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- PDB-5hk9: Crystal structure of the CFTR inhibitory factor Cif bound to a ur... -

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Basic information

Entry
Database: PDB / ID: 5hk9
TitleCrystal structure of the CFTR inhibitory factor Cif bound to a urea inhibitor
ComponentsCFTR inhibitory factor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Bacterial Epoxide Hydrolase / Inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
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
Chem-64O / Putative hydrolase / CFTR inhibitory factor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHvorecny, K.L. / Madden, D.R.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Rational Design of Potent and Selective Inhibitors of an Epoxide Hydrolase Virulence Factor from Pseudomonas aeruginosa.
Authors: Kitamura, S. / Hvorecny, K.L. / Niu, J. / Hammock, B.D. / Madden, D.R. / Morisseau, C.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CFTR inhibitory factor
B: CFTR inhibitory factor
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,0407
Polymers136,6594
Non-polymers1,3813
Water20,3571130
1
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2504
Polymers68,3292
Non-polymers9212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-23 kcal/mol
Surface area20630 Å2
MethodPISA
2
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7903
Polymers68,3292
Non-polymers4601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-23 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.270, 84.066, 89.153
Angle α, β, γ (deg.)90.00, 100.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-689-

HOH

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Components

#1: Protein
CFTR inhibitory factor /


Mass: 34164.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: PA14_26090 / Plasmid: pDPM73 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: A0A0M3KL26, UniProt: A0A0H2ZD27*PLUS
#2: Chemical ChemComp-64O / N-(4-{[4'-(carbamoylamino)-6-hydroxybiphenyl-3-yl]oxy}-3,5-dichlorophenyl)propanamide


Mass: 460.310 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H19Cl2N3O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1130 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 8000, Calcium Chloride, Sodium Acetate, Dimethylsulfoxide

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.8→19.828 Å / Num. obs: 111909 / % possible obs: 98.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.26 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
XDSJanuary 10, 2014data reduction
XDSJanuary 10, 2014data scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 1.8→19.828 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1977 5589 4.99 %
Rwork0.1687 --
obs0.1701 111894 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.787 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5586 Å2-0 Å20.2732 Å2
2---4.4863 Å20 Å2
3---3.9278 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9447 0 93 1130 10670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079947
X-RAY DIFFRACTIONf_angle_d1.11513527
X-RAY DIFFRACTIONf_dihedral_angle_d13.9663640
X-RAY DIFFRACTIONf_chiral_restr0.0781380
X-RAY DIFFRACTIONf_plane_restr0.0061780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82040.29182750.26673487X-RAY DIFFRACTION98
1.8204-1.84191000000000.25733609X-RAY DIFFRACTION97
1.8419-1.86430.27882770.24343373X-RAY DIFFRACTION97
1.8643-1.88790.2862800.2343446X-RAY DIFFRACTION98
1.8879-1.91271000000000.21513684X-RAY DIFFRACTION98
1.9127-1.93890.23462770.19353374X-RAY DIFFRACTION98
1.9389-1.96660.22232740.18463435X-RAY DIFFRACTION98
1.9666-1.99591000000000.18143681X-RAY DIFFRACTION98
1.9959-2.0270.2152750.17683417X-RAY DIFFRACTION98
2.027-2.06020.21442770.17373422X-RAY DIFFRACTION98
2.0602-2.09571000000000.17383728X-RAY DIFFRACTION98
2.0957-2.13380.20852790.16393371X-RAY DIFFRACTION98
2.1338-2.17480.19962770.16663460X-RAY DIFFRACTION98
2.1748-2.21911000000000.16793717X-RAY DIFFRACTION99
2.2191-2.26730.18082810.16643453X-RAY DIFFRACTION98
2.2673-2.320.19852790.16753407X-RAY DIFFRACTION98
2.32-2.37791000000000.16373729X-RAY DIFFRACTION99
2.3779-2.44210.20992830.16813446X-RAY DIFFRACTION98
2.4421-2.51380.19712800.17373421X-RAY DIFFRACTION98
2.5138-2.59481000000000.16923768X-RAY DIFFRACTION99
2.5948-2.68730.20262830.17063462X-RAY DIFFRACTION99
2.6873-2.79460.20252810.16283484X-RAY DIFFRACTION99
2.7946-2.92141000000000.16753766X-RAY DIFFRACTION99
2.9214-3.07490.20882800.17223468X-RAY DIFFRACTION99
3.0749-3.26680.18222820.15963473X-RAY DIFFRACTION99
3.2668-3.51771000000000.15283796X-RAY DIFFRACTION99
3.5177-3.86930.15692820.14883480X-RAY DIFFRACTION99
3.8693-4.42380.14882830.13353523X-RAY DIFFRACTION99
4.4238-5.55321000000000.14083818X-RAY DIFFRACTION99
5.5532-19.82930.20452840.18643607X-RAY DIFFRACTION100
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)
10.79710.08470.00650.9756-0.07760.9246-0.0119-0.066-0.07020.0788-0.01730.03920.1123-0.02270.02740.0770.00430.01220.0715-0.00030.0605-22.125611.565627.2932
21.1341-0.3946-0.1311.2552-0.04440.579-0.00040.00710.1518-0.03740.01270.0006-0.0752-0.0223-0.00990.06580.0084-0.01540.0669-0.00290.079-31.283151.243115.6453
30.75940.08570.0911.07740.13650.9371-0.0162-0.03380.09880.0492-0.0127-0.0713-0.09550.03820.02390.06920.0076-0.00490.06180.00410.08865.774544.335526.9085
41.0615-0.2340.12681.11050.06570.41330.01710.0187-0.0646-0.037-0.0027-0.06610.04820.0144-0.01290.07320.01630.01130.0767-0.00140.049914.83934.81315.5853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:320)
2X-RAY DIFFRACTION2(chain B and resid 25:321)
3X-RAY DIFFRACTION3(chain C and resid 25:317)
4X-RAY DIFFRACTION4(chain D and resid 25:321)

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