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

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Basic information

Entry
Database: PDB / ID: 5tnn
TitleCrystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted (S)-1,2-Epoxyoctane 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
(2R)-octane-1,2-diol / Putative hydrolase / CFTR inhibitory factor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHvorecny, K.L. / Madden, D.R.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI091699 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM113132 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106394 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK097154 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008704 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES002710 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES004699 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES024806 United States
Cystic Fibrosis FoundationSTANTO19R0 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 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)137,2408
Polymers136,6554
Non-polymers5854
Water12,502694
1
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6204
Polymers68,3272
Non-polymers2922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-23 kcal/mol
Surface area20750 Å2
MethodPISA
2
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6204
Polymers68,3272
Non-polymers2922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-23 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.582, 84.030, 89.581
Angle α, β, γ (deg.)90.00, 100.19, 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-7F2 / (2R)-octane-1,2-diol


Mass: 146.227 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 45.99 %
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: SSRL / Beamline: BL14-1 / Wavelength: 1.181 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
ReflectionResolution: 1.95→19.837 Å / Num. obs: 89284 / % possible obs: 99.5 % / Redundancy: 3.73 % / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.63
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 3.26 / CC1/2: 0.87 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSOct 15, 2015data reduction
XDSOct 15, 2015data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 1.95→19.837 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1897 4440 4.97 %
Rwork0.1475 --
obs0.1495 89272 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→19.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9387 0 36 694 10117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079890
X-RAY DIFFRACTIONf_angle_d0.79913449
X-RAY DIFFRACTIONf_dihedral_angle_d15.9565845
X-RAY DIFFRACTIONf_chiral_restr0.0511382
X-RAY DIFFRACTIONf_plane_restr0.0051772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97210.28592220.22962725X-RAY DIFFRACTION99
1.9721-1.99531000000000.22342972X-RAY DIFFRACTION100
1.9953-2.01960.28882220.19972705X-RAY DIFFRACTION99
2.0196-2.04520.23892220.19622802X-RAY DIFFRACTION100
2.0452-2.07211000000000.18642897X-RAY DIFFRACTION100
2.0721-2.10040.2712220.18122767X-RAY DIFFRACTION100
2.1004-2.13040.23922220.17992734X-RAY DIFFRACTION100
2.1304-2.16211000000000.17042961X-RAY DIFFRACTION100
2.1621-2.19590.23432220.1652767X-RAY DIFFRACTION100
2.1959-2.23180.21082220.15632728X-RAY DIFFRACTION100
2.2318-2.27031000000000.15832953X-RAY DIFFRACTION99
2.2703-2.31150.22642220.15742723X-RAY DIFFRACTION100
2.3115-2.35590.21682220.15332773X-RAY DIFFRACTION99
2.3559-2.40391000000000.15632967X-RAY DIFFRACTION99
2.4039-2.45610.21232220.15562729X-RAY DIFFRACTION100
2.4561-2.51310.2052220.15892744X-RAY DIFFRACTION99
2.5131-2.57581000000000.15812950X-RAY DIFFRACTION100
2.5758-2.64530.21012220.15492771X-RAY DIFFRACTION100
2.6453-2.7230.18712220.15252759X-RAY DIFFRACTION100
2.723-2.81061000000000.152941X-RAY DIFFRACTION99
2.8106-2.91080.20552220.15222789X-RAY DIFFRACTION99
2.9108-3.02690.18362220.15892726X-RAY DIFFRACTION100
3.0269-3.16421000000000.15492975X-RAY DIFFRACTION100
3.1642-3.33020.17922220.14772777X-RAY DIFFRACTION100
3.3302-3.53780.15522220.13222749X-RAY DIFFRACTION100
3.5378-3.80921000000000.13222999X-RAY DIFFRACTION100
3.8092-4.18930.17162220.12152767X-RAY DIFFRACTION100
4.1893-4.7880.12022220.11072791X-RAY DIFFRACTION100
4.788-6.00451000000000.12943034X-RAY DIFFRACTION100
6.0045-19.8380.20512220.14022857X-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)
11.0730.08280.09591.0446-0.00810.83260.0216-0.099-0.07710.0469-0.03320.05260.0921-0.01940.01050.18540.0051-0.01640.2130.00930.1858-21.942513.269327.2241
21.1701-0.26610.05411.3778-0.10150.5983-0.0190.01820.1415-0.04720.00940.068-0.0778-0.01720.00960.1740.0171-0.03710.19710.00140.2352-30.808552.07715.6239
30.84420.0503-0.02041.11360.10790.79070.0189-0.04140.13520.0527-0.0317-0.0688-0.09410.0210.0130.18930.001-0.01420.2085-0.00340.23325.919345.004327.0113
41.1756-0.3216-0.0471.35970.1840.57990.0250.068-0.0394-0.0164-0.0149-0.10220.05530.0059-0.00870.1920.0216-0.01390.2218-0.00150.187614.99225.737515.7232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 25:317 )A25 - 317
2X-RAY DIFFRACTION2( CHAIN B AND RESID 25:317 )B25 - 317
3X-RAY DIFFRACTION3( CHAIN C AND RESID 25:317 )C25 - 317
4X-RAY DIFFRACTION4( CHAIN D AND RESID 25:321 )D25 - 321

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