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

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Basic information

Entry
Database: PDB / ID: 5tnr
TitleCrystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 16,17-EpDPE 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-7EZ / 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 18, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: CFTR inhibitory factor
D: CFTR inhibitory factor
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,1058
Polymers136,6554
Non-polymers1,4504
Water22,0861226
1
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0524
Polymers68,3272
Non-polymers7252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-23 kcal/mol
Surface area20490 Å2
MethodPISA
2
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0524
Polymers68,3272
Non-polymers7252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-21 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.846, 168.912, 176.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-501-

HOH

21D-801-

HOH

31D-831-

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-7EZ / (4Z,7Z,10Z,13Z,16R,17R,19Z)-16,17-dihydroxydocosa-4,7,10,13,19-pentaenoic acid


Mass: 362.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H34O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1226 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.18 %
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: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→46.743 Å / Num. obs: 115528 / % possible obs: 99.8 % / Redundancy: 6.75 % / CC1/2: 0.997 / Rmerge(I) obs: 0.145 / Net I/σ(I): 13.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.83 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 3.98 / CC1/2: 0.944 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSMay 1, 2016data reduction
XDSMay 1, 2016data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 1.8→46.743 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1893 5759 4.99 %
Rwork0.1614 --
obs0.1628 115459 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→46.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9352 0 100 1226 10678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079853
X-RAY DIFFRACTIONf_angle_d0.85613373
X-RAY DIFFRACTIONf_dihedral_angle_d16.0885803
X-RAY DIFFRACTIONf_chiral_restr0.0541370
X-RAY DIFFRACTIONf_plane_restr0.0061773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.28252880.24863582X-RAY DIFFRACTION100
1.8205-1.84191000000000.2263782X-RAY DIFFRACTION100
1.8419-1.86430.2432880.22093512X-RAY DIFFRACTION100
1.8643-1.88790.25072880.21333558X-RAY DIFFRACTION100
1.8879-1.91281000000000.2073811X-RAY DIFFRACTION100
1.9128-1.9390.23762870.19323519X-RAY DIFFRACTION100
1.939-1.96670.2242880.1953556X-RAY DIFFRACTION100
1.9667-1.9961000000000.1863813X-RAY DIFFRACTION100
1.996-2.02720.22382880.18653483X-RAY DIFFRACTION100
2.0272-2.06050.22112880.18093520X-RAY DIFFRACTION99
2.0605-2.0961000000000.17643841X-RAY DIFFRACTION99
2.096-2.13410.20752880.1653524X-RAY DIFFRACTION100
2.1341-2.17520.22542880.16273523X-RAY DIFFRACTION100
2.1752-2.21961000000000.16723838X-RAY DIFFRACTION100
2.2196-2.26780.19152880.15723542X-RAY DIFFRACTION100
2.2678-2.32060.17932880.16123541X-RAY DIFFRACTION100
2.3206-2.37861000000000.15633842X-RAY DIFFRACTION100
2.3786-2.44290.19382880.16193558X-RAY DIFFRACTION100
2.4429-2.51480.19132880.15953507X-RAY DIFFRACTION99
2.5148-2.5961000000000.15533870X-RAY DIFFRACTION100
2.596-2.68870.18952880.16183571X-RAY DIFFRACTION100
2.6887-2.79640.19352880.15653566X-RAY DIFFRACTION100
2.7964-2.92361000000000.15753841X-RAY DIFFRACTION100
2.9236-3.07770.18022880.16523590X-RAY DIFFRACTION100
3.0777-3.27050.17952880.15673591X-RAY DIFFRACTION100
3.2705-3.52291000000000.14183873X-RAY DIFFRACTION100
3.5229-3.87730.14962880.13933601X-RAY DIFFRACTION100
3.8773-4.4380.13342880.13073638X-RAY DIFFRACTION100
4.438-5.58991000000000.13063951X-RAY DIFFRACTION100
5.5899-46.75880.18652880.16383756X-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)
10.83330.00760.06130.8478-0.04130.7371-0.01910.0447-0.0931-0.07810.02490.13830.0555-0.0997-0.00450.08060.0012-0.0160.08360.00590.1022-16.0845-5.9703-27.0516
20.7214-0.22090.04990.9625-0.06980.4032-0.0122-0.0066-0.05310.03650.0052-0.0586-0.00190.04770.00820.08270.0218-0.00490.08420.01040.061822.8969-14.998-15.64
30.69260.01140.01040.83630.15840.68-0.00520.0830.0546-0.11610.0172-0.0887-0.050.0988-0.00460.08490.00030.01560.08650.00680.065516.274921.9881-27.33
41.1611-0.4043-0.12891.1781-0.01050.58640.0253-0.01470.01910.0082-0.02320.1778-0.018-0.0944-0.00130.07270.01410.00540.0877-0.01250.1046-22.990730.8803-15.6512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 25:317 )C25 - 317
2X-RAY DIFFRACTION2( CHAIN D AND RESID 25:317 )D25 - 317
3X-RAY DIFFRACTION3( CHAIN A AND RESID 25:317 )A25 - 317
4X-RAY DIFFRACTION4( CHAIN B AND RESID 25:317 )B25 - 317

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