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- PDB-7jqz: Crystal structure of Cfl2 wild-type from Burkholderia cenocepacia -

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Basic information

Entry
Database: PDB / ID: 7jqz
TitleCrystal structure of Cfl2 wild-type from Burkholderia cenocepacia
ComponentsAlpha/beta hydrolase fold
KeywordsHYDROLASE / decamer / alpha/beta hydrolase fold
Function / homologyAlpha/beta hydrolase family / Epoxide hydrolase-like / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Alpha/beta hydrolase fold
Function and homology information
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTaher, N.M. / Madden, D.R.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI091699 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM113240 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37-AI83256-06 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20-GM113132 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30-DK117469 United States
Cystic Fibrosis FoundationSTANTO19R0 United States
CitationJournal: Curr Res Struct Biol / Year: 2021
Title: Biochemical and structural characterization of two cif-like epoxide hydrolases from Burkholderia cenocepacia .
Authors: Taher, N.M. / Hvorecny, K.L. / Burke, C.M. / Gilman, M.S.A. / Heussler, G.E. / Adolf-Bryfogle, J. / Bahl, C.D. / O'Toole, G.A. / Madden, D.R.
History
DepositionAug 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase fold
B: Alpha/beta hydrolase fold
C: Alpha/beta hydrolase fold
D: Alpha/beta hydrolase fold
E: Alpha/beta hydrolase fold
F: Alpha/beta hydrolase fold
G: Alpha/beta hydrolase fold
H: Alpha/beta hydrolase fold
I: Alpha/beta hydrolase fold
J: Alpha/beta hydrolase fold


Theoretical massNumber of molelcules
Total (without water)345,40910
Polymers345,40910
Non-polymers00
Water20,5551141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25580 Å2
ΔGint-147 kcal/mol
Surface area101830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.734, 210.471, 86.956
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein
Alpha/beta hydrolase fold


Mass: 34540.922 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (strain MC0-3) (bacteria)
Strain: MC0-3 / Gene: Bcenmc03_3580 / Production host: Escherichia coli (E. coli) / References: UniProt: B1K378
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1141 / 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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 784 mM sodium thiocyanate, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 2.2→48.54 Å / Num. obs: 170389 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 37.33 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.097 / Net I/σ(I): 16.6
Reflection shellResolution: 2.2→2.33 Å / Mean I/σ(I) obs: 2.45 / Num. unique obs: 27173 / CC1/2: 0.822 / Rrim(I) all: 0.841

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 2.2→48.54 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 8500 4.99 %Random selection in thin resolution shells
Rwork0.1848 161762 --
obs0.1863 170263 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.23 Å2 / Biso mean: 39.4107 Å2 / Biso min: 19.76 Å2
Refinement stepCycle: final / Resolution: 2.2→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23260 0 0 1141 24401
Biso mean---41.6 -
Num. residues----2940

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