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

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Basic information

Entry
Database: PDB / ID: 5tnj
TitleCrystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 4-Vinyl-1-cyclohexene 1,2-epoxide 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
(1S,2S,4S)-4-ethenylcyclohexane-1,2-diol / (1R,2R,4R)-4-ethenylcyclohexane-1,2-diol / (1R,2R,4S)-4-ethenylcyclohexane-1,2-diol / (1S,2S,4R)-4-ethenylcyclohexane-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, 5items
OrganizationGrant numberCountry
Cystic Fibrosis Foundation United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) 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 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)137,79212
Polymers136,6554
Non-polymers1,1388
Water20,5011138
1
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8966
Polymers68,3272
Non-polymers5694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-23 kcal/mol
Surface area20650 Å2
MethodPISA
2
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8966
Polymers68,3272
Non-polymers5694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-22 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.351, 83.436, 89.377
Angle α, β, γ (deg.)90.00, 100.45, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-761-

HOH

21A-766-

HOH

31D-790-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 1146 molecules

#2: Chemical ChemComp-AVH / (1R,2R,4R)-4-ethenylcyclohexane-1,2-diol


Mass: 142.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O2
#3: Chemical ChemComp-8MD / (1S,2S,4S)-4-ethenylcyclohexane-1,2-diol


Mass: 142.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O2
#4: Chemical ChemComp-BVH / (1R,2R,4S)-4-ethenylcyclohexane-1,2-diol


Mass: 142.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H14O2
#5: Chemical ChemComp-DVH / (1S,2S,4R)-4-ethenylcyclohexane-1,2-diol


Mass: 142.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H14O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1138 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsLigand AVH ((1R,2R,4R)-4-ethenylcyclohexane-1,2-diol) or 8MD ((1S,2S,4S)-4-ethenylcyclohexane-1,2- ...Ligand AVH ((1R,2R,4R)-4-ethenylcyclohexane-1,2-diol) or 8MD ((1S,2S,4S)-4-ethenylcyclohexane-1,2-diol ) covalently linked to the protein Cif-E153Q, via its C1 atom to OD1 on Asp129 of the protein chain A; In chain B, C and D, ligand BVH ((1R,2R,4S)-4-ethenylcyclohexane-1,2-diol) or DVH ((1S,2S,4R)-4-ethenylcyclohexane-1,2-diol) covalently linked to the protein Cif-E153Q, via its C6 atom to OD1 on Asp129 of the protein.

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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: 2.24 Å3/Da / Density % sol: 45.19 %
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: Mar 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→19.905 Å / Num. obs: 145788 / % possible obs: 99.8 % / Redundancy: 7.49 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Net I/σ(I): 28.02
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 6.99 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 6.08 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSSept 26, 2012data reduction
XDSJuly 4, 2012data scaling
PHENIX1.10_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 1.65→19.905 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 15.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1725 7288 5 %
Rwork0.1446 --
obs0.146 145781 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→19.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9360 0 80 1138 10578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069958
X-RAY DIFFRACTIONf_angle_d0.83213562
X-RAY DIFFRACTIONf_dihedral_angle_d14.4485851
X-RAY DIFFRACTIONf_chiral_restr0.0531403
X-RAY DIFFRACTIONf_plane_restr0.0061776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66870.19663540.16954338X-RAY DIFFRACTION97
1.6687-1.68841000000000.15854827X-RAY DIFFRACTION99
1.6884-1.70890.19033650.15934488X-RAY DIFFRACTION100
1.7089-1.73060.20123650.15834458X-RAY DIFFRACTION100
1.7306-1.75331000000000.15724850X-RAY DIFFRACTION100
1.7533-1.77730.19483650.15084550X-RAY DIFFRACTION100
1.7773-1.80270.17683650.14354423X-RAY DIFFRACTION100
1.8027-1.82961000000000.1514841X-RAY DIFFRACTION100
1.8296-1.85820.19633650.15684498X-RAY DIFFRACTION100
1.8582-1.88860.18543650.15834480X-RAY DIFFRACTION100
1.8886-1.92111000000000.14494841X-RAY DIFFRACTION100
1.9211-1.9560.17273650.1434482X-RAY DIFFRACTION100
1.956-1.99360.18943650.1464490X-RAY DIFFRACTION100
1.9936-2.03431000000000.14734868X-RAY DIFFRACTION100
2.0343-2.07850.18333650.14454492X-RAY DIFFRACTION100
2.0785-2.12680.16713650.14114472X-RAY DIFFRACTION100
2.1268-2.17991000000000.14374859X-RAY DIFFRACTION100
2.1799-2.23880.16553650.14074505X-RAY DIFFRACTION100
2.2388-2.30450.16223640.14264452X-RAY DIFFRACTION100
2.3045-2.37881000000000.14114883X-RAY DIFFRACTION100
2.3788-2.46370.15713650.15224514X-RAY DIFFRACTION100
2.4637-2.56210.17573650.15074485X-RAY DIFFRACTION100
2.5621-2.67851000000000.15174856X-RAY DIFFRACTION100
2.6785-2.81930.16843650.14614517X-RAY DIFFRACTION100
2.8193-2.99540.18333650.15424524X-RAY DIFFRACTION100
2.9954-3.22581000000000.15194885X-RAY DIFFRACTION100
3.2258-3.54880.16913650.13744496X-RAY DIFFRACTION100
3.5488-4.05850.15243650.13714564X-RAY DIFFRACTION100
4.0585-5.0991000000000.12094920X-RAY DIFFRACTION100
5.099-19.90670.17163650.14674635X-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)
10.68260.01520.10430.6573-0.00530.72880.0063-0.0773-0.07040.0572-0.02350.04160.0929-0.03620.01890.090.00360.00860.09570.00470.073562.089154.522227.2305
20.9967-0.26320.03041.1473-0.1530.5641-0.01860.00840.1388-0.04670.01120.0751-0.0846-0.03020.00580.09070.0181-0.02140.089-0.0040.116953.199193.30415.4789
30.6878-0.01330.05980.89980.070.75330.0061-0.02130.12290.0452-0.0377-0.0928-0.09810.02910.030.09410.00620.00120.09080.00510.120789.885586.122127.1154
41.0253-0.2216-0.08760.92520.15530.53910.02210.0559-0.0457-0.0107-0.0152-0.10650.04860.0123-0.00530.09070.02570.0070.10.00150.072798.863747.547615.7693
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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