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

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Basic information

Entry
Database: PDB / ID: 5tnp
TitleCrystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted Styrene oxide 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
(1R)-1-phenylethane-1,2-diol / Putative hydrolase / CFTR inhibitory factor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)R01AI091699 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113132 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM106394 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)U24DK097154 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008704 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01ES002710 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)P42ES004699 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)K99ES024806 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R00ES024806 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 1.1Apr 13, 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

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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)137,76012
Polymers136,6554
Non-polymers1,1058
Water14,016778
1
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8806
Polymers68,3272
Non-polymers5534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-23 kcal/mol
Surface area20640 Å2
MethodPISA
2
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8806
Polymers68,3272
Non-polymers5534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-24 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.015, 84.013, 89.459
Angle α, β, γ (deg.)90.00, 100.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-519-

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-FEH / (1R)-1-phenylethane-1,2-diol


Mass: 138.164 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H10O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 778 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsFEH represents bound form of Styrene oxide. C1 atom of FEH 327 (or C3 atom of FEH 326) covalently ...FEH represents bound form of Styrene oxide. C1 atom of FEH 327 (or C3 atom of FEH 326) covalently bound to OD1 atom of residues 129 (ASP) of polymer.

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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: 2.22 Å3/Da / Density % sol: 44.67 %
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: 1.85→19.823 Å / Num. obs: 104019 / % possible obs: 99.6 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.28
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.68 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 3.44 / CC1/2: 0.865 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSOct 15, 2015data reduction
XDSOct 15, 2015data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 1.85→19.823 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 5220 5.02 %
Rwork0.1666 --
obs0.1687 104010 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→19.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9352 0 80 778 10210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069910
X-RAY DIFFRACTIONf_angle_d0.79813484
X-RAY DIFFRACTIONf_dihedral_angle_d15.6775812
X-RAY DIFFRACTIONf_chiral_restr0.051382
X-RAY DIFFRACTIONf_plane_restr0.0061777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8710.28342610.25853218X-RAY DIFFRACTION99
1.871-1.8931000000000.23563399X-RAY DIFFRACTION100
1.893-1.91610.26662610.20793230X-RAY DIFFRACTION100
1.9161-1.94030.2412610.19373166X-RAY DIFFRACTION100
1.9403-1.96581000000000.19123456X-RAY DIFFRACTION100
1.9658-1.99270.23482610.19043204X-RAY DIFFRACTION100
1.9927-2.02120.23212610.18333181X-RAY DIFFRACTION100
2.0212-2.05131000000000.17673476X-RAY DIFFRACTION100
2.0513-2.08330.23132610.17783181X-RAY DIFFRACTION99
2.0833-2.11740.24042610.17313164X-RAY DIFFRACTION100
2.1174-2.15391000000000.16863465X-RAY DIFFRACTION100
2.1539-2.1930.21442610.17123212X-RAY DIFFRACTION100
2.193-2.23520.21662610.17113203X-RAY DIFFRACTION100
2.2352-2.28071000000000.16913435X-RAY DIFFRACTION100
2.2807-2.33020.21742610.16553205X-RAY DIFFRACTION100
2.3302-2.38440.22552610.17123195X-RAY DIFFRACTION100
2.3844-2.44391000000000.17323448X-RAY DIFFRACTION100
2.4439-2.50980.23342610.1753227X-RAY DIFFRACTION100
2.5098-2.58350.21272610.16783218X-RAY DIFFRACTION100
2.5835-2.66671000000000.17463443X-RAY DIFFRACTION100
2.6667-2.76180.20942610.173210X-RAY DIFFRACTION99
2.7618-2.87210.22642610.17493188X-RAY DIFFRACTION100
2.8721-3.00241000000000.18133503X-RAY DIFFRACTION100
3.0024-3.160.2162610.17423171X-RAY DIFFRACTION100
3.16-3.35710.19442610.16623248X-RAY DIFFRACTION100
3.3571-3.61491000000000.14943478X-RAY DIFFRACTION100
3.6149-3.97610.17612610.15253206X-RAY DIFFRACTION100
3.9761-4.54530.16152610.13873230X-RAY DIFFRACTION100
4.5453-5.70391000000000.14343513X-RAY DIFFRACTION100
5.7039-19.82380.20722610.16213317X-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)
11.01460.03680.12021.0939-0.09860.73880.019-0.0821-0.10760.0893-0.02030.04720.0763-0.02140.00380.15250.00670.00750.15850.010.1422-22.0817-31.727827.0638
21.072-0.3621-0.03821.6176-0.24120.598-0.00670.01620.1397-0.05080.02130.063-0.0719-0.0274-0.01360.12020.0188-0.0190.1370.00270.1703-30.7317.110415.6553
30.86770.02630.05611.18920.09340.711-0.0003-0.04560.16230.0675-0.0225-0.0833-0.08950.01810.0230.15390.00560.00380.1587-0.0040.18386.00370.025727.0019
41.0416-0.3333-0.06421.39050.1640.5210.01610.0387-0.0636-0.0185-0.0035-0.11360.05610.027-0.01130.13960.02160.01130.1499-0.00560.133714.76-38.866315.7861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:317)
2X-RAY DIFFRACTION2(chain B and resid 25:317)
3X-RAY DIFFRACTION3(chain C and resid 25:317)
4X-RAY DIFFRACTION4(chain D and resid 25:317)

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