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

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Basic information

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


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-7P8 / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / 4Fe-4S cluster-binding domain-containing protein
Similarity search - Component
Biological speciesStreptomyces spectabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89931293521 Å
AuthorsZhou, J.H. / Hou, X.L.
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 1.1May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: 4Fe-4S cluster-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,80335
Polymers72,0292
Non-polymers4,77433
Water6,431357
1
A: 4Fe-4S cluster-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,44017
Polymers36,0151
Non-polymers2,42516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-63 kcal/mol
Surface area12910 Å2
MethodPISA
2
B: 4Fe-4S cluster-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,36318
Polymers36,0151
Non-polymers2,34917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-130 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.280, 93.579, 108.146
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 3 - 299 / Label seq-ID: 23 - 319

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain 'A' and resid 3 through 299)AA
2chain 'B'BB

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 36014.637 Da / Num. of mol.: 2
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 , 9 types, 390 molecules

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


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-7P8 / (1~{S},2~{R},4~{S},5~{R})-2,4-bis(methylamino)-6-[(2~{S},3~{R},4~{S},6~{R})-6-methyl-3,4-bis(oxidanyl)oxan-2-yl]oxy-cyclohexane-1,3,5-triol


Mass: 336.381 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28N2O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.5 M Sodium cacodylate trihydrate (pH 6.5), 1.7 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: BL17U1 / Wavelength: 0.97917 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2020
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.89→70.77 Å / Num. obs: 53042 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Net I/σ(I): 16.7
Reflection shellResolution: 1.89→2 Å / Num. unique obs: 7642 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.89931293521→70.7643857242 Å / SU ML: 0.240473563064 / Cross valid method: THROUGHOUT / σ(F): 1.32609457704 / Phase error: 25.1162430572
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234886035528 2621 4.9522909778 %
Rwork0.199954106414 50304 -
obs0.201665248867 52925 99.8886456289 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.2001153623 Å2
Refinement stepCycle: LAST / Resolution: 1.89931293521→70.7643857242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4711 0 243 357 5311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005839658368125065
X-RAY DIFFRACTIONf_angle_d1.030341761836916
X-RAY DIFFRACTIONf_chiral_restr0.0558061660191749
X-RAY DIFFRACTIONf_plane_restr0.00488825874692871
X-RAY DIFFRACTIONf_dihedral_angle_d16.52445046182962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93390.3515589331231210.2811311654852614X-RAY DIFFRACTION100
1.9339-1.9710.3187646171631520.2709628113272608X-RAY DIFFRACTION99.9275887038
1.971-2.01130.2622095601231110.2527666591222633X-RAY DIFFRACTION100
2.0113-2.0550.2791054660551340.2452327268612621X-RAY DIFFRACTION100
2.055-2.10280.3109955026621150.2371950020862641X-RAY DIFFRACTION100
2.1028-2.15540.2832561822761490.2262667510762597X-RAY DIFFRACTION99.9635966509
2.1554-2.21370.2743704939931480.2269916278182611X-RAY DIFFRACTION99.9637681159
2.2137-2.27880.260353792741400.2194498208042638X-RAY DIFFRACTION100
2.2788-2.35240.2980418521971610.2217810853442588X-RAY DIFFRACTION99.9272991639
2.3524-2.43650.2655947721451360.2126766261962608X-RAY DIFFRACTION100
2.4365-2.5340.2498705501771250.2116992396492685X-RAY DIFFRACTION100
2.534-2.64940.2641120239151360.2151060189312628X-RAY DIFFRACTION100
2.6494-2.78910.2607399436851350.2148406499822631X-RAY DIFFRACTION99.9638597759
2.7891-2.96380.2501789310321280.2066428846472681X-RAY DIFFRACTION99.9644128114
2.9638-3.19260.2297932634611380.2081791757692654X-RAY DIFFRACTION99.9641962048
3.1926-3.51390.2362538474751530.1876647753222651X-RAY DIFFRACTION99.9643493761
3.5139-4.02240.2093967601891570.170359644712677X-RAY DIFFRACTION99.859055673
4.0224-5.06750.1794613670341450.1641013317712723X-RAY DIFFRACTION100
5.0675-70.760.202452785491370.1926662006562815X-RAY DIFFRACTION98.5642737896
Refinement TLS params.Method: refined / Origin x: -4.07118898352 Å / Origin y: 16.4696925026 Å / Origin z: -27.1929538399 Å
111213212223313233
T0.271122031729 Å2-0.00129135143829 Å2-0.0285049217168 Å2-0.270963538512 Å2-0.0231394214167 Å2--0.299365306757 Å2
L0.201092773855 °2-0.143419118171 °2-0.330344103255 °2-0.274475061628 °20.0716244249962 °2--1.20228761352 °2
S0.0290009113255 Å °0.0543538660945 Å °-0.0394879353383 Å °0.0106124050023 Å °-0.0238094205087 Å °-0.0336923657734 Å °0.0287188156834 Å °-0.0661208315085 Å °0.000379629273652 Å °
Refinement TLS groupSelection details: all

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