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- PDB-8irz: Carbon Sulfoxide lyase -

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Basic information

Entry
Database: PDB / ID: 8irz
TitleCarbon Sulfoxide lyase
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
PYRIDOXAL-5'-PHOSPHATE / Probable hercynylcysteine sulfoxide lyase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 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

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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)83,1884
Polymers82,6932
Non-polymers4942
Water37821
1
A: Probable hercynylcysteine sulfoxide lyase
hetero molecules

A: Probable hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1884
Polymers82,6932
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5200 Å2
ΔGint-16 kcal/mol
Surface area28100 Å2
MethodPISA
2
B: Probable hercynylcysteine sulfoxide lyase
hetero molecules

B: Probable hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1884
Polymers82,6932
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5210 Å2
ΔGint-16 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.966, 174.395, 84.089
Angle α, β, γ (deg.)90.00, 125.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-503-

HOH

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Components

#1: Protein Probable hercynylcysteine sulfoxide lyase


Mass: 41346.645 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.92 Å3/Da / Density % sol: 68.6 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES-Na, pH 7.5, 1M NaCl, 0.1M LiSO4, 10% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.86→50 Å / Num. obs: 29006 / % possible obs: 99.5 % / Redundancy: 4.6 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.043 / Rrim(I) all: 0.095 / Χ2: 2.315 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.88-2.934.70.54514590.8330.9530.2780.6140.47799
2.93-2.984.70.47314260.8920.9710.240.5310.52199.1
2.98-3.044.70.39114640.9040.9750.20.4410.5499.7
3.04-3.14.70.34514290.9170.9780.1760.3880.57199.4
3.1-3.174.70.28614210.9420.9850.1460.3220.64299.3
3.17-3.244.60.24615010.9630.990.1270.2780.81299.6
3.24-3.324.60.19814130.9750.9940.1020.2230.87999.3
3.32-3.414.30.18114380.9750.9940.0960.2051.15399.6
3.41-3.514.20.16214590.9780.9940.0870.1851.32199.1
3.51-3.634.70.13614200.9820.9960.0680.1531.69898.6
3.63-3.764.80.1314290.9860.9960.0640.1452.08199.8
3.76-3.914.80.11514750.9870.9970.0570.1292.41199.7
3.91-4.094.80.10114350.9910.9980.050.1133.35999.7
4.09-4.34.70.09514660.9910.9980.0480.1073.92899.7
4.3-4.574.50.0914580.990.9970.0460.1024.68699.9
4.57-4.924.20.08114570.9910.9980.0430.0924.84699.8
4.92-5.424.80.07614550.9940.9980.0380.0854.24899.9
5.42-6.24.70.06614650.9950.9990.0330.0733.755100
6.2-7.814.30.05614620.9950.9990.030.0644.29499.7
7.81-504.30.04714740.9960.9990.0250.0534.39898.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→39.75 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.856 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.507 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20288 1433 4.9 %RANDOM
Rwork0.17094 ---
obs0.17247 27573 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.06 Å2
2--0.2 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.86→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5527 0 0 21 5548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125642
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165148
X-RAY DIFFRACTIONr_angle_refined_deg0.9411.6287723
X-RAY DIFFRACTIONr_angle_other_deg0.3291.54411933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.691052
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98310810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0440.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026652
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021063
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_it3.798.4532998
X-RAY DIFFRACTIONr_mcbond_other3.798.4542998
X-RAY DIFFRACTIONr_mcangle_it5.96712.6623744
X-RAY DIFFRACTIONr_mcangle_other5.96612.6633745
X-RAY DIFFRACTIONr_scbond_it4.0568.9192644
X-RAY DIFFRACTIONr_scbond_other4.0488.9212641
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5213.2283980
X-RAY DIFFRACTIONr_long_range_B_refined8.6995934
X-RAY DIFFRACTIONr_long_range_B_other8.6985935
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.861→2.935 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 105 -
Rwork0.319 1871 -
obs--91.91 %

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