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

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Basic information

Entry
Database: PDB / ID: 4dln
TitleCrystal structure of the CFTR inhibitory factor Cif with the D129S 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: 1.55 Å
AuthorsBahl, C.D. / Amacher, J.F. / 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 6, 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 1.5Nov 20, 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)136,5474
Polymers136,5474
Non-polymers00
Water22,0501224
1
A: Putative hydrolase
B: Putative hydrolase


Theoretical massNumber of molelcules
Total (without water)68,2732
Polymers68,2732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-23 kcal/mol
Surface area20870 Å2
MethodPISA
2
C: Putative hydrolase
D: Putative hydrolase


Theoretical massNumber of molelcules
Total (without water)68,2732
Polymers68,2732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-23 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.174, 83.953, 89.169
Angle α, β, γ (deg.)90.00, 100.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-676-

HOH

21C-678-

HOH

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Components

#1: Protein
Putative hydrolase


Mass: 34136.691 Da / Num. of mol.: 4 / Fragment: Cif (UNP Residues 25-319) / Mutation: D129S
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.: 1224 / 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: 45.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 16% 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: 1.55→46.087 Å / Num. obs: 173094 / % possible obs: 98 % / Redundancy: 4.2 % / Rsym value: 0.056 / Net I/σ(I): 16.9
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 12570 / Rsym value: 0.284 / % possible all: 96.7

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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: 1.55→46.087 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 15.48 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1759 8686 5.02 %thin shells
Rwork0.1593 ---
obs0.1602 173079 98.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.766 Å2 / ksol: 0.374 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7139 Å2-0 Å20.3504 Å2
2---0.9305 Å2-0 Å2
3---1.6444 Å2
Refinement stepCycle: LAST / Resolution: 1.55→46.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9484 0 0 1224 10708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069860
X-RAY DIFFRACTIONf_angle_d1.08313394
X-RAY DIFFRACTIONf_dihedral_angle_d12.9353600
X-RAY DIFFRACTIONf_chiral_restr0.0781378
X-RAY DIFFRACTIONf_plane_restr0.0051763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.56760.20354280.17155278X-RAY DIFFRACTION97
1.5676-1.58611000000000.16665661X-RAY DIFFRACTION97
1.5861-1.60540.19254350.16415198X-RAY DIFFRACTION97
1.6054-1.62570.19534340.16315294X-RAY DIFFRACTION97
1.6257-1.64711000000000.1595721X-RAY DIFFRACTION97
1.6471-1.66970.18454330.15545210X-RAY DIFFRACTION97
1.6697-1.69360.18484300.15275224X-RAY DIFFRACTION97
1.6936-1.71881000000000.15685766X-RAY DIFFRACTION97
1.7188-1.74570.19814340.15765310X-RAY DIFFRACTION98
1.7457-1.77430.18314310.15625278X-RAY DIFFRACTION97
1.7743-1.80491000000000.14765713X-RAY DIFFRACTION98
1.8049-1.83770.18014310.15295249X-RAY DIFFRACTION97
1.8377-1.87310.17574320.15395287X-RAY DIFFRACTION97
1.8731-1.91131000000000.15185786X-RAY DIFFRACTION98
1.9113-1.95290.16854310.1495316X-RAY DIFFRACTION98
1.9529-1.99830.18414330.15125320X-RAY DIFFRACTION98
1.9983-2.04831000000000.14935797X-RAY DIFFRACTION98
2.0483-2.10370.16874350.14785296X-RAY DIFFRACTION98
2.1037-2.16560.16714310.14785356X-RAY DIFFRACTION98
2.1656-2.23551000000000.15185823X-RAY DIFFRACTION99
2.2355-2.31530.18064350.15275328X-RAY DIFFRACTION99
2.3153-2.4080.18964360.15775413X-RAY DIFFRACTION99
2.408-2.51761000000000.15745764X-RAY DIFFRACTION99
2.5176-2.65040.15964380.15695386X-RAY DIFFRACTION99
2.6504-2.81640.16674380.15165414X-RAY DIFFRACTION99
2.8164-3.03381000000000.16415884X-RAY DIFFRACTION99
3.0338-3.3390.16044400.15495424X-RAY DIFFRACTION99
3.339-3.8220.1434410.14085462X-RAY DIFFRACTION99
3.822-4.81451000000000.1315892X-RAY DIFFRACTION99
4.8145-46.10780.15584400.16195543X-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)
10.28430.06430.04020.5652-0.01090.41030.0128-0.01290.04760.0267-0.027-0.0474-0.04940.0103-00.02680.00760.00440.0236-0.00060.03675.684641.054527.1069
20.5684-0.1584-0.01090.60360.14080.32250.01890.0174-0.0242-0.01970.0072-0.08730.02280.007400.03150.020.00680.0335-0.00040.019214.80791.168415.6506
30.34120.040.08740.37890.09580.44040.0153-0.0552-0.03460.031-0.02740.02210.0547-0.0487-00.02670.00280.00520.04240.00520.0163-21.96487.996827.2913
40.7111-0.2658-0.04230.6212-0.08250.2502-0.01130.00720.1072-0.03210.00940.0125-0.0355-0.001300.03380.0172-0.01960.0282-0.00550.0515-30.966947.644715.6348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:321)
2X-RAY DIFFRACTION2(chain B and resid 25:322)
3X-RAY DIFFRACTION3(chain C and resid 25:321)
4X-RAY DIFFRACTION4(chain D and resid 25:320)

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