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- PDB-3kd2: Crystal structure of the CFTR inhibitory factor Cif -

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Basic information

Entry
Database: PDB / ID: 3kd2
TitleCrystal structure of the CFTR inhibitory factor Cif
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: 1.8 Å
AuthorsBahl, C.D. / Madden, D.R.
Citation
Journal: 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.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Purification, crystallization and preliminary X-ray diffraction analysis of Cif, a virulence factor secreted by Pseudomonas aeruginosa.
Authors: Bahl, C.D. / MacEachran, D.P. / 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 1.3Nov 27, 2024Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)136,6594
Polymers136,6594
Non-polymers00
Water15,799877
1
A: CFTR inhibitory factor (Cif)
B: CFTR inhibitory factor (Cif)


Theoretical massNumber of molelcules
Total (without water)68,3292
Polymers68,3292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-23 kcal/mol
Surface area20780 Å2
MethodPISA
2
D: CFTR inhibitory factor (Cif)
C: CFTR inhibitory factor (Cif)


Theoretical massNumber of molelcules
Total (without water)68,3292
Polymers68,3292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-23 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.181, 83.887, 88.977
Angle α, β, γ (deg.)90.00, 100.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
CFTR inhibitory factor (Cif)


Mass: 34164.699 Da / Num. of mol.: 4
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: pDPM73 / 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.: 877 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
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: 0.9787 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 17, 2007 / Details: Toroidal focusing mirror
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.8→29.55 Å / Num. obs: 112393 / % possible obs: 99.8 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.49
Reflection shellResolution: 1.8→1.87 Å / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 5.16 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.553 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.2 / σ(F): 2 / Phase error: 16.62 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.182 5733 5.1 %
Rwork0.167 21452 -
obs0.167 112388 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.689 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 64.99 Å2 / Biso mean: 15.328 Å2 / Biso min: 1.95 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9352 0 0 877 10229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049737
X-RAY DIFFRACTIONf_angle_d0.82513229
X-RAY DIFFRACTIONf_dihedral_angle_d16.9333515
X-RAY DIFFRACTIONf_chiral_restr0.061362
X-RAY DIFFRACTIONf_plane_restr0.0041745
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8210.2043694369599
1.82-1.8420.1913723100
1.842-1.8640.1843727100
1.864-1.8880.2227620.18629543716100
1.888-1.9120.1873765100
1.912-1.9390.183689100
1.939-1.9660.2044710.17432873758100
1.966-1.9960.2021910.17435643755100
1.996-2.0270.1753708100
2.027-2.060.1951660.16935553721100
2.06-2.0950.1864230.16732923715100
2.095-2.1340.1623755100
2.134-2.1750.1815260.16532123738100
2.175-2.2190.1683760100
2.219-2.2670.165372099
2.267-2.320.1795020.16232243726100
2.32-2.3780.1653729100
2.378-2.4420.1924170.16733253742100
2.442-2.5140.1653730100
2.514-2.5950.1733830.16433763759100
2.595-2.6880.1673779100
2.688-2.7950.1753320.16634113743100
2.795-2.9220.1782740.16834693743100
2.922-3.0760.1793755100
3.076-3.2690.2042400.16435293769100
3.269-3.5210.172340.1535373771100
3.521-3.8750.1591950.1535673762100
3.875-4.4340.1741670.13536183785100
4.434-5.580.1212190.13935893808100
5.58-29.5570.1662300.1733612384299
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)
1-0.04390.01690.00090.1654-0.00850.010.0051-0.0152-0.01760.0214-0.02060.04660.0315-0.0237-0.0030.00310.00770.00670.03180.00590.0614-22.11453.999927.0274
2-0.0290.01760.00210.172-0.0021-0.0010.0199-0.0129-0.02850.00690.0151-0.08610.0165-0.00560.0013-0.08860.10560.0286-0.0339-0.0190.070814.561747.389115.5425
3-0.03610.0121-0.00750.17040.0002-0.0015-0.0167-0.00990.0515-0.02090.01430.0618-0.0098-0.01210.001-0.09350.0979-0.0278-0.04070.00640.1153-30.95599.322315.4493
4-0.04850.019-0.00470.16110.00360.00750.00780.00540.01830.019-0.0227-0.0601-0.02530.01440.0030.00490.01470.00280.0141-0.00070.08995.97912.849826.8201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 25:317)A25 - 317
2X-RAY DIFFRACTION2(chain B and resid 25:317)D25 - 317
3X-RAY DIFFRACTION3(chain C and resid 25:317)B25 - 317
4X-RAY DIFFRACTION4(chain D and resid 25:317)C25 - 317

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