.15214069X-RAY DIFFRACTION100
2.1579-2.20480.17993020.15533756X-RAY DIFFRACTION100
2.2048-2.25610.19483050.15013761X-RAY DIFFRACTION100
2.2561-2.31251000000000.15124060X-RAY DIFFRACTION100
2.3125-2.3750.18523050.14793779X-RAY DIFFRACTION100
2.375-2.44490.19553050.15593744X-RAY DIFFRACTION100
2.4449-2.52381000000000.15594103X-RAY DIFFRACTION100
2.5238-2.61390.19173040.1533766X-RAY DIFFRACTION100
2.6139-2.71860.17373030.15183770X-RAY DIFFRACTION100
2.7186-2.84221000000000.15124087X-RAY DIFFRACTION100
2.8422-2.9920.19523050.15823771X-RAY DIFFRACTION100
2.992-3.17940.18683050.15463766X-RAY DIFFRACTION100
3.1794-3.42471000000000.13994093X-RAY DIFFRACTION100
3.4247-3.7690.15163050.13313801X-RAY DIFFRACTION100
3.769-4.31370.14443040.12843802X-RAY DIFFRACTION100
4.3137-5.43191000000000.12164115X-RAY DIFFRACTION100
5.4319-36.56180.16463050.15653895X-RAY DIFFRACTION99
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)
10.745-0.06930.07680.64020.01970.73030.01770.0753-0.0799-0.0531-0.024-0.04110.08850.0320.00670.0955-0.00250.00120.1013-0.01080.09721.878212.1967-27.2866
20.98150.32690.02140.92290.18350.4853-0.0183-0.00260.13320.03980.0205-0.0765-0.07960.0342-0.00220.0945-0.0164-0.02250.0941-0.00390.150430.921851.6794-15.5563
30.693-0.04120.04110.7285-0.03760.70160.01450.03280.1217-0.0352-0.03390.0664-0.0949-0.02440.01980.1012-0.0015-0.00150.09930.00480.1426-5.834744.9214-27.0694
40.88980.1943-0.08180.8432-0.13510.44240.0102-0.0437-0.05320.0076-0.0070.08250.046-0.0075-0.00340.0999-0.02310.00210.11150.00430.0924-14.8345.3179-15.6887
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:321)
2X-RAY DIFFRACTION2(chain B and resid 25:320)
3X-RAY DIFFRACTION3(chain C and resid 25:321)
4X-RAY DIFFRACTION4(chain D and resid 25:320)

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