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

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Basic information

Entry
Database: PDB / ID: 4dmc
TitleCrystal structure of the CFTR inhibitory factor Cif with the E153Q mutation
ComponentsPutative hydrolase
KeywordsHYDROLASE / Alpha Beta Hydrolase / Epoxide Hydrolase / 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
Putative hydrolase / Putative hydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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 7, 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 / 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative hydrolase
B: Putative hydrolase
C: Putative hydrolase
D: Putative hydrolase


Theoretical massNumber of molelcules
Total (without water)136,6554
Polymers136,6554
Non-polymers00
Water15,673870
1
A: Putative hydrolase
B: Putative hydrolase


Theoretical massNumber of molelcules
Total (without water)68,3272
Polymers68,3272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-23 kcal/mol
Surface area21040 Å2
MethodPISA
2
C: Putative hydrolase
D: Putative hydrolase


Theoretical massNumber of molelcules
Total (without water)68,3272
Polymers68,3272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-22 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.385, 83.948, 89.510
Angle α, β, γ (deg.)90.00, 100.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-597-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 870 / 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: 45.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 14% PEG 8000, 0.125M calcium chloride, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 31, 2010 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→46.13 Å / Num. all: 144645 / Num. obs: 140472 / % possible obs: 97.1 % / Redundancy: 7.5 % / Rsym value: 0.09 / Net I/σ(I): 16.5
Reflection shellResolution: 1.66→1.7 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 71953 / Rsym value: 0.564 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAIN A OF PDB ENTRY 3KD2

3kd2


Resolution: 1.66→36.265 Å / SU ML: 0.21 / σ(F): 1.99 / Phase error: 18.85 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.208 7020 5 %thin shells
Rwork0.1812 ---
obs0.1825 140462 97.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.056 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6332 Å2-0 Å2-0.3842 Å2
2---2.0996 Å2-0 Å2
3---3.7328 Å2
Refinement stepCycle: LAST / Resolution: 1.66→36.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9452 0 0 870 10322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069796
X-RAY DIFFRACTIONf_angle_d1.02813296
X-RAY DIFFRACTIONf_dihedral_angle_d13.1633576
X-RAY DIFFRACTIONf_chiral_restr0.0781365
X-RAY DIFFRACTIONf_plane_restr0.0051751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.67890.22733460.19284268X-RAY DIFFRACTION96
1.6789-1.69861000000000.19014608X-RAY DIFFRACTION96
1.6986-1.71930.23773410.19164214X-RAY DIFFRACTION96
1.7193-1.74110.22323460.18834262X-RAY DIFFRACTION96
1.7411-1.7641000000000.19214601X-RAY DIFFRACTION96
1.764-1.78820.22223490.18244280X-RAY DIFFRACTION96
1.7882-1.81370.22233520.17434255X-RAY DIFFRACTION96
1.8137-1.84081000000000.1764638X-RAY DIFFRACTION96
1.8408-1.86960.21593470.17514277X-RAY DIFFRACTION96
1.8696-1.90020.19923480.17664267X-RAY DIFFRACTION97
1.9002-1.9331000000000.17314653X-RAY DIFFRACTION97
1.933-1.96810.21373490.17444294X-RAY DIFFRACTION97
1.9681-2.0060.20873480.17774333X-RAY DIFFRACTION97
2.006-2.04691000000000.17984690X-RAY DIFFRACTION97
2.0469-2.09140.22353420.17984297X-RAY DIFFRACTION97
2.0914-2.14010.21613490.17474311X-RAY DIFFRACTION97
2.1401-2.19361000000000.17934690X-RAY DIFFRACTION97
2.1936-2.25290.20793510.17424283X-RAY DIFFRACTION97
2.2529-2.31910.19853540.174363X-RAY DIFFRACTION97
2.3191-2.3941000000000.17354674X-RAY DIFFRACTION98
2.394-2.47950.21173550.17434404X-RAY DIFFRACTION98
2.4795-2.57880.20123570.17774315X-RAY DIFFRACTION98
2.5788-2.69611000000000.17974747X-RAY DIFFRACTION98
2.6961-2.83820.18773530.17384369X-RAY DIFFRACTION98
2.8382-3.01590.20893560.18324374X-RAY DIFFRACTION98
3.0159-3.24871000000000.1824792X-RAY DIFFRACTION98
3.2487-3.57530.18363610.16544397X-RAY DIFFRACTION98
3.5753-4.09210.16983580.1644467X-RAY DIFFRACTION99
4.0921-5.15321000000000.14354786X-RAY DIFFRACTION99
5.1532-36.27370.19833580.1864533X-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)
10.4162-0.01760.02860.40030.0060.3380.0155-0.00080.11450.0098-0.0254-0.052-0.05510.0190.00720.04160.0030.00630.0332-0.00140.0575.796429.854627.1348
20.6033-0.2089-0.02350.45730.0930.28210.00620.022-0.0397-0.01740.0051-0.06620.0346-0.0051-0.00630.04040.02450.00770.0336-0.00070.021614.7372-9.714915.7808
30.441-0.04120.05150.36180.00750.4340.0182-0.0363-0.07690.0209-0.02110.04690.061-0.030.00240.04340.00340.00050.03650.00720.0367-21.9889-2.827527.312
40.6693-0.3259-0.00990.5945-0.11280.2902-0.0130.01540.0944-0.03650.01560.0334-0.04930.00070.00650.03440.0231-0.01630.02810.00550.057-30.972836.715.7321
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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