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- PDB-8is0: Carbon Sulfoxide lyase - Y106F -

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Basic information

Entry
Database: PDB / ID: 8is0
TitleCarbon Sulfoxide lyase - Y106F
ComponentsProbable hercynylcysteine sulfoxide lyase
KeywordsLYASE / Carbon Sulfoxide lyase / EgtE
Function / homology
Function and homology information


Lyases; Carbon-sulfur lyases / hercynylcysteine sulfoxide lyase activity (ergothioneine-forming) / ergothioneine biosynthesis from histidine via gamma-glutamyl-hercynylcysteine sulfoxide
Similarity search - Function
Pyridoxal-phosphate-dependent protein EgtE / Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
2-AMINO-ACRYLIC ACID / PYRIDOXAL-5'-PHOSPHATE / Probable hercynylcysteine sulfoxide lyase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsGong, W.M. / Wei, L.L. / Liu, L.
Funding support China, Israel, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Israel Ministry of Science and Technology Israel
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structure of mycobacterial ergothioneine-biosynthesis C-S lyase EgtE.
Authors: Wei, L. / Liu, L. / Gong, W.
History
DepositionMar 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable hercynylcysteine sulfoxide lyase
B: Probable hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3306
Polymers82,6612
Non-polymers6684
Water68538
1
A: Probable hercynylcysteine sulfoxide lyase
hetero molecules

A: Probable hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3306
Polymers82,6612
Non-polymers6684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area5280 Å2
ΔGint-20 kcal/mol
Surface area26850 Å2
MethodPISA
2
B: Probable hercynylcysteine sulfoxide lyase
hetero molecules

B: Probable hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3306
Polymers82,6612
Non-polymers6684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y,-z+31
Buried area5130 Å2
ΔGint-18 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.518, 173.275, 82.858
Angle α, β, γ (deg.)90.00, 125.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-516-

HOH

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Components

#1: Protein Probable hercynylcysteine sulfoxide lyase


Mass: 41330.645 Da / Num. of mol.: 2 / Mutation: Y106F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: egtE, MSMEG_6246, MSMEI_6085 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R5M7, Lyases; Carbon-sulfur lyases
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DHA / 2-AMINO-ACRYLIC ACID / 2,3-DIDEHYDROALANINE


Type: peptide linking / Mass: 87.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.8 Å3/Da / Density % sol: 67.63 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES-Na, pH 7.5, 12% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 23776 / % possible obs: 99.2 % / Redundancy: 6.9 % / CC1/2: 0.912 / CC star: 0.977 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.075 / Rrim(I) all: 0.201 / Χ2: 2.431 / Net I/σ(I): 3.6 / Num. measured all: 164337
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3-3.056.91.3911920.6870.9020.5641.5020.46599.9
3.05-3.116.91.20911880.7570.9280.4951.3080.518100
3.11-3.176.90.97711990.7780.9360.41.0570.5499.8
3.17-3.236.80.73311830.8850.9690.3010.7930.50899.9
3.23-3.36.80.64312090.9120.9770.2660.6970.52899.5
3.3-3.386.70.66611790.8820.9680.2750.7220.63599.5
3.38-3.466.70.46511840.9430.9850.1930.5040.58499.5
3.46-3.566.70.35611870.9560.9890.1470.3860.54399.2
3.56-3.666.60.32111710.9550.9880.1330.3480.85798.2
3.66-3.786.40.27911530.9710.9930.1170.3030.60797.8
3.78-3.9160.23912010.9730.9930.1040.2611.06198
3.91-4.075.50.15911370.9870.9970.0720.1751.03795
4.07-4.265.80.13911560.9790.9950.0610.1521.69598.2
4.26-4.487.20.13811990.9860.9960.0550.1481.74100
4.48-4.767.80.12112110.9850.9960.0460.1291.578100
4.76-5.137.70.11911890.9740.9930.0460.1272.626100
5.13-5.647.70.10211890.9920.9980.0390.111.395100
5.64-6.467.70.10212120.9750.9940.0390.112.806100
6.46-8.137.70.09412100.9650.9910.0360.14.653100
8.13-507.50.14812270.9050.9750.0580.15920.33100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SCALEPACKdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→34.36 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.9 / SU B: 18.579 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R: 3.867 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24047 1198 5 %RANDOM
Rwork0.19695 ---
obs0.19915 22555 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.773 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.01 Å2
2---0.01 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 3.02→34.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 0 38 5604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125683
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165202
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.6297763
X-RAY DIFFRACTIONr_angle_other_deg0.4171.54412064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3575748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.3321053
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69910828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0530.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026681
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021071
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.8218.2192998
X-RAY DIFFRACTIONr_mcbond_other5.8218.222998
X-RAY DIFFRACTIONr_mcangle_it8.78912.2763744
X-RAY DIFFRACTIONr_mcangle_other8.78912.2773745
X-RAY DIFFRACTIONr_scbond_it5.568.6012685
X-RAY DIFFRACTIONr_scbond_other5.5588.6012684
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.28512.7714019
X-RAY DIFFRACTIONr_long_range_B_refined11.5436366
X-RAY DIFFRACTIONr_long_range_B_other11.5426365
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.02→3.098 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 84 -
Rwork0.329 1459 -
obs--86.15 %

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