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- PDB-7kq3: Structure of isethionate sulfite-lyase from Bilophila wadsworthia... -

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Basic information

Entry
Database: PDB / ID: 7kq3
TitleStructure of isethionate sulfite-lyase from Bilophila wadsworthia with substrate isethionate bound
ComponentsIsethionate sulfite-lyase
KeywordsLYASE / glycyl radical enzyme / isethionate-sulfite lyase / carbon-sulfur bond cleavage / microbiome
Function / homology
Function and homology information


isethionate sulfite-lyase / alkanesulfonate catabolic process / lyase activity / cytosol
Similarity search - Function
: / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile.
Similarity search - Domain/homology
2-hydroxyethylsulfonic acid / Isethionate sulfite-lyase
Similarity search - Component
Biological speciesBilophila wadsworthia
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.688 Å
AuthorsDawson, C.D. / Backman, L.R.F. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM069857 United States
CitationJournal: Cell Chem Biol / Year: 2021
Title: Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase.
Authors: Dawson, C.D. / Irwin, S.M. / Backman, L.R.F. / Le, C. / Wang, J.X. / Vennelakanti, V. / Yang, Z. / Kulik, H.J. / Drennan, C.L. / Balskus, E.P.
History
DepositionNov 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Isethionate sulfite-lyase
B: Isethionate sulfite-lyase
C: Isethionate sulfite-lyase
D: Isethionate sulfite-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)376,8318
Polymers376,3274
Non-polymers5054
Water16,988943
1
A: Isethionate sulfite-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2082
Polymers94,0821
Non-polymers1261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isethionate sulfite-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2082
Polymers94,0821
Non-polymers1261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Isethionate sulfite-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2082
Polymers94,0821
Non-polymers1261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Isethionate sulfite-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2082
Polymers94,0821
Non-polymers1261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.954, 163.754, 181.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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: GLU / Beg label comp-ID: GLU / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 6 - 830 / Label seq-ID: 6 - 830

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

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Components

#1: Protein
Isethionate sulfite-lyase / Glycyl radical enzyme IslA / GRE IslA


Mass: 94081.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bilophila wadsworthia (strain 3_1_6) (bacteria)
Strain: 3_1_6 / Gene: islA, iseG, HMPREF0179_00639 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E5Y378, Lyases; Carbon-sulfur lyases
#2: Chemical
ChemComp-8X3 / 2-hydroxyethylsulfonic acid / 2-oxidanylethanesulfonic acid


Mass: 126.132 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 943 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.16 M sodium bromide, 20% PEG 3350, and 10 mM sodium isethionate. Paraffin oil was used as a cryoprotectant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.688→50 Å / Num. obs: 107420 / % possible obs: 98.9 % / Redundancy: 4.1 % / CC1/2: 0.969 / Net I/σ(I): 7
Reflection shellResolution: 2.6881→2.7186 Å / Num. unique obs: 10625 / CC1/2: 0.496

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FAU

5fau


Resolution: 2.688→49.223 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 5364 5 %
Rwork0.1837 101933 -
obs0.1856 107297 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.34 Å2 / Biso mean: 36.722 Å2 / Biso min: 20.34 Å2
Refinement stepCycle: final / Resolution: 2.688→49.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26332 0 28 943 27303
Biso mean--31.49 34.46 -
Num. residues----3300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00426992
X-RAY DIFFRACTIONf_angle_d0.62336556
X-RAY DIFFRACTIONf_dihedral_angle_d14.29616176
X-RAY DIFFRACTIONf_chiral_restr0.0453892
X-RAY DIFFRACTIONf_plane_restr0.0054788
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A16345X-RAY DIFFRACTION8.279TORSIONAL
12B16345X-RAY DIFFRACTION8.279TORSIONAL
13C16345X-RAY DIFFRACTION8.279TORSIONAL
14D16345X-RAY DIFFRACTION8.279TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6881-2.71860.30771540.2724292886
2.7186-2.75060.31761770.274336199
2.7506-2.78410.31121780.2652338799
2.7841-2.81940.28281780.2562337799
2.8194-2.85650.30871800.2447341799
2.8565-2.89560.27071780.2392337299
2.8956-2.9370.28591790.2431340099
2.937-2.98080.28411800.2315344799
2.9808-3.02740.26991790.2276337699
3.0274-3.0770.26911780.223337399
3.077-3.130.24631780.2136339199
3.13-3.18690.27121780.219339199
3.1869-3.24820.26371780.2177337199
3.2482-3.31450.2451790.2268340299
3.3145-3.38660.29581800.2069342299
3.3866-3.46530.23091790.1993340799
3.4653-3.5520.21091800.1902343599
3.552-3.6480.21051770.1774338099
3.648-3.75530.23261800.1738339899
3.7553-3.87640.22671790.1597340399
3.8764-4.01490.19091790.1614339999
4.0149-4.17560.17691780.1474339499
4.1756-4.36550.19021830.1469347099
4.3655-4.59550.18891800.14373417100
4.5955-4.88320.17631820.14263470100
4.8832-5.25990.18371830.1505346499
5.2599-5.78840.21591810.1706345899
5.7884-6.62430.21351810.1731341697
6.6243-8.33940.18131800.1616343597
8.3394-49.2230.17111880.1554357296

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