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- PDB-7jqx: Crystal structure of Cfl1 wild-type from Burkholderia cenocepacia -

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Basic information

Entry
Database: PDB / ID: 7jqx
TitleCrystal structure of Cfl1 wild-type from Burkholderia cenocepacia
ComponentsCif-like 1 wild-type
KeywordsHYDROLASE / Octamer / alpha/beta hydrolase fold
Function / homologyEpoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Hydrolase
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cif-like 1 wild-type
B: Cif-like 1 wild-type
C: Cif-like 1 wild-type
D: Cif-like 1 wild-type


Theoretical massNumber of molelcules
Total (without water)138,1574
Polymers138,1574
Non-polymers00
Water10,881604
1
A: Cif-like 1 wild-type
C: Cif-like 1 wild-type

A: Cif-like 1 wild-type
C: Cif-like 1 wild-type

A: Cif-like 1 wild-type
C: Cif-like 1 wild-type

A: Cif-like 1 wild-type
C: Cif-like 1 wild-type


Theoretical massNumber of molelcules
Total (without water)276,3158
Polymers276,3158
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area18110 Å2
ΔGint-102 kcal/mol
Surface area78300 Å2
MethodPISA
2
B: Cif-like 1 wild-type
D: Cif-like 1 wild-type

B: Cif-like 1 wild-type
D: Cif-like 1 wild-type

B: Cif-like 1 wild-type
D: Cif-like 1 wild-type

B: Cif-like 1 wild-type
D: Cif-like 1 wild-type


Theoretical massNumber of molelcules
Total (without water)276,3158
Polymers276,3158
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area17670 Å2
ΔGint-105 kcal/mol
Surface area79090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.150, 132.150, 341.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-463-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 11 - 304 / Label seq-ID: 11 - 304

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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Components

#1: Protein
Cif-like 1 wild-type


Mass: 34539.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: BCAM1529 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EJL9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 750 mM potassium sodium tartrate, 100 mM HEPES pH 8.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→48.63 Å / Num. obs: 76696 / % possible obs: 99.5 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rrim(I) all: 0.178 / Net I/σ(I): 11.71
Reflection shellResolution: 2.2→2.33 Å / Num. unique obs: 11911 / CC1/2: 0.794

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 2.2→48.63 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 3819 4.99 %
Rwork0.1801 72782 -
obs0.1817 76601 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.92 Å2 / Biso mean: 42.2694 Å2 / Biso min: 24.56 Å2
Refinement stepCycle: final / Resolution: 2.2→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9276 0 0 604 9880
Biso mean---44.48 -
Num. residues----1176
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5672X-RAY DIFFRACTION8.791TORSIONAL
12B5672X-RAY DIFFRACTION8.791TORSIONAL
13C5672X-RAY DIFFRACTION8.791TORSIONAL
14D5672X-RAY DIFFRACTION8.791TORSIONAL

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