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- PDB-8irk: Carbon Sulfoxide lyase -

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Basic information

Entry
Database: PDB / ID: 8irk
TitleCarbon Sulfoxide lyase
ComponentsProbable hercynylcysteine sulfoxide lyase
KeywordsLYASE
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 / PYRUVIC ACID / Probable hercynylcysteine sulfoxide lyase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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: To Be Published
Title: Structure of Mycobacterial ergothioneine-biosynthesis C-S lyase EgtE
Authors: Gong, W.M. / Wei, L.L. / Liu, L.
History
DepositionMar 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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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
C: Probable hercynylcysteine sulfoxide lyase
D: Probable hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,5919
Polymers165,5154
Non-polymers1,0775
Water5,386299
1
A: Probable hercynylcysteine sulfoxide lyase
C: Probable hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3405
Polymers82,7572
Non-polymers5823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-11 kcal/mol
Surface area27660 Å2
MethodPISA
2
B: Probable hercynylcysteine sulfoxide lyase
D: Probable hercynylcysteine sulfoxide lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2524
Polymers82,7572
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-18 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.314, 90.372, 101.531
Angle α, β, γ (deg.)110.77, 105.95, 103.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Probable hercynylcysteine sulfoxide lyase


Mass: 41378.711 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 3.83 Å3/Da / Density % sol: 67.89 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M citric acid, pH 6.5, 15% PEG 8000, 15% glycol

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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: Oct 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 95080 / % possible obs: 93.4 % / Redundancy: 1.6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.045 / Rrim(I) all: 0.064 / Χ2: 0.801 / Net I/σ(I): 7.2 / Num. measured all: 154794
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.34-2.381.70.646590.6880.9030.60.8480.44492.5
2.38-2.421.60.47247240.7770.9350.4720.6680.4192.5
2.42-2.471.60.40747570.8230.950.4070.5760.46693.4
2.47-2.521.60.31747680.9010.9740.3170.4480.42693.8
2.52-2.581.60.31247600.8580.9610.3120.4410.49292.6
2.58-2.641.60.28247320.880.9680.2820.3990.49393.4
2.64-2.71.60.24247320.910.9760.2420.3420.47293.5
2.7-2.771.60.19246710.9510.9870.1920.2710.4892.1
2.77-2.861.70.14648320.9590.9890.1460.2060.48694.4
2.86-2.951.70.11847820.9740.9930.1180.1670.54494
2.95-3.051.70.09848470.9680.9920.0980.1380.9494.7
3.05-3.181.70.07447760.9880.9970.0740.1040.62994.6
3.18-3.321.60.05748210.9920.9980.0570.0810.75394.2
3.32-3.51.60.04746450.9940.9990.0470.0660.69891.6
3.5-3.711.70.03748650.9950.9990.0370.0520.76595.1
3.71-41.70.03148110.9960.9990.0310.0431.10895.1
4-4.41.60.02847400.9960.9990.0280.0391.27593
4.4-5.041.60.02546740.9970.9990.0250.0361.31291.6
5.04-6.351.60.02548460.9960.9990.0250.0361.45695.2
6.35-501.60.02546380.9960.9990.0250.0362.61191.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→41.81 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.468 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24596 4786 5 %RANDOM
Rwork0.19757 ---
obs0.2 90294 92.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.243 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0.08 Å20.08 Å2
2--0.05 Å20.04 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 2.35→41.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11064 0 66 299 11429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01311365
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710746
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.63115538
X-RAY DIFFRACTIONr_angle_other_deg1.3481.56824647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35151496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06420.56571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.232151659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.08115105
X-RAY DIFFRACTIONr_chiral_restr0.0810.21497
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022482
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_it4.5415.2965996
X-RAY DIFFRACTIONr_mcbond_other4.5395.2965995
X-RAY DIFFRACTIONr_mcangle_it6.4917.947488
X-RAY DIFFRACTIONr_mcangle_other6.4917.9417489
X-RAY DIFFRACTIONr_scbond_it5.0035.7195369
X-RAY DIFFRACTIONr_scbond_other5.0045.725366
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2438.4338051
X-RAY DIFFRACTIONr_long_range_B_refined9.04163.35212252
X-RAY DIFFRACTIONr_long_range_B_other9.04663.34512221
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.408 Å
RfactorNum. reflection% reflection
Rfree0.383 295 -
Rwork0.382 5838 -
obs--81.17 %

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