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

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Basic information

Entry
Database: PDB / ID: 5tnf
TitleCrystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 19,20-EpDPE hydrolysis intermediate
ComponentsCFTR inhibitory factor
Keywordshydrolase/hydrolase inhibitor / epoxide hydrolase / hydroxyalkyl-enzyme intermediate / hydrolase-hydrolase inhibitor complex
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-7HW / 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, 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 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)138,1058
Polymers136,6554
Non-polymers1,4504
Water19,1861065
1
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 area2780 Å2
ΔGint-23 kcal/mol
Surface area21110 Å2
MethodPISA
2
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 area2770 Å2
ΔGint-23 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.551, 83.922, 89.678
Angle α, β, γ (deg.)90.00, 100.35, 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-7HW / (4Z,7Z,10Z,13Z,16Z,19R,20R)-19,20-dihydroxydocosa-4,7,10,13,16-pentaenoic acid


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


Mass: 18.015 Da / Num. of mol.: 1065 / 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: 45.77 %
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, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→46.158 Å / Num. obs: 120855 / % possible obs: 97.6 % / Redundancy: 5.75 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 20.76
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 5.79 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 5.24 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSDec 6, 2010data reduction
XDSDec 6, 2010data scaling
PHENIX1.10_2155: ???phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 1.75→46.158 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1747 6053 5.01 %
Rwork0.1463 --
obs0.1477 120849 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→46.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9492 0 100 1065 10657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610032
X-RAY DIFFRACTIONf_angle_d0.81613634
X-RAY DIFFRACTIONf_dihedral_angle_d16.0285958
X-RAY DIFFRACTIONf_chiral_restr0.0521395
X-RAY DIFFRACTIONf_plane_restr0.0061790
LS refinement shellResolution: 1.75→1.7699 Å
RfactorNum. reflection% reflection
Rfree0.206 297 -
Rwork0.1668 3637 -
obs--96 %
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)
10.86160.04520.16430.82830.01640.75850.01280.0995-0.0919-0.0765-0.0143-0.05150.10070.04020.0060.0824-0.00250.00490.0869-0.00860.062721.786711.991-27.339
21.09750.3980.01471.22670.10120.66-0.0222-0.02150.14720.04070.0127-0.0562-0.11070.02530.00520.089-0.0181-0.02130.077-0.00090.101931.049351.7358-15.7387
30.8369-0.0075-0.0511.0941-0.02180.83240.01610.04890.1511-0.0618-0.02670.1001-0.1103-0.04950.01030.0807-0.0040.00140.07820.00230.1096-5.576844.9447-27.2865
41.08520.2939-0.09811.0014-0.14110.59820.018-0.0701-0.08220.0145-0.02080.0840.0686-0.00370.00470.0894-0.02680.01180.09610.00150.0637-14.89475.2015-15.7423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 25:321 )A25 - 321
2X-RAY DIFFRACTION2( CHAIN B AND RESID 25:321 )B25 - 321
3X-RAY DIFFRACTION3( CHAIN C AND RESID 25:321 )C25 - 321
4X-RAY DIFFRACTION4( CHAIN D AND RESID 25:321 )D25 - 321

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