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- PDB-4dm7: Crystal structure of the CFTR inhibitory factor Cif with the E153... -

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Basic information

Entry
Database: PDB / ID: 4dm7
TitleCrystal structure of the CFTR inhibitory factor Cif with the E153D mutation
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
Putative hydrolase / Putative hydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsBahl, C.D. / Madden, D.R.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Inhibiting an Epoxide Hydrolase Virulence Factor from Pseudomonas aeruginosa Protects CFTR.
Authors: Bahl, C.D. / Hvorecny, K.L. / Bomberger, J.M. / Stanton, B.A. / Hammock, B.D. / Morisseau, C. / Madden, D.R.
History
DepositionFeb 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 16, 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: Putative hydrolase
B: Putative hydrolase
C: Putative hydrolase
D: Putative hydrolase


Theoretical massNumber of molelcules
Total (without water)136,6034
Polymers136,6034
Non-polymers00
Water17,781987
1
A: Putative hydrolase
B: Putative hydrolase


Theoretical massNumber of molelcules
Total (without water)68,3012
Polymers68,3012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-24 kcal/mol
Surface area20710 Å2
MethodPISA
2
C: Putative hydrolase
D: Putative hydrolase


Theoretical massNumber of molelcules
Total (without water)68,3012
Polymers68,3012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-24 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.353, 84.138, 89.166
Angle α, β, γ (deg.)90.00, 100.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-587-

HOH

21A-656-

HOH

31C-626-

HOH

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Components

#1: Protein
Putative hydrolase


Mass: 34150.676 Da / Num. of mol.: 4 / Fragment: Cif (UNP Residues 25-319) / Mutation: E153D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: PA14_26090 / Plasmid: pMQ70 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q02P97, UniProt: A0A0H2ZD27*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 987 / 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: 45.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 14% PEG 8000, 0.125M calcium chloride, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9782 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 2, 2009 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 1.36→44.07 Å / Num. all: 261685 / Num. obs: 258302 / % possible obs: 98.7 % / Redundancy: 5.8 % / Rsym value: 0.075 / Net I/σ(I): 13.6
Reflection shellResolution: 1.36→1.45 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 44425 / Rsym value: 0.454 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAIN A OF PDB ENTRY 3KD2

3kd2


Resolution: 1.36→43.662 Å / SU ML: 0.21 / σ(F): 2 / Phase error: 20.52 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.223 12908 5 %thin shells
Rwork0.2118 ---
obs0.2124 258287 98.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.751 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2833 Å2-0 Å2-0.0509 Å2
2---0.6076 Å2-0 Å2
3---2.8909 Å2
Refinement stepCycle: LAST / Resolution: 1.36→43.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9402 0 0 987 10389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069751
X-RAY DIFFRACTIONf_angle_d1.06213244
X-RAY DIFFRACTIONf_dihedral_angle_d12.3363556
X-RAY DIFFRACTIONf_chiral_restr0.0761366
X-RAY DIFFRACTIONf_plane_restr0.0051743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.37550.26536330.23897746X-RAY DIFFRACTION97
1.3755-1.39161000000000.23428532X-RAY DIFFRACTION97
1.3916-1.40860.24656350.22747822X-RAY DIFFRACTION97
1.4086-1.42640.24146400.22577858X-RAY DIFFRACTION98
1.4264-1.44521000000000.22098470X-RAY DIFFRACTION98
1.4452-1.4650.22946400.20947864X-RAY DIFFRACTION98
1.465-1.48590.23626410.21687878X-RAY DIFFRACTION98
1.4859-1.50811000000000.21518468X-RAY DIFFRACTION98
1.5081-1.53170.24096400.20777948X-RAY DIFFRACTION98
1.5317-1.55680.23616370.20417895X-RAY DIFFRACTION98
1.5568-1.58371000000000.20568543X-RAY DIFFRACTION98
1.5837-1.61250.23586480.20037903X-RAY DIFFRACTION98
1.6125-1.64350.21976430.19667933X-RAY DIFFRACTION99
1.6435-1.6771000000000.19398599X-RAY DIFFRACTION99
1.677-1.71350.21996510.19247969X-RAY DIFFRACTION99
1.7135-1.75330.21816420.19617927X-RAY DIFFRACTION99
1.7533-1.79721000000000.19478619X-RAY DIFFRACTION99
1.7972-1.84580.2086490.1878005X-RAY DIFFRACTION99
1.8458-1.90010.21246490.1957941X-RAY DIFFRACTION99
1.9001-1.96141000000000.19418657X-RAY DIFFRACTION99
1.9614-2.03150.20676530.19398020X-RAY DIFFRACTION100
2.0315-2.11290.20786440.19278036X-RAY DIFFRACTION99
2.1129-2.2091000000000.1978677X-RAY DIFFRACTION100
2.209-2.32550.21456530.19168058X-RAY DIFFRACTION100
2.3255-2.47120.21556540.19988080X-RAY DIFFRACTION100
2.4712-2.66191000000000.20248697X-RAY DIFFRACTION100
2.6619-2.92980.21226540.2058085X-RAY DIFFRACTION100
2.9298-3.35360.21276520.20798125X-RAY DIFFRACTION100
3.3536-4.22461000000000.19718789X-RAY DIFFRACTION100
4.2246-43.68450.19396500.21788235X-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)
10.3876-0.0420.00550.3429-0.02280.28270.02180.02850.0601-0.0158-0.01980.034-0.0307-0.007200.0393-0.00230.00330.04010.00830.0409-5.8453-37.2415-27.0427
20.5260.1978-0.03310.4355-0.10990.27310.0091-0.0212-0.0210.02230.00610.07130.0417-0.016800.0424-0.01920.00580.03870.00450.0338-14.6969-76.6236-15.6315
30.3861-0.0220.0490.25890.02620.31580.02390.0373-0.0546-0.0091-0.018-0.02260.03750.0103-00.0387-0.00270.00050.0372-0.00920.030922.0442-70.1291-27.2248
40.47610.2120.05380.47910.08940.30.0029-0.02460.05760.03930.0012-0.0436-0.04130.017200.0426-0.0191-0.00930.04-0.00460.051630.8881-30.6836-15.6301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:320)
2X-RAY DIFFRACTION2(chain B and resid 25:318)
3X-RAY DIFFRACTION3(chain C and resid 25:320)
4X-RAY DIFFRACTION4(chain D and resid 25:317)

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