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- PDB-7wzx: The structure of a Twitch Radical SAM Dehydrogenase SpeY -

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Basic information

Entry
Database: PDB / ID: 7wzx
TitleThe structure of a Twitch Radical SAM Dehydrogenase SpeY
Components4Fe-4S cluster-binding domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / Spectinomycin / Twitch Radical SAM Dehydrogenase / Epimerase
Function / homology
Function and homology information


heme biosynthetic process / catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Radical SAM superfamily / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-7PK / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / 4Fe-4S cluster-binding domain-containing protein
Similarity search - Component
Biological speciesStreptomyces spectabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98001304567 Å
AuthorsHou, X.L. / Zhou, J.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Dioxane Bridge Formation during the Biosynthesis of Spectinomycin Involves a Twitch Radical S -Adenosyl Methionine Dehydrogenase That May Have Evolved from an Epimerase.
Authors: Zhang, J. / Hou, X. / Chen, Z. / Ko, Y. / Ruszczycky, M.W. / Chen, Y. / Zhou, J. / Liu, H.W.
History
DepositionFeb 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 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

Downloads & links

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Assembly

Deposited unit
A: 4Fe-4S cluster-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,01111
Polymers36,0151
Non-polymers1,99710
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-21 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.930, 93.930, 143.420
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 4Fe-4S cluster-binding domain-containing protein / SpeY


Mass: 36014.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces spectabilis (bacteria) / Gene: speY, FH965_34950 / Production host: Escherichia coli (E. coli) / References: UniProt: A8WEZ7

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Non-polymers , 6 types, 91 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-7PK / (2~{S},4~{S},6~{R})-2-[(2~{S},3~{R},5~{S},6~{R})-3,5-bis(methylamino)-2,4,6-tris(oxidanyl)cyclohexyl]oxy-6-methyl-4-oxidanyl-oxan-3-one


Mass: 334.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H26N2O7 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.5 M Sodium cacodylate trihydrate (pH 6.0), 1.8 M Ammonium sulfate and 0.05 M Magnesium acetate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97846 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97846 Å / Relative weight: 1
ReflectionResolution: 1.98→44.63 Å / Num. obs: 26783 / % possible obs: 100 % / Redundancy: 37.9 % / Biso Wilson estimate: 34.0387505161 Å2 / CC1/2: 1 / Net I/σ(I): 42.3
Reflection shellResolution: 1.98→2.03 Å / Rmerge(I) obs: 0.963 / Num. unique obs: 1844 / CC1/2: 0.949

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WZV

7wzv


Resolution: 1.98001304567→41.2158933488 Å / SU ML: 0.250812795788 / Cross valid method: FREE R-VALUE / σ(F): 1.35002947799 / Phase error: 24.4586368563
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.23413175987 1284 4.80466995959 %
Rwork0.209269199281 25440 -
obs0.210486832907 26724 99.9850344208 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.3943035328 Å2
Refinement stepCycle: LAST / Resolution: 1.98001304567→41.2158933488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 100 81 2544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005025387404082525
X-RAY DIFFRACTIONf_angle_d0.9498854053383450
X-RAY DIFFRACTIONf_chiral_restr0.0704139939232374
X-RAY DIFFRACTIONf_plane_restr0.00512339223812438
X-RAY DIFFRACTIONf_dihedral_angle_d20.65759459861481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05930.3021387966251270.2822111537622768X-RAY DIFFRACTION100
2.0593-2.1530.2974718321441630.2707080932652743X-RAY DIFFRACTION100
2.153-2.26650.2891281255391360.2591020872512771X-RAY DIFFRACTION99.9656121045
2.2665-2.40850.3066888099971390.2557280790922796X-RAY DIFFRACTION100
2.4085-2.59440.2909206821791340.2534770887982795X-RAY DIFFRACTION100
2.5944-2.85550.2836343779641350.2407397670912818X-RAY DIFFRACTION99.9661475965
2.8555-3.26850.2422063489491470.2279578387072817X-RAY DIFFRACTION100
3.2685-4.11740.2227276964361360.1872153847992883X-RAY DIFFRACTION100
4.1174-41.20.179864237311670.1659446968753049X-RAY DIFFRACTION99.937849596
Refinement TLS params.Method: refined / Origin x: 2.63957130723 Å / Origin y: 36.4786141394 Å / Origin z: 2.53794544531 Å
111213212223313233
T0.36761856863 Å20.117428032635 Å2-0.176898941616 Å2-0.429976655369 Å2-0.134285777342 Å2--0.375434579503 Å2
L1.8216062328 °20.39524735173 °20.81922413769 °2-2.03073489195 °20.586523457384 °2--2.05001537213 °2
S0.0267497786942 Å °-0.400290466163 Å °0.111326059899 Å °-0.315844936503 Å °-0.303240691671 Å °0.244046998416 Å °-0.12384236794 Å °-0.58237654549 Å °0.139724801104 Å °
Refinement TLS groupSelection details: all

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