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- PDB-7vob: The crystal structure of a Radical SAM Enzyme BlsE involved in th... -

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Basic information

Entry
Database: PDB / ID: 7vob
TitleThe crystal structure of a Radical SAM Enzyme BlsE involved in the Biosynthesis of Blasticidin S
ComponentsCytosylglucuronate decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / Radical SAM Enzyme / Dehydratase / Blasticidin S
Function / homology
Function and homology information


catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Cytosylglucuronate decarboxylase / : / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Cytosylglucuronate decarboxylase
Similarity search - Component
Biological speciesStreptomyces griseochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09224113188 Å
AuthorsHou, X.L. / Zhou, J.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Radical S -Adenosyl Methionine Enzyme BlsE Catalyzes a Radical-Mediated 1,2-Diol Dehydration during the Biosynthesis of Blasticidin S.
Authors: Lee, Y.H. / Hou, X. / Chen, R. / Feng, J. / Liu, X. / Ruszczycky, M.W. / Gao, J.M. / Wang, B. / Zhou, J. / Liu, H.W.
History
DepositionOct 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Cytosylglucuronate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,65711
Polymers39,9671
Non-polymers1,69010
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-22 kcal/mol
Surface area13730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.293, 164.293, 157.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11C-580-

HOH

21C-630-

HOH

31C-633-

HOH

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Components

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Protein , 1 types, 1 molecules C

#1: Protein Cytosylglucuronate decarboxylase


Mass: 39967.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseochromogenes (bacteria)
Gene: AVL59_19980 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B1AYF2

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Non-polymers , 5 types, 143 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 6.64 Å3/Da / Density % sol: 81.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M 2-(N-morpholino) ethanesulfonic acid monohydrate (MES) at pH 5.66, 3.0 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97921 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.09→66.57 Å / Num. obs: 63221 / % possible obs: 99.9 % / Redundancy: 26.7 % / Biso Wilson estimate: 48.3833276048 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.5
Reflection shellResolution: 2.09→2.21 Å / Num. unique obs: 63221 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.09224113188→28.1760170488 Å / SU ML: 0.255279438098 / Cross valid method: FREE R-VALUE / σ(F): 1.36413587268 / Phase error: 24.4679440888
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237064861224 3201 5.0631910283 %
Rwork0.222669703871 60020 -
obs0.223417269732 63221 99.9446692804 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.3103775108 Å2
Refinement stepCycle: LAST / Resolution: 2.09224113188→28.1760170488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 80 133 2762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009165434808342690
X-RAY DIFFRACTIONf_angle_d0.9633640270443657
X-RAY DIFFRACTIONf_chiral_restr0.052762410448384
X-RAY DIFFRACTIONf_plane_restr0.00605398411115478
X-RAY DIFFRACTIONf_dihedral_angle_d13.46444744381606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0922411319-2.12350.354213140151280.2950115330442588X-RAY DIFFRACTION100
2.1235-2.15660.3212571462041610.283848438092548X-RAY DIFFRACTION100
2.1566-2.1920.2801243664651500.2801243664652602X-RAY DIFFRACTION100
2.192-2.22980.2819515929991400.2727994607452556X-RAY DIFFRACTION100
2.2298-2.27030.2875623459461400.2685559313462562X-RAY DIFFRACTION99.9630040696
2.2703-2.31390.2710501513081170.2638960195862601X-RAY DIFFRACTION100
2.3139-2.36110.2781831869021190.2501830431562588X-RAY DIFFRACTION100
2.3611-2.41250.2552952633151400.2532968960552599X-RAY DIFFRACTION100
2.4125-2.46850.2731766642321400.2516253050812596X-RAY DIFFRACTION99.9634636463
2.4685-2.53020.2326482727291280.2326482727292606X-RAY DIFFRACTION100
2.5302-2.59860.2674688741251150.2595923421882608X-RAY DIFFRACTION100
2.5986-2.6750.2538743117181350.2538743117182571X-RAY DIFFRACTION99.9630587366
2.675-2.76130.2698826816511410.2583292357682615X-RAY DIFFRACTION99.9637286906
2.7613-2.85990.2719395885551250.2614047761522627X-RAY DIFFRACTION100
2.8599-2.97430.2958995969341370.2543355586632580X-RAY DIFFRACTION100
2.9743-3.10950.2884981911821450.250151069042607X-RAY DIFFRACTION100
3.1095-3.27320.2880563758521400.2475301809012616X-RAY DIFFRACTION100
3.2732-3.47790.2473363698541290.2348872874512622X-RAY DIFFRACTION100
3.4779-3.74590.2626786037971380.2183276049872631X-RAY DIFFRACTION99.963898917
3.7459-4.12180.2029309787461500.2046931743132643X-RAY DIFFRACTION100
4.1218-4.71580.188909370951440.1921144884852648X-RAY DIFFRACTION100
4.7158-5.93230.2283593814341600.1981217697582660X-RAY DIFFRACTION100
5.9323-28.17601704880.1993578259451790.1862529570762746X-RAY DIFFRACTION99.0182802979

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