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- PDB-4eus: Crystal structure of the CFTR inhibitory factor Cif bound to 1,2-... -

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Basic information

Entry
Database: PDB / ID: 4eus
TitleCrystal structure of the CFTR inhibitory factor Cif bound to 1,2-hexanediol
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
(2S)-hexane-1,2-diol / Putative hydrolase / Putative hydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionApr 25, 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: Refinement description / Category: software
Revision 1.4Sep 13, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 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
A: Putative hydrolase
B: Putative hydrolase
C: Putative hydrolase
D: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,8956
Polymers136,6594
Non-polymers2362
Water24,0321334
1
A: Putative hydrolase
B: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4483
Polymers68,3292
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-24 kcal/mol
Surface area20610 Å2
MethodPISA
2
C: Putative hydrolase
D: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4483
Polymers68,3292
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-23 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.768, 84.249, 90.132
Angle α, β, γ (deg.)90.00, 100.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-712-

HOH

21C-635-

HOH

31C-646-

HOH

41D-589-

HOH

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Components

#1: Protein
Putative hydrolase


Mass: 34164.699 Da / Num. of mol.: 4
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-0RE / (2S)-hexane-1,2-diol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1334 / 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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 14% PEG 8000, 0.125M calcium chloride, 0.1M sodium acetate, 0.02M 1,2-hexanediol, 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: Feb 24, 2012 / 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: 1.65→46.45 Å / Num. obs: 149966 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rsym value: 0.058 / Net I/σ(I): 15.63
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.59 / Num. unique all: 12794 / Rsym value: 0.377 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Chain A of PDB ENTRY 3KD2

3kd2


Resolution: 1.65→46.45 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 17.02 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1974 7520 5.01 %thin shells
Rwork0.1687 ---
obs0.1701 149955 99.95 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.488 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8506 Å2-0 Å20.4012 Å2
2---1.3604 Å20 Å2
3---2.2109 Å2
Refinement stepCycle: LAST / Resolution: 1.65→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9352 0 16 1334 10702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069776
X-RAY DIFFRACTIONf_angle_d1.06113278
X-RAY DIFFRACTIONf_dihedral_angle_d13.4413570
X-RAY DIFFRACTIONf_chiral_restr0.0771371
X-RAY DIFFRACTIONf_plane_restr0.0051750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66880.28283760.24584633X-RAY DIFFRACTION100
1.6688-1.688400.23475003X-RAY DIFFRACTION100
1.6884-1.7090.26593760.23434552X-RAY DIFFRACTION100
1.709-1.73060.24463760.22474616X-RAY DIFFRACTION100
1.7306-1.753400.21384986X-RAY DIFFRACTION100
1.7534-1.77740.22723760.2024541X-RAY DIFFRACTION100
1.7774-1.80280.22343760.20264617X-RAY DIFFRACTION100
1.8028-1.829700.18634977X-RAY DIFFRACTION100
1.8297-1.85830.22883760.19094646X-RAY DIFFRACTION100
1.8583-1.88880.22223760.18644569X-RAY DIFFRACTION100
1.8888-1.921300.17484992X-RAY DIFFRACTION100
1.9213-1.95630.19193760.16384631X-RAY DIFFRACTION100
1.9563-1.99390.19383760.16544581X-RAY DIFFRACTION100
1.9939-2.034600.16394977X-RAY DIFFRACTION100
2.0346-2.07880.19653760.16434610X-RAY DIFFRACTION100
2.0788-2.12720.18443760.16384596X-RAY DIFFRACTION100
2.1272-2.180400.16185004X-RAY DIFFRACTION100
2.1804-2.23940.20133760.16544626X-RAY DIFFRACTION100
2.2394-2.30520.21463760.17334643X-RAY DIFFRACTION100
2.3052-2.379700.16154979X-RAY DIFFRACTION100
2.3797-2.46470.19013760.16724619X-RAY DIFFRACTION100
2.4647-2.56340.18793760.16534636X-RAY DIFFRACTION100
2.5634-2.6800.16384985X-RAY DIFFRACTION100
2.68-2.82130.18333760.16554644X-RAY DIFFRACTION100
2.8213-2.9980.19133760.17124637X-RAY DIFFRACTION100
2.998-3.229500.17185020X-RAY DIFFRACTION100
3.2295-3.55440.18823760.15674639X-RAY DIFFRACTION100
3.5544-4.06840.17463760.15094654X-RAY DIFFRACTION100
4.0684-5.124700.12635062X-RAY DIFFRACTION100
5.1247-46.46790.18883760.18584760X-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)
10.59930.04340.07250.6217-0.03660.61910.0030.0631-0.0529-0.0484-0.0191-0.06280.07660.06040.010.080.00120.01180.0814-0.00510.060821.927812.3684-27.4424
20.80470.2526-0.02560.70150.04850.3728-0.01850.02130.12010.03610.0063-0.0315-0.0619-0.00260.00570.0708-0.0137-0.01770.06180.00610.086231.071151.3549-15.8003
30.5488-0.01640.040.7523-0.09260.7013-0.00480.01430.0844-0.0155-0.01450.0923-0.084-0.05280.01050.0629-0.00190.00380.0543-0.00230.0717-5.661944.3894-27.275
40.73990.0786-0.0360.5389-0.11750.3630.0160.0066-0.0444-0.0076-0.00140.0740.0223-0.007-0.00930.0532-0.02370.00710.06420.00150.0466-14.70635.4248-15.7749
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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