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

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Basic information

Entry
Database: PDB / ID: 5hka
TitleCrystal structure of the CFTR inhibitory factor Cif bound to an amide inhibitor
ComponentsCFTR inhibitory factor
KeywordsHydrolase/Hydrolase inhibitor / Bacterial Epoxide Hydrolase / Inhibitor / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


soluble epoxide hydrolase / epoxide hydrolase activity / host cell / extracellular region
Similarity search - Function
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-64N / CFTR inhibitory factor / CFTR inhibitory factor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 / diffrn_radiation_wavelength / 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
Revision 1.3Nov 20, 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
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)138,4408
Polymers136,6594
Non-polymers1,7814
Water13,565753
1
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2204
Polymers68,3292
Non-polymers8912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-24 kcal/mol
Surface area20600 Å2
MethodPISA
2
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2204
Polymers68,3292
Non-polymers8912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-22 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.971, 83.711, 88.879
Angle α, β, γ (deg.)90.00, 100.68, 90.00
Int Tables number5
Space group name H-MC121

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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-64N / 5'-[2,6-dichloro-4-(propanoylamino)phenoxy]-2'-hydroxybiphenyl-4-carboxamide


Mass: 445.295 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H18Cl2N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 45.58 %
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: 2.05→20 Å / Num. obs: 75324 / % possible obs: 98.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 15.25
Reflection shellResolution: 2.05→2.08 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 3.53 / % possible all: 97.2

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Processing

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

3kd2


Resolution: 2.05→19.967 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1974 3764 5 %
Rwork0.1621 --
obs0.1639 75318 98.62 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.269 Å2 / ksol: 0.395 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6854 Å2-0 Å20.3962 Å2
2---2.3175 Å20 Å2
3---3.0029 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9422 0 120 753 10295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079914
X-RAY DIFFRACTIONf_angle_d1.12913473
X-RAY DIFFRACTIONf_dihedral_angle_d14.6023631
X-RAY DIFFRACTIONf_chiral_restr0.0761367
X-RAY DIFFRACTIONf_plane_restr0.0051771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07590.21681840.20052541X-RAY DIFFRACTION97
2.0759-2.10321000000000.19782760X-RAY DIFFRACTION98
2.1032-2.1320.22681890.18592563X-RAY DIFFRACTION98
2.132-2.16240.25831860.18552550X-RAY DIFFRACTION98
2.1624-2.19470.25181860.18352592X-RAY DIFFRACTION98
2.1947-2.22891000000000.17672764X-RAY DIFFRACTION98
2.2289-2.26540.22491830.16872577X-RAY DIFFRACTION98
2.2654-2.30440.25391880.17712576X-RAY DIFFRACTION98
2.3044-2.34630.22961870.17162581X-RAY DIFFRACTION98
2.3463-2.39131000000000.17432775X-RAY DIFFRACTION99
2.3913-2.440.20751880.16552578X-RAY DIFFRACTION98
2.44-2.4930.19761880.16332601X-RAY DIFFRACTION99
2.493-2.55090.19931870.1752607X-RAY DIFFRACTION99
2.5509-2.61451000000000.16852801X-RAY DIFFRACTION99
2.6145-2.68510.21881890.15882578X-RAY DIFFRACTION99
2.6851-2.76390.17571890.14912590X-RAY DIFFRACTION99
2.7639-2.85290.18881900.15922614X-RAY DIFFRACTION99
2.8529-2.95451000000000.16752800X-RAY DIFFRACTION99
2.9545-3.07240.21491890.17542580X-RAY DIFFRACTION99
3.0724-3.21170.21681900.15882627X-RAY DIFFRACTION99
3.2117-3.38020.1805530.15462755X-RAY DIFFRACTION99
3.3802-3.59090.19911360.15672678X-RAY DIFFRACTION99
3.5909-3.86630.18411910.15532614X-RAY DIFFRACTION99
3.8663-4.2520.15491900.14012645X-RAY DIFFRACTION99
4.252-4.85951000000000.12232822X-RAY DIFFRACTION99
4.8595-6.09340.14291900.16862662X-RAY DIFFRACTION99
6.0934-19.96770.20261910.17542723X-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)
10.77110.1765-0.00211.0027-0.00380.9645-0.0294-0.0811-0.07890.0883-0.01990.02970.1180.00160.04870.10410.01090.01540.09410.00330.0812-22.044811.674427.179
21.0197-0.3592-0.1671.2219-0.06940.6266-0.00210.01420.1522-0.03160.0160.0347-0.083-0.0358-0.010.08260.0118-0.02260.09380.00040.1192-31.094550.993815.4655
30.69720.08480.07461.28290.16611.0194-0.011-0.03150.0880.0733-0.0279-0.0828-0.1020.02210.03870.09360.0099-0.0040.09240.00970.10615.644544.498226.8302
40.8146-0.12020.12120.98970.16980.57660.0270.0256-0.0638-0.0522-0.0051-0.08670.03520.0109-0.01730.08890.0220.01570.09910.00180.074114.83565.109315.5722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:321)
2X-RAY DIFFRACTION2(chain B and resid 25:317)
3X-RAY DIFFRACTION3(chain C and resid 25:317)
4X-RAY DIFFRACTION4(chain D and resid 25:321)

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