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

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Basic information

Entry
Database: PDB / ID: 5tnk
TitleCrystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 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: 1.65 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 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 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
Water22,1041227
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 area2820 Å2
ΔGint-23 kcal/mol
Surface area20830 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-22 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.207, 84.093, 89.246
Angle α, β, γ (deg.)90.00, 100.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-745-

HOH

21A-778-

HOH

31D-816-

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-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.: 1227 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
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: 1.0781 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.65→19.696 Å / Num. obs: 146707 / % possible obs: 99.9 % / Redundancy: 7.52 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 23.14
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 7.43 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.64 / CC1/2: 0.918 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSMarch 30, 2013data reduction
XDSJuly 4, 2012data scaling
PHENIX(1.10_2155: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 1.65→19.696 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.39
RfactorNum. reflection% reflection
Rfree0.1757 7340 5 %
Rwork0.1511 --
obs0.1523 146702 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→19.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9417 0 36 1227 10680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069831
X-RAY DIFFRACTIONf_angle_d0.8113343
X-RAY DIFFRACTIONf_dihedral_angle_d14.0845779
X-RAY DIFFRACTIONf_chiral_restr0.0521366
X-RAY DIFFRACTIONf_plane_restr0.0061753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66870.22823670.1844429X-RAY DIFFRACTION100
1.6687-1.68841000000000.17974897X-RAY DIFFRACTION100
1.6884-1.70890.20993670.16794502X-RAY DIFFRACTION100
1.7089-1.73060.19053670.16744492X-RAY DIFFRACTION100
1.7306-1.75331000000000.16544896X-RAY DIFFRACTION100
1.7533-1.77730.19823670.16054508X-RAY DIFFRACTION100
1.7773-1.80270.19313670.15664497X-RAY DIFFRACTION100
1.8027-1.82961000000000.16194887X-RAY DIFFRACTION100
1.8296-1.85820.19743670.16434481X-RAY DIFFRACTION100
1.8582-1.88860.20993670.16494533X-RAY DIFFRACTION100
1.8886-1.92111000000000.1574868X-RAY DIFFRACTION100
1.9211-1.9560.16113670.15144503X-RAY DIFFRACTION100
1.956-1.99360.1983670.15344502X-RAY DIFFRACTION100
1.9936-2.03431000000000.15574845X-RAY DIFFRACTION100
2.0343-2.07850.18113670.15224567X-RAY DIFFRACTION100
2.0785-2.12680.17883670.14834495X-RAY DIFFRACTION100
2.1268-2.17991000000000.15114884X-RAY DIFFRACTION100
2.1799-2.23870.183670.15094562X-RAY DIFFRACTION100
2.2387-2.30450.1753670.15274456X-RAY DIFFRACTION100
2.3045-2.37881000000000.14794906X-RAY DIFFRACTION100
2.3788-2.46360.17163670.15254521X-RAY DIFFRACTION100
2.4636-2.56210.17333670.1574525X-RAY DIFFRACTION100
2.5621-2.67841000000000.15394887X-RAY DIFFRACTION100
2.6784-2.81930.16463670.14794534X-RAY DIFFRACTION100
2.8193-2.99530.17433670.15784545X-RAY DIFFRACTION100
2.9953-3.22571000000000.15474928X-RAY DIFFRACTION100
3.2257-3.54860.16023670.14144533X-RAY DIFFRACTION100
3.5486-4.05810.14783670.14144567X-RAY DIFFRACTION100
4.0581-5.09811000000000.12574949X-RAY DIFFRACTION100
5.0981-19.69720.1813670.15444663X-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)
10.74450.0460.14050.67410.05140.63660.0122-0.1069-0.07830.0575-0.01720.04890.0809-0.04780.00730.08030.00040.00740.09340.01280.062162.145154.20627.3236
21.0535-0.379-0.0141.1308-0.07240.5207-0.01760.01370.1495-0.04010.01320.043-0.0832-0.02790.00340.08520.0133-0.0220.07840.00410.107553.24393.385415.6409
30.65040.06430.02520.84810.04920.65940.0034-0.05280.1170.0369-0.0209-0.0854-0.07710.03570.01740.07970.00460.00280.0822-0.00510.100489.952186.211126.9233
41.0012-0.2923-0.06610.96680.14690.49710.02640.0409-0.0412-0.0207-0.0136-0.10630.04190.0156-0.01040.08160.0190.00780.0837-0.00170.0698.827246.997915.7291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 25:325 )A25 - 325
2X-RAY DIFFRACTION2( CHAIN B AND RESID 25:317 )B25 - 317
3X-RAY DIFFRACTION3( CHAIN C AND RESID 26:317 )C26 - 317
4X-RAY DIFFRACTION4( CHAIN D AND RESID 25:325 )D25 - 325

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