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- PDB-3kda: Crystal structure of the CFTR inhibitory factor Cif with the H269... -

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Basic information

Entry
Database: PDB / ID: 3kda
TitleCrystal structure of the CFTR inhibitory factor Cif with the H269A mutation
ComponentsCFTR inhibitory factor (Cif)
KeywordsHYDROLASE / Alpha/beta hydrolase
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 UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBahl, C.D. / Madden, D.R.
CitationJournal: J.Bacteriol. / Year: 2010
Title: Crystal structure of the cystic fibrosis transmembrane conductance regulator inhibitory factor Cif reveals novel active-site features of an epoxide hydrolase virulence factor.
Authors: Bahl, C.D. / Morisseau, C. / Bomberger, J.M. / Stanton, B.A. / Hammock, B.D. / O'Toole, G.A. / Madden, D.R.
History
DepositionOct 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 12, 2011Group: Other
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: CFTR inhibitory factor (Cif)
C: CFTR inhibitory factor (Cif)
A: CFTR inhibitory factor (Cif)
B: CFTR inhibitory factor (Cif)


Theoretical massNumber of molelcules
Total (without water)136,3914
Polymers136,3914
Non-polymers00
Water20,0151111
1
D: CFTR inhibitory factor (Cif)
C: CFTR inhibitory factor (Cif)


Theoretical massNumber of molelcules
Total (without water)68,1952
Polymers68,1952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-23 kcal/mol
Surface area21120 Å2
MethodPISA
2
A: CFTR inhibitory factor (Cif)
B: CFTR inhibitory factor (Cif)


Theoretical massNumber of molelcules
Total (without water)68,1952
Polymers68,1952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-23 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.960, 83.640, 88.930
Angle α, β, γ (deg.)90.00, 100.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
CFTR inhibitory factor (Cif)


Mass: 34097.633 Da / Num. of mol.: 4 / Mutation: H269A
Source method: isolated from a genetically manipulated source
Details: Secreted protein
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Strain: PA14 / Gene: PA14_26090 / Plasmid: pDMP77 / 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.: 1111 / 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: 45.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG 8000, 0.55M 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: 0.9464 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 27, 2007 / Details: Toroidal focusing mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9464 Å / Relative weight: 1
ReflectionResolution: 1.5→45.98 Å / Num. all: 193185 / Num. obs: 192680 / % possible obs: 99.7 % / Rsym value: 0.063 / Net I/σ(I): 22.59
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 5.25 / Rsym value: 0.314 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: initial model obtained from SAD with selenomethionine labeled Cif

Resolution: 1.5→30.722 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.17 / σ(F): 1.99 / Phase error: 16.38 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.183 9636 5 %
Rwork0.169 183037 -
obs0.17 192673 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.589 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso max: 61.76 Å2 / Biso mean: 14.536 Å2 / Biso min: 3.44 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9512 0 0 1111 10623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059866
X-RAY DIFFRACTIONf_angle_d1.06613397
X-RAY DIFFRACTIONf_dihedral_angle_d17.0943541
X-RAY DIFFRACTIONf_chiral_restr0.0761376
X-RAY DIFFRACTIONf_plane_restr0.0061766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.21923080.19966073X-RAY DIFFRACTION100
1.517-1.53490.23913310.19626085X-RAY DIFFRACTION100
1.5349-1.55360.19543020.18776080X-RAY DIFFRACTION100
1.5536-1.57330.19523090.17786065X-RAY DIFFRACTION100
1.5733-1.5940.19943440.17336082X-RAY DIFFRACTION100
1.594-1.61580.18633060.1756086X-RAY DIFFRACTION100
1.6158-1.63890.19713090.17356115X-RAY DIFFRACTION100
1.6389-1.66340.19783550.16776033X-RAY DIFFRACTION100
1.6634-1.68930.19323220.17226069X-RAY DIFFRACTION100
1.6893-1.7170.1863550.16566077X-RAY DIFFRACTION100
1.717-1.74660.19013350.16736078X-RAY DIFFRACTION100
1.7466-1.77840.19182810.1656138X-RAY DIFFRACTION100
1.7784-1.81260.18323520.16116059X-RAY DIFFRACTION100
1.8126-1.84960.18473330.16286111X-RAY DIFFRACTION100
1.8496-1.88980.19633300.16616050X-RAY DIFFRACTION100
1.8898-1.93380.18453500.16576071X-RAY DIFFRACTION100
1.9338-1.98210.19813240.16776038X-RAY DIFFRACTION100
1.9821-2.03570.16713240.1616157X-RAY DIFFRACTION100
2.0357-2.09560.17663270.15956080X-RAY DIFFRACTION100
2.0956-2.16320.18553230.15926075X-RAY DIFFRACTION100
2.1632-2.24050.18512930.16026125X-RAY DIFFRACTION100
2.2405-2.33020.16573110.16046117X-RAY DIFFRACTION100
2.3302-2.43620.17232920.16716137X-RAY DIFFRACTION100
2.4362-2.56460.16862990.16756121X-RAY DIFFRACTION100
2.5646-2.72520.17043130.16856132X-RAY DIFFRACTION100
2.7252-2.93540.19143350.17166111X-RAY DIFFRACTION100
2.9354-3.23050.19283200.1726155X-RAY DIFFRACTION100
3.2305-3.69730.1583110.1526156X-RAY DIFFRACTION100
3.6973-4.65560.14613340.14176149X-RAY DIFFRACTION100
4.6556-30.72810.1533080.17076212X-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)
10.4822-0.1588-0.09160.20730.10790.1786-0.0210.0319-0.04060.01030.0091-0.02180.0153-0.00310.01030.01730.02370.00670.0368-0.00350.050714.6798-5.800115.6305
20.08910.01960.00450.3528-0.06250.31550.01510.00220.01570.0321-0.0268-0.0467-0.03670.02030.01280.02720.0065-0.00550.0343-0.00460.07685.984433.871427.0672
30.09710.06780.02950.33680.11270.32060.0031-0.01310.02460.0383-0.0280.03710.0382-0.02150.02230.02090.00290.01450.03830.00380.046-22.09410.603327.1173
40.4851-0.42550.11050.2401-0.05990.254-0.0381-0.01660.057-0.0120.027-0.0073-0.0364-0.02120.0130.02410.0186-0.01610.0285-0.00530.0981-30.970640.272515.4238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 25:319)D25 - 319
2X-RAY DIFFRACTION2(chain B and resid 25:319)C25 - 319
3X-RAY DIFFRACTION3(chain C and resid 25:319)A25 - 319
4X-RAY DIFFRACTION4(chain D and resid 25:319)B25 - 319

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