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- PDB-5tns: Crystal structure of the D129S mutant of the CFTR inhibitory fact... -

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Basic information

Entry
Database: PDB / ID: 5tns
TitleCrystal structure of the D129S mutant of the CFTR inhibitory factor Cif containing 1,2-Epoxycyclohexane
ComponentsCFTR inhibitory factor
Keywordshydrolase/hydrolase inhibitor / epoxide hydrolase / hydroxyalkyl-enzyme intermediate / 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
(1R,6S)-7-oxabicyclo[4.1.0]heptane / Putative hydrolase / CFTR inhibitory factor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHvorecny, K.L. / Madden, D.R.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI091699 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM113132 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106394 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK097154 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008704 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES002710 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES004699 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES024806 United States
Cystic Fibrosis FoundationSTANTO19R0 United States
CitationJournal: Structure / Year: 2017
Title: Active-Site Flexibility and Substrate Specificity in a Bacterial Virulence Factor: Crystallographic Snapshots of an Epoxide Hydrolase.
Authors: Hvorecny, K.L. / Bahl, C.D. / Kitamura, S. / Lee, K.S.S. / Hammock, B.D. / Morisseau, C. / Madden, D.R.
History
DepositionOct 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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)136,6455
Polymers136,5474
Non-polymers981
Water19,5101083
1
A: CFTR inhibitory factor
B: CFTR inhibitory factor


Theoretical massNumber of molelcules
Total (without water)68,2732
Polymers68,2732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-23 kcal/mol
Surface area21110 Å2
MethodPISA
2
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3723
Polymers68,2732
Non-polymers981
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-24 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.944, 83.690, 89.175
Angle α, β, γ (deg.)90.00, 100.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
CFTR inhibitory factor


Mass: 34136.691 Da / Num. of mol.: 4 / Mutation: D129S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: PA14_26090 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: A0A0M3KL26, UniProt: A0A0H2ZD27*PLUS
#2: Chemical ChemComp-7EX / (1R,6S)-7-oxabicyclo[4.1.0]heptane


Mass: 98.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1083 / 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: 45.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: sodium acetate, pH5 calcium chloride PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→46.158 Å / Num. obs: 120855 / % possible obs: 97.6 % / Redundancy: 5.75 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 20.76
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 5.79 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 5.24 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSDec 6, 2010data reduction
XDSDec 6, 2010data scaling
PHENIX1.10_2155: ???phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 1.75→39.233 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1832 5930 5.02 %
Rwork0.1512 --
obs0.1528 118202 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→39.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9453 0 7 1083 10543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069902
X-RAY DIFFRACTIONf_angle_d0.81113476
X-RAY DIFFRACTIONf_dihedral_angle_d15.0095882
X-RAY DIFFRACTIONf_chiral_restr0.0521390
X-RAY DIFFRACTIONf_plane_restr0.0061774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.21022980.18313626X-RAY DIFFRACTION95
1.7699-1.79071000000000.18373801X-RAY DIFFRACTION95
1.7907-1.81260.22512980.17473551X-RAY DIFFRACTION95
1.8126-1.83550.25412960.18293603X-RAY DIFFRACTION95
1.8355-1.85961000000000.17733910X-RAY DIFFRACTION96
1.8596-1.88510.23712960.17133568X-RAY DIFFRACTION96
1.8851-1.91210.17492910.16343628X-RAY DIFFRACTION96
1.9121-1.94061000000000.15453867X-RAY DIFFRACTION96
1.9406-1.97090.212920.15643574X-RAY DIFFRACTION96
1.9709-2.00320.18842930.15533620X-RAY DIFFRACTION96
2.0032-2.03781000000000.15883958X-RAY DIFFRACTION96
2.0378-2.07480.18882960.16043598X-RAY DIFFRACTION96
2.0748-2.11470.20652920.15483588X-RAY DIFFRACTION96
2.1147-2.15791000000000.15043926X-RAY DIFFRACTION96
2.1579-2.20480.19322960.15423627X-RAY DIFFRACTION97
2.2048-2.25610.17953010.15123628X-RAY DIFFRACTION97
2.2561-2.31251000000000.14843936X-RAY DIFFRACTION97
2.3125-2.3750.19752960.15383655X-RAY DIFFRACTION97
2.375-2.44490.18872960.1563631X-RAY DIFFRACTION97
2.4449-2.52381000000000.15713982X-RAY DIFFRACTION97
2.5238-2.6140.18332970.15663660X-RAY DIFFRACTION97
2.614-2.71860.17572980.15273654X-RAY DIFFRACTION97
2.7186-2.84231000000000.15043988X-RAY DIFFRACTION97
2.8423-2.99210.18572970.16053678X-RAY DIFFRACTION97
2.9921-3.17950.17952980.15553680X-RAY DIFFRACTION98
3.1795-3.42491000000000.14534003X-RAY DIFFRACTION98
3.4249-3.76930.16013020.13763722X-RAY DIFFRACTION98
3.7693-4.31410.15022960.13143734X-RAY DIFFRACTION98
4.3141-5.4331000000000.12354038X-RAY DIFFRACTION98
5.433-39.24290.17583010.15753838X-RAY DIFFRACTION98
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)
10.5831-0.0680.06260.6451-0.07370.73620.0150.0857-0.0651-0.0666-0.0389-0.03060.09140.07170.02450.0917-0.00630.00220.1069-0.00430.068521.876312.1064-27.3289
21.10950.4046-0.04621.08130.12350.4722-0.0216-0.0070.1680.02410.0216-0.0301-0.07120.02420.00090.0992-0.0251-0.02740.08890.0020.120630.937851.8388-15.5645
30.4947-0.04020.06910.8992-0.04110.68880.0160.01420.0882-0.0364-0.03980.0856-0.0842-0.02910.02280.0906-0.01140.00260.0897-0.00420.107-6.015544.9655-26.9559
40.98120.2649-0.02570.8152-0.14640.48110.0228-0.0292-0.05080.0123-0.00010.08680.0379-0.0067-0.02020.0926-0.02740.00410.08980.00280.0626-14.80155.4861-15.6309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 25:321 )A25 - 321
2X-RAY DIFFRACTION2( CHAIN B AND RESID 25:321 )B25 - 321
3X-RAY DIFFRACTION3( CHAIN C AND RESID 25:318 )C25 - 318
4X-RAY DIFFRACTION4( CHAIN D AND RESID 25:321 )D25 - 321

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