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- PDB-4dnf: Crystal structure of the CFTR inhibitory factor Cif with the E153... -

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Basic information

Entry
Database: PDB / ID: 4dnf
TitleCrystal structure of the CFTR inhibitory factor Cif with the E153Q mutation adducted with the epibromohydrin hydrolysis intermediate
ComponentsPutative hydrolase
KeywordsHYDROLASE / Alpha Beta Hydrolase / Epoxide Hydrolase / covalently adducted with the epibromohydrin hydrolysis intermediate / 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
(2S)-1-bromopropan-2-ol / Putative hydrolase / Putative hydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBahl, C.D. / Madden, D.R.
CitationJournal: Biochemistry / Year: 2016
Title: Visualizing the Mechanism of Epoxide Hydrolysis by the Bacterial Virulence Enzyme Cif.
Authors: Bahl, C.D. / Hvorecny, K.L. / Morisseau, C. / Gerber, S.A. / Madden, D.R.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Feb 24, 2016Group: 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 / Derived calculations / 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 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: Putative hydrolase
B: Putative hydrolase
C: Putative hydrolase
D: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,2118
Polymers136,6554
Non-polymers5564
Water14,934829
1
A: Putative hydrolase
B: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6054
Polymers68,3272
Non-polymers2782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-21 kcal/mol
Surface area20730 Å2
MethodPISA
2
C: Putative hydrolase
D: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6054
Polymers68,3272
Non-polymers2782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-22 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.147, 83.959, 89.536
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
Putative hydrolase


Mass: 34163.715 Da / Num. of mol.: 4 / Fragment: Cif (UNP Residues 25-319) / Mutation: E153Q
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: Chemical
ChemComp-EBH / (2S)-1-bromopropan-2-ol


Mass: 138.991 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7BrO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 829 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 14% PEG 8000, 0.125M calcium chloride, 0.1M sodium acetate, 0.01M epibromohydrin, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8984 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 20, 2008 / Details: Toroidal focusing mirror
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8984 Å / Relative weight: 1
ReflectionResolution: 1.8→46.14 Å / Num. obs: 112816 / % possible obs: 99.4 % / Redundancy: 4.1 % / Rsym value: 0.09 / Net I/σ(I): 11.87
Reflection shellResolution: 1.8→1.97 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.77 / Num. unique all: 110996 / Rsym value: 0.278 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAIN A OF PDB ENTRY 3KD2

3kd2


Resolution: 1.8→38.541 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 21.6 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 5797 5.14 %thin shells
Rwork0.1892 ---
obs0.1911 112809 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.966 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.8119 Å2-0 Å20.1493 Å2
2---2.8979 Å2-0 Å2
3---3.6299 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9452 0 20 829 10301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069833
X-RAY DIFFRACTIONf_angle_d1.01213349
X-RAY DIFFRACTIONf_dihedral_angle_d16.6063545
X-RAY DIFFRACTIONf_chiral_restr0.0741374
X-RAY DIFFRACTIONf_plane_restr0.0051754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8205010.20713741X-RAY DIFFRACTION100
1.8205-1.84191000000000.19993785X-RAY DIFFRACTION100
1.8419-1.86431000000000.19323756X-RAY DIFFRACTION100
1.8643-1.88790.25617420.19113037X-RAY DIFFRACTION100
1.8879-1.91281000000000.19563715X-RAY DIFFRACTION100
1.9128-1.9391000000000.18663720X-RAY DIFFRACTION100
1.939-1.96671000000000.18563761X-RAY DIFFRACTION100
1.9667-1.9960.2396580.18633128X-RAY DIFFRACTION100
1.996-2.02721000000000.17713708X-RAY DIFFRACTION100
2.0272-2.06051000000000.17493751X-RAY DIFFRACTION99
2.0605-2.0960.21956090.17493155X-RAY DIFFRACTION100
2.096-2.13411000000000.18593756X-RAY DIFFRACTION100
2.1341-2.17510.24941160.18083612X-RAY DIFFRACTION100
2.1751-2.21950.23664600.17913310X-RAY DIFFRACTION100
2.2195-2.26781000000000.16733756X-RAY DIFFRACTION99
2.2678-2.32050.20624680.17833263X-RAY DIFFRACTION99
2.3205-2.37861000000000.18583772X-RAY DIFFRACTION99
2.3786-2.44290.23274460.18493287X-RAY DIFFRACTION99
2.4429-2.51471000000000.18473759X-RAY DIFFRACTION99
2.5147-2.59590.22553950.18263366X-RAY DIFFRACTION99
2.5959-2.68861000000000.18763772X-RAY DIFFRACTION99
2.6886-2.79630.2333350.18773442X-RAY DIFFRACTION99
2.7963-2.92351000000000.19243732X-RAY DIFFRACTION99
2.9235-3.07750.22813120.20153444X-RAY DIFFRACTION99
3.0775-3.27030.24412480.19843507X-RAY DIFFRACTION99
3.2703-3.52260.20282220.18313581X-RAY DIFFRACTION99
3.5226-3.87680.19781850.17563579X-RAY DIFFRACTION99
3.8768-4.43710.17411430.1693639X-RAY DIFFRACTION99
4.4371-5.58750.17622200.16493589X-RAY DIFFRACTION99
5.5875-38.54970.21142370.20693589X-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)
10.30230.02390.16860.1899-0.04340.2584-0.0176-0.0217-0.14620.0491-0.0730.16270.0854-0.0391-0.05330.00360.0035-0.02560.0060.044-0.0872-21.967511.949427.2513
20.3965-0.27450.01620.3956-0.16840.1659-0.01140.02340.0707-0.04770.01170.0584-0.0395-0.01330.02720.02290.0215-0.01680.0167-0.00030.0345-30.860951.559815.7372
30.34290.0743-0.08330.2740.0480.29410.0099-0.01640.13810.0053-0.0413-0.104-0.04970.0502-0.03770.0060.00140.0050.0025-0.0199-0.01425.877544.691327.2357
40.3125-0.2177-0.00510.34940.13590.11820.0020.0235-0.0135-0.02490.0034-0.07030.01510.0052-0.00940.02730.01840.01150.0294-0.0041-0.003314.79765.067815.7568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:320)
2X-RAY DIFFRACTION2(chain B and resid 25:320)
3X-RAY DIFFRACTION3(chain C and resid 25:320)
4X-RAY DIFFRACTION4(chain D and resid 25:320)

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