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

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Basic information

Entry
Database: PDB / ID: 7voc
TitleThe crystal structure of a Radical SAM Enzyme BlsE involved in the Biosynthesis of Blasticidin S
ComponentsCytosylglucuronate decarboxylase
KeywordsDehydratase / Radical SAM Enzyme / Blasticidin S / enzyme catalysis
Function / homology
Function and homology information


iron-sulfur cluster binding / catalytic activity / 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
Chem-7QO / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Cytosylglucuronate decarboxylase
Similarity search - Component
Biological speciesStreptomyces griseochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62005420008 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 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Cytosylglucuronate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8106
Polymers40,3291
Non-polymers1,4815
Water27015
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 area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.920, 163.920, 158.810
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

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Components

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Protein , 1 types, 1 molecules C

#1: Protein Cytosylglucuronate decarboxylase


Mass: 40329.426 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, 20 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-7QO / (2~{S},3~{S},4~{S},5~{R},6~{R})-6-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid


Mass: 287.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N3O7
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 6.67 Å3/Da / Density % sol: 81.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: 0.1 M MES monohydrate pH 6.07 , 2.8 M NaCl / PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.62→27.32 Å / Num. obs: 32642 / % possible obs: 99.9 % / Redundancy: 26.3 % / Biso Wilson estimate: 72.1936256233 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.211 / Net I/σ(I): 11.1
Reflection shellResolution: 2.62→2.69 Å / Num. unique obs: 32642 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VOB

7vob


Resolution: 2.62005420008→27.2212916085 Å / SU ML: 0.311886517668 / Cross valid method: FREE R-VALUE / σ(F): 1.34358397052 / Phase error: 25.7667448123
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234201946906 1536 4.70559401997 %
Rwork0.213790999671 31106 -
obs0.214761018098 32642 99.8806646063 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.7818123831 Å2
Refinement stepCycle: LAST / Resolution: 2.62005420008→27.2212916085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 69 15 2633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003174213925372686
X-RAY DIFFRACTIONf_angle_d0.6700485242433663
X-RAY DIFFRACTIONf_chiral_restr0.0464946438415389
X-RAY DIFFRACTIONf_plane_restr0.0053947655311480
X-RAY DIFFRACTIONf_dihedral_angle_d20.57965744791596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6201-2.70450.3372285738481350.3033667524212798X-RAY DIFFRACTION99.8978201635
2.7045-2.80110.2487899669881200.2894757326072787X-RAY DIFFRACTION100
2.8011-2.91310.2896112084981310.2795327247262810X-RAY DIFFRACTION100
2.9131-3.04560.2760415637891620.261817392782775X-RAY DIFFRACTION100
3.0456-3.20590.3274411283571280.2514295743292803X-RAY DIFFRACTION100
3.2059-3.40640.2911722534321490.2586267930352800X-RAY DIFFRACTION99.9661016949
3.4064-3.66880.2631947073731560.2271452155152794X-RAY DIFFRACTION99.9322493225
3.6688-4.0370.2039450429221250.2030827907812852X-RAY DIFFRACTION99.9664204164
4.037-4.61870.1894411791761430.1879292276992833X-RAY DIFFRACTION100
4.6187-5.80970.2242628347061470.1942425460962872X-RAY DIFFRACTION99.9668874172
5.8097-27.221290.2108778607051400.1911967968412982X-RAY DIFFRACTION99.0168093879
Refinement TLS params.Method: refined / Origin x: 0.132429976342 Å / Origin y: 23.2992855155 Å / Origin z: -66.3173996159 Å
111213212223313233
T0.578612463132 Å20.00484379554344 Å20.0155887745532 Å2-0.413287373164 Å2-0.101298696129 Å2--0.632738281937 Å2
L2.9506359713 °20.600000337267 °2-0.0538481228143 °2-2.29045173403 °20.614959928648 °2--2.42647780362 °2
S0.0143875853569 Å °-0.244556066931 Å °0.0771753802566 Å °0.24499823151 Å °0.0363624133695 Å °-0.0212279357753 Å °-0.111301503719 Å °0.00874355574801 Å °-0.0546788365465 Å °
Refinement TLS groupSelection details: all

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