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- PDB-4dmf: Crystal structure of the CFTR inhibitory factor Cif with the H177... -

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Basic information

Entry
Database: PDB / ID: 4dmf
TitleCrystal structure of the CFTR inhibitory factor Cif with the H177A 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: 2.12 Å
AuthorsBahl, C.D. / Madden, D.R.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Inhibiting an Epoxide Hydrolase Virulence Factor from Pseudomonas aeruginosa Protects CFTR.
Authors: Bahl, C.D. / Hvorecny, K.L. / Bomberger, J.M. / Stanton, B.A. / Hammock, B.D. / Morisseau, C. / Madden, D.R.
History
DepositionFeb 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)136,3914
Polymers136,3914
Non-polymers00
Water9,998555
1
A: Putative hydrolase
B: Putative hydrolase


Theoretical massNumber of molelcules
Total (without water)68,1952
Polymers68,1952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-23 kcal/mol
Surface area20660 Å2
MethodPISA
2
C: Putative hydrolase
D: Putative hydrolase


Theoretical massNumber of molelcules
Total (without water)68,1952
Polymers68,1952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-23 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.766, 83.784, 89.045
Angle α, β, γ (deg.)90.00, 100.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Putative hydrolase /


Mass: 34097.633 Da / Num. of mol.: 4 / Fragment: Cif (UNP Residues 25-319) / Mutation: H177A
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 / Water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

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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: 45.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 16% 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: 0.977 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 11, 2009 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.12→45.981 Å / Num. obs: 68803 / % possible obs: 99.8 % / Redundancy: 4.2 % / Rsym value: 0.097 / Net I/σ(I): 12.7
Reflection shellResolution: 2.12→2.2 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4 / Num. unique all: 30057 / Rsym value: 0.382 / % possible all: 99.7

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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
Resolution: 2.12→45.981 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 18.82 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 3454 5.02 %thin shells
Rwork0.1664 ---
obs0.1683 68795 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.287 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1482 Å2-0 Å2-0.1439 Å2
2---1.9211 Å2-0 Å2
3---5.0693 Å2
Refinement stepCycle: LAST / Resolution: 2.12→45.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9332 0 0 555 9887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079625
X-RAY DIFFRACTIONf_angle_d0.99413061
X-RAY DIFFRACTIONf_dihedral_angle_d13.873495
X-RAY DIFFRACTIONf_chiral_restr0.071349
X-RAY DIFFRACTIONf_plane_restr0.0051718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.1490.23511730.16992572X-RAY DIFFRACTION100
2.149-2.17970.23221730.17692576X-RAY DIFFRACTION100
2.1797-2.21231000000000.17962711X-RAY DIFFRACTION100
2.2123-2.24680.24751730.16972535X-RAY DIFFRACTION100
2.2468-2.28370.2421720.18042630X-RAY DIFFRACTION100
2.2837-2.32310.22771730.16072521X-RAY DIFFRACTION100
2.3231-2.36530.22991730.16622565X-RAY DIFFRACTION100
2.3653-2.41081000000000.17042755X-RAY DIFFRACTION100
2.4108-2.460.22641730.17292578X-RAY DIFFRACTION100
2.46-2.51350.22931730.16762535X-RAY DIFFRACTION100
2.5135-2.57190.23571730.17052590X-RAY DIFFRACTION100
2.5719-2.63630.21721730.17022587X-RAY DIFFRACTION100
2.6363-2.70751000000000.16642739X-RAY DIFFRACTION100
2.7075-2.78720.2181730.16542594X-RAY DIFFRACTION100
2.7872-2.87710.20521730.16992562X-RAY DIFFRACTION100
2.8771-2.980.22681730.182561X-RAY DIFFRACTION100
2.98-3.09920.21571730.18412584X-RAY DIFFRACTION100
3.0992-3.24031000000000.16492763X-RAY DIFFRACTION100
3.2403-3.4110.18471730.15242573X-RAY DIFFRACTION100
3.411-3.62470.20491730.15322572X-RAY DIFFRACTION100
3.6247-3.90440.17051720.14742604X-RAY DIFFRACTION100
3.9044-4.29710.14911710.13362582X-RAY DIFFRACTION100
4.2971-4.91821000000000.11912790X-RAY DIFFRACTION100
4.9182-6.19410.14241720.14272610X-RAY DIFFRACTION100
6.1941-45.99220.15441720.1562652X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.24990.07090.11880.42040.12180.4680.0073-0.0357-0.03810.0459-0.02990.04270.0722-0.0337-00.05880.00690.01420.06220.010.0442-22.0821-78.369127.068
20.4677-0.3076-0.07650.5194-0.19960.2233-0.01690.01140.1122-0.02010.02010.0026-0.0411-0.012600.05220.0187-0.02040.0532-0.00150.0979-30.7774-39.163915.5054
30.09380.06970.09260.6148-0.02590.3579-0.0120.01050.0580.0333-0.0352-0.0646-0.05790.015500.04980.01140.00260.0545-0.00640.07055.9211-45.760826.9155
40.4113-0.2627-0.01110.52980.21670.13320.00630.03380.0086-0.00180.0136-0.07410.00330.004600.05140.02390.00650.056-0.00030.024114.5792-85.03115.6716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:317)
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 25:317)

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