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- PDB-4ehb: Crystal structure of the CFTR inhibitory factor Cif with the D129... -

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Basic information

Entry
Database: PDB / ID: 4ehb
TitleCrystal structure of the CFTR inhibitory factor Cif with the D129S mutation bound to epoxyhexane
ComponentsPutative hydrolase
KeywordsHYDROLASE / Alpha Beta Hydrolase / Epoxide Hydrolase / secreted
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)-2-butyloxirane / Putative hydrolase / Putative hydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PDB ENTRY 3KD2 CHAIN A / Resolution: 1.85 Å
AuthorsHvorecny, K.L. / Bahl, C.D. / Madden, D.R.
CitationJournal: Biochemistry / Year: 2016
Title: Visualizing the Mechanism of Epoxide Hydrolysis by the Bacterial Virulence Enzyme Cif.
Authors: Bahl, C.D. / Hvorecny, K.L. / Morisseau, C. / Gerber, S.A. / Madden, D.R.
History
DepositionApr 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Feb 24, 2016Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative hydrolase
B: Putative hydrolase
C: Putative hydrolase
D: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,9478
Polymers136,5474
Non-polymers4014
Water19,0781059
1
A: Putative hydrolase
B: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4744
Polymers68,2732
Non-polymers2002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-22 kcal/mol
Surface area20580 Å2
MethodPISA
2
C: Putative hydrolase
D: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4744
Polymers68,2732
Non-polymers2002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-22 kcal/mol
Surface area20840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.430, 83.920, 88.740
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
11A-594-

HOH

21A-612-

HOH

31D-691-

HOH

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Components

#1: Protein
Putative hydrolase


Mass: 34136.691 Da / Num. of mol.: 4 / Fragment: Cif / Mutation: D129S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA14 / Gene: PA14_26090 / Plasmid: pMQ70 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q02P97, UniProt: A0A0H2ZD27*PLUS
#2: Chemical
ChemComp-0PZ / (2R)-2-butyloxirane


Mass: 100.159 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1059 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 13% PEG 8000, 0.125M calcium chloride, 0.1M sodium acetate, 0.02M epoxyhexane, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→43.43 Å / Num. obs: 99966 / % possible obs: 96.9 % / Redundancy: 5.8 % / Rsym value: 0.072 / Net I/σ(I): 18.1
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 7549 / Rsym value: 0.392 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: PDB ENTRY 3KD2 CHAIN A / Resolution: 1.85→43.43 Å / SU ML: 0.24 / σ(F): 1.99 / Phase error: 20.82 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 4990 4.99 %thin shells
Rwork0.1771 ---
obs0.1789 99957 96.95 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.4 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.8184 Å2-0 Å2-0.2477 Å2
2---2.3618 Å20 Å2
3---8.1802 Å2
Refinement stepCycle: LAST / Resolution: 1.85→43.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9464 0 28 1059 10551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610002
X-RAY DIFFRACTIONf_angle_d1.03613600
X-RAY DIFFRACTIONf_dihedral_angle_d16.2633710
X-RAY DIFFRACTIONf_chiral_restr0.0751397
X-RAY DIFFRACTIONf_plane_restr0.0051794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.87110.29712490.23773018X-RAY DIFFRACTION96
1.8711-1.89311000000000.2343250X-RAY DIFFRACTION96
1.8931-1.91620.30082480.22823053X-RAY DIFFRACTION96
1.9162-1.94040.26692440.21153065X-RAY DIFFRACTION96
1.9404-1.96591000000000.19273264X-RAY DIFFRACTION96
1.9659-1.99290.25822470.19363057X-RAY DIFFRACTION96
1.9929-2.02140.25612520.1853041X-RAY DIFFRACTION97
2.0214-2.05151000000000.18623280X-RAY DIFFRACTION96
2.0515-2.08360.22572480.18073071X-RAY DIFFRACTION97
2.0836-2.11770.22492510.17433036X-RAY DIFFRACTION96
2.1177-2.15431000000000.17373325X-RAY DIFFRACTION96
2.1543-2.19340.21862520.17413056X-RAY DIFFRACTION97
2.1934-2.23560.25582530.17733065X-RAY DIFFRACTION97
2.2356-2.28121000000000.18033345X-RAY DIFFRACTION97
2.2812-2.33080.23692500.1723057X-RAY DIFFRACTION97
2.3308-2.38510.2412480.1833048X-RAY DIFFRACTION97
2.3851-2.44471000000000.17573335X-RAY DIFFRACTION97
2.4447-2.51080.23052490.17733069X-RAY DIFFRACTION97
2.5108-2.58470.22122510.17073088X-RAY DIFFRACTION97
2.5847-2.66811000000000.17413379X-RAY DIFFRACTION97
2.6681-2.76340.20992490.17293086X-RAY DIFFRACTION97
2.7634-2.8740.21292480.17313105X-RAY DIFFRACTION97
2.874-3.00481000000000.17633344X-RAY DIFFRACTION98
3.0048-3.16320.212500.17413148X-RAY DIFFRACTION98
3.1632-3.36130.18712480.16983105X-RAY DIFFRACTION97
3.3613-3.62071000000000.16933383X-RAY DIFFRACTION98
3.6207-3.98490.18812560.16823129X-RAY DIFFRACTION98
3.9849-4.56090.14842510.1423146X-RAY DIFFRACTION98
4.5609-5.74421000000000.15243398X-RAY DIFFRACTION98
5.7442-43.44160.20642460.22583221X-RAY DIFFRACTION97
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)
10.1867-0.02350.07480.1354-0.02050.17150.01770.0229-0.0405-0.0028-0.0211-0.01430.0320.03170.00160.0502-0.0075-0.00280.049300.029121.980512.1571-27.0419
20.04010.0216-0.00340.06230.01440.0397-0.0039-0.00790.0450.0050.0065-0.0137-0.01550.00460.00610.0561-0.053-0.01850.0544-0.00190.06830.788451.8044-15.4811
30.10580.01320.01710.150.01060.12820.01590.01060.0479-0.004-0.02820.0333-0.0222-0.00840.00640.046-0.00960.01170.03960.00070.0441-5.860644.8752-27.0292
40.07230.0271-0.02790.087-0.0240.0248-0.0006-0.0079-0.00670.00340.01040.03190.00910.00030.03090.057-0.04780.00790.05370.00910.0314-14.77745.3269-15.5223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:319)
2X-RAY DIFFRACTION2(chain B and resid 25:321)
3X-RAY DIFFRACTION3(chain C and resid 25:321)
4X-RAY DIFFRACTION4(chain D and resid 25:321)

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