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- PDB-5tnd: Crystal structure of the E153Q mutant of the CFTR inhibitory fact... -

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Basic information

Entry
Database: PDB / ID: 5tnd
TitleCrystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 1,2-Epoxycyclohexane hydrolysis intermediate
ComponentsCFTR inhibitory factor
KeywordsHYDROLASE / epoxide hydrolase / hydroxyalkyl-enzyme intermediate
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
(1S,2S)-cyclohexane-1,2-diol / (1R,2R)-cyclohexane-1,2-diol / Putative hydrolase / CFTR inhibitory factor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsHvorecny, K.L. / Madden, D.R.
Funding support United States, 5items
OrganizationGrant numberCountry
Cystic Fibrosis Foundation United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) 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 1.1Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.4Nov 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
C: CFTR inhibitory factor
D: CFTR inhibitory factor
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,58412
Polymers136,6554
Non-polymers9298
Water21,8161211
1
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7926
Polymers68,3272
Non-polymers4654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-22 kcal/mol
Surface area21110 Å2
MethodPISA
2
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7926
Polymers68,3272
Non-polymers4654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-23 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.339, 83.926, 89.287
Angle α, β, γ (deg.)90.00, 100.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-808-

HOH

21A-756-

HOH

31A-769-

HOH

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Components

#1: Protein
CFTR inhibitory factor


Mass: 34163.715 Da / Num. of mol.: 4 / Mutation: E153Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: PA14_26090 / Plasmid: pMQ70 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: A0A0M3KL26, UniProt: A0A0H2ZD27*PLUS
#2: Chemical
ChemComp-40O / (1R,2R)-cyclohexane-1,2-diol


Mass: 116.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O2
#3: Chemical
ChemComp-3ZQ / (1S,2S)-cyclohexane-1,2-diol


Mass: 116.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1211 / 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: 45.56 %
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: 1.55→46.105 Å / Num. obs: 176815 / % possible obs: 99.9 % / Redundancy: 5.54 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.19
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 5.55 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 4.08 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSDec 6, 2010data reduction
XDSDec 6, 2010data scaling
PHENIX1.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 1.55→46.105 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 15.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1736 8839 5 %
Rwork0.1502 --
obs0.1513 176807 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→46.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9492 0 56 1211 10759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610064
X-RAY DIFFRACTIONf_angle_d0.84813703
X-RAY DIFFRACTIONf_dihedral_angle_d15.1835932
X-RAY DIFFRACTIONf_chiral_restr0.0541409
X-RAY DIFFRACTIONf_plane_restr0.0061800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.56760.2194420.18445473X-RAY DIFFRACTION100
1.5676-1.58611000000000.17495821X-RAY DIFFRACTION100
1.5861-1.60540.19874420.16835430X-RAY DIFFRACTION100
1.6054-1.62570.19684420.17325495X-RAY DIFFRACTION100
1.6257-1.64711000000000.17415869X-RAY DIFFRACTION100
1.6471-1.66970.21794420.16635368X-RAY DIFFRACTION100
1.6697-1.69350.19574420.15965409X-RAY DIFFRACTION100
1.6935-1.71881000000000.15995923X-RAY DIFFRACTION100
1.7188-1.74570.19274420.15715449X-RAY DIFFRACTION100
1.7457-1.77430.19164420.1545429X-RAY DIFFRACTION100
1.7743-1.80491000000000.15125870X-RAY DIFFRACTION100
1.8049-1.83770.17494420.14895404X-RAY DIFFRACTION100
1.8377-1.87310.18154420.15245421X-RAY DIFFRACTION100
1.8731-1.91131000000000.1575895X-RAY DIFFRACTION100
1.9113-1.95280.16874420.15185457X-RAY DIFFRACTION100
1.9528-1.99830.18054420.15815453X-RAY DIFFRACTION100
1.9983-2.04821000000000.14815886X-RAY DIFFRACTION100
2.0482-2.10360.15624420.14325414X-RAY DIFFRACTION100
2.1036-2.16550.17664420.14455415X-RAY DIFFRACTION100
2.1655-2.23541000000000.15155941X-RAY DIFFRACTION100
2.2354-2.31530.17944420.14795424X-RAY DIFFRACTION100
2.3153-2.4080.17344420.15035499X-RAY DIFFRACTION100
2.408-2.51761000000000.15865833X-RAY DIFFRACTION100
2.5176-2.65030.18264420.1565466X-RAY DIFFRACTION100
2.6503-2.81630.18474410.15065465X-RAY DIFFRACTION100
2.8163-3.03381000000000.15765945X-RAY DIFFRACTION100
3.0338-3.3390.15334420.15035467X-RAY DIFFRACTION100
3.339-3.82190.14514420.13685519X-RAY DIFFRACTION100
3.8219-4.81441000000000.1265937X-RAY DIFFRACTION100
4.8144-46.12560.17174420.14945591X-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)
10.546-0.01540.00320.7689-0.05430.59220.01480.03720.1046-0.0397-0.02920.078-0.0859-0.01830.01370.0879-0.00490.00150.08550.00280.11-5.682229.6234-27.1567
20.91770.2356-0.06240.8464-0.17370.4970.0209-0.0468-0.04750.0118-0.01170.08850.048-0.0133-0.00570.0801-0.02090.00670.08550.00080.0652-14.8531-9.8752-15.7201
30.5911-0.0140.1130.55840.00080.58260.01160.0721-0.0697-0.051-0.0171-0.04080.08090.02720.00630.082-0.00380.00470.0859-0.00890.067622.0807-2.6638-27.3206
40.93720.25210.00420.99950.10560.4792-0.0153-0.01570.15140.03870.01-0.0526-0.08830.03270.00410.0874-0.0171-0.0210.0767-0.00230.112531.161236.8563-15.5474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 25:321 )C25 - 321
2X-RAY DIFFRACTION2( CHAIN D AND RESID 25:321 )D25 - 321
3X-RAY DIFFRACTION3( CHAIN A AND RESID 25:321 )A25 - 321
4X-RAY DIFFRACTION4( CHAIN B AND RESID 25:321 )B25 - 321

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