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

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Basic information

Entry
Database: PDB / ID: 5tnl
TitleCrystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted (S)-1,2-Epoxyhexane 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)-hexane-1,2-diol / Putative hydrolase / CFTR inhibitory factor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)137,1288
Polymers136,6554
Non-polymers4734
Water15,565864
1
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5644
Polymers68,3272
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-22 kcal/mol
Surface area20820 Å2
MethodPISA
2
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5644
Polymers68,3272
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-21 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.492, 83.789, 89.570
Angle α, β, γ (deg.)90.00, 100.39, 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-7FB / (2R)-hexane-1,2-diol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 864 / 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: 45.94 %
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: ALS / Beamline: 5.0.3 / Wavelength: 0.999999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999 Å / Relative weight: 1
ReflectionResolution: 1.8→19.984 Å / Num. obs: 111128 / % possible obs: 97.9 % / Redundancy: 3.74 % / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.19
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.73 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 6.34 / CC1/2: 0.956 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSJan 10, 2014data reduction
XDSJan 10, 2014data scaling
PHENIX(1.10_2155: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 1.8→19.984 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.78
RfactorNum. reflection% reflection
Rfree0.1874 5565 5.01 %
Rwork0.1576 --
obs0.1591 111123 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9482 0 28 864 10374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069963
X-RAY DIFFRACTIONf_angle_d0.79813548
X-RAY DIFFRACTIONf_dihedral_angle_d15.8025880
X-RAY DIFFRACTIONf_chiral_restr0.0521391
X-RAY DIFFRACTIONf_plane_restr0.0061785
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82040.22872660.20143224X-RAY DIFFRACTION93
1.8204-1.84181000000000.18893651X-RAY DIFFRACTION97
1.8418-1.86430.22522770.18543396X-RAY DIFFRACTION98
1.8643-1.88790.22652810.18073396X-RAY DIFFRACTION97
1.8879-1.91271000000000.16453680X-RAY DIFFRACTION98
1.9127-1.93890.1882770.15263364X-RAY DIFFRACTION98
1.9389-1.96660.18242780.15363406X-RAY DIFFRACTION98
1.9666-1.99591000000000.1613709X-RAY DIFFRACTION98
1.9959-2.0270.2172780.16213377X-RAY DIFFRACTION98
2.027-2.06020.20932800.16253394X-RAY DIFFRACTION98
2.0602-2.09571000000000.16213713X-RAY DIFFRACTION98
2.0957-2.13380.192800.16023437X-RAY DIFFRACTION98
2.1338-2.17480.18942760.15593382X-RAY DIFFRACTION98
2.1748-2.21911000000000.15953709X-RAY DIFFRACTION98
2.2191-2.26730.19122810.15173422X-RAY DIFFRACTION98
2.2673-2.320.1862750.15713432X-RAY DIFFRACTION98
2.32-2.37791000000000.15623737X-RAY DIFFRACTION99
2.3779-2.44210.20892770.16833426X-RAY DIFFRACTION98
2.4421-2.51380.21592820.17753431X-RAY DIFFRACTION98
2.5138-2.59481000000000.17283713X-RAY DIFFRACTION98
2.5948-2.68730.2042770.16813455X-RAY DIFFRACTION98
2.6873-2.79460.20142770.16243451X-RAY DIFFRACTION98
2.7946-2.92151000000000.16543710X-RAY DIFFRACTION98
2.9215-3.0750.19932770.17333451X-RAY DIFFRACTION99
3.075-3.26680.19422770.16543427X-RAY DIFFRACTION98
3.2668-3.51781000000000.14873779X-RAY DIFFRACTION99
3.5178-3.86950.1482830.14323461X-RAY DIFFRACTION99
3.8695-4.42420.14642820.13453480X-RAY DIFFRACTION99
4.4242-5.55411000000000.13113777X-RAY DIFFRACTION99
5.5541-19.9850.17492840.15813568X-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)
10.7620.06260.04030.83540.01210.7320.0192-0.0772-0.08560.0536-0.03170.04120.0814-0.02340.010.08870.0047-0.01050.10390.00460.0578-22.018712.443927.3054
20.9713-0.2551-0.02721.1119-0.14930.5852-0.01120.01870.1367-0.04920.01870.0636-0.0813-0.03080.0020.09190.0192-0.03610.09430.00130.0942-31.088751.74515.6782
30.76580.03210.03660.95690.12030.74020.0145-0.04190.12520.0401-0.0342-0.0674-0.09580.02810.01930.09460.0049-0.00870.10260.00180.09235.74644.628227.2368
40.919-0.2733-0.09520.94450.15860.54010.02030.0247-0.0536-0.0247-0.0068-0.09410.05530.0207-0.01270.09670.023-0.00420.1054-0.00280.059514.86035.236415.7321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 25:320 )A25 - 320
2X-RAY DIFFRACTION2( CHAIN B AND RESID 25:325 )B25 - 325
3X-RAY DIFFRACTION3( CHAIN C AND RESID 25:325 )C25 - 325
4X-RAY DIFFRACTION4( CHAIN D AND RESID 25:325 )D25 - 325

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