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- PDB-5v1x: Carbon Sulfoxide lyase, Egt2 Y134F in complex with its substrate -

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Basic information

Entry
Database: PDB / ID: 5v1x
TitleCarbon Sulfoxide lyase, Egt2 Y134F in complex with its substrate
ComponentsHercynylcysteine sulfoxide lyase
KeywordsLYASE / C-S lyase / PLP dependent
Function / homology
Function and homology information


Lyases; Carbon-sulfur lyases / hercynylcysteine sulfoxide lyase activity (ergothioneine-forming) / nucleus / cytoplasm
Similarity search - Function
Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-8VV / FORMIC ACID / Hercynylcysteine sulfoxide lyase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.558 Å
AuthorsIrani, S. / Zhang, Y.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Snapshots of C-S Cleavage in Egt2 Reveals Substrate Specificity and Reaction Mechanism.
Authors: Irani, S. / Naowarojna, N. / Tang, Y. / Kathuria, K.R. / Wang, S. / Dhembi, A. / Lee, N. / Yan, W. / Lyu, H. / Costello, C.E. / Liu, P. / Zhang, Y.J.
History
DepositionMar 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Oct 4, 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4May 15, 2024Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Hercynylcysteine sulfoxide lyase
F: Hercynylcysteine sulfoxide lyase
D: Hercynylcysteine sulfoxide lyase
C: Hercynylcysteine sulfoxide lyase
A: Hercynylcysteine sulfoxide lyase
B: Hercynylcysteine sulfoxide lyase
G: Hercynylcysteine sulfoxide lyase
H: Hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)452,30715
Polymers451,4108
Non-polymers8977
Water5,386299
1
E: Hercynylcysteine sulfoxide lyase
F: Hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8993
Polymers112,8532
Non-polymers461
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-19 kcal/mol
Surface area32030 Å2
MethodPISA
2
D: Hercynylcysteine sulfoxide lyase
C: Hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2324
Polymers112,8532
Non-polymers3792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-25 kcal/mol
Surface area33060 Å2
MethodPISA
3
A: Hercynylcysteine sulfoxide lyase
B: Hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2324
Polymers112,8532
Non-polymers3792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-23 kcal/mol
Surface area31840 Å2
MethodPISA
4
G: Hercynylcysteine sulfoxide lyase
H: Hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9454
Polymers112,8532
Non-polymers922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-24 kcal/mol
Surface area32820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.898, 195.067, 107.604
Angle α, β, γ (deg.)90.00, 91.34, 90.00
Int Tables number4
Space group name H-MP1211
DetailsDimer as determined by gel filtration

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Components

#1: Protein
Hercynylcysteine sulfoxide lyase / Ergothioneine biosynthesis protein 2 / PLP-binding cysteine desulfurase / PLP-dependent C-S lyase


Mass: 56426.262 Da / Num. of mol.: 8 / Mutation: Y134F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: egt-2, NCU11365 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A7UX13, Lyases; Carbon-sulfur lyases
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-8VV / (1S)-2-{2-[(R)-(2R)-2-amino-2-carboxyethanesulfinyl]-1H-imidazol-4-yl}-1-carboxy-N,N,N-trimethylethan-1-aminium


Mass: 333.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H21N4O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 3350, 50mM HEPES pH 7.0, 0.2M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.558→50 Å / Num. obs: 135254 / % possible obs: 99.4 % / Redundancy: 3.1 % / Net I/σ(I): 10.69

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UTS

5uts


Resolution: 2.558→48.806 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2793 1978 1.46 %
Rwork0.2225 --
obs0.2234 135254 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.558→48.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27978 0 59 299 28336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00428667
X-RAY DIFFRACTIONf_angle_d0.63238849
X-RAY DIFFRACTIONf_dihedral_angle_d15.57317235
X-RAY DIFFRACTIONf_chiral_restr0.0444294
X-RAY DIFFRACTIONf_plane_restr0.0045010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5576-2.62160.38011150.32467792X-RAY DIFFRACTION80
2.6216-2.69240.36981430.31929590X-RAY DIFFRACTION99
2.6924-2.77170.40781350.3049575X-RAY DIFFRACTION99
2.7717-2.86110.33181520.28049626X-RAY DIFFRACTION99
2.8611-2.96340.32651400.26359666X-RAY DIFFRACTION100
2.9634-3.0820.33191470.26069650X-RAY DIFFRACTION100
3.082-3.22220.33491400.25289664X-RAY DIFFRACTION100
3.2222-3.39210.27361530.2479636X-RAY DIFFRACTION100
3.3921-3.60450.31961320.23479749X-RAY DIFFRACTION100
3.6045-3.88270.28891420.21149650X-RAY DIFFRACTION100
3.8827-4.27330.24731430.1949641X-RAY DIFFRACTION100
4.2733-4.89110.21521510.17899698X-RAY DIFFRACTION100
4.8911-6.16040.26221410.19869687X-RAY DIFFRACTION100
6.1604-48.81520.22411440.17849652X-RAY DIFFRACTION98

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