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- PDB-7x0b: The structure of a Twitch Radical SAM Dehydrogenase SpeY -

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Basic information

Entry
Database: PDB / ID: 7x0b
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


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
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: 2.02027524648 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 21, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / 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)75,39725
Polymers72,0292
Non-polymers3,36823
Water4,774265
1
A: 4Fe-4S cluster-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,91115
Polymers36,0151
Non-polymers1,89614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13130 Å2
MethodPISA
2
B: 4Fe-4S cluster-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,48710
Polymers36,0151
Non-polymers1,4729
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-23 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.932, 94.196, 107.577
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: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 2 - 300 / Label seq-ID: 22 - 320

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain 'A'AA
2(chain 'B' and resid 2 through 301)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 , 7 types, 288 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.5 M Sodium cacodylate trihydrate (pH 6.5), 1.8 M Ammonium sulfate and 0.15 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: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 43975 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 23.6981167031 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.172
Reflection shellResolution: 2.02→2.05 Å / Num. unique obs: 43975 / CC1/2: 0.722

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WZV

7wzv


Resolution: 2.02027524648→35.9348943832 Å / SU ML: 0.252689238447 / Cross valid method: FREE R-VALUE / σ(F): 1.34479052676 / Phase error: 27.4294657737
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.246870960004 2058 4.9921164342 %
Rwork0.217687876118 39167 -
obs0.219159562088 41225 93.7166109709 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.7303697378 Å2
Refinement stepCycle: LAST / Resolution: 2.02027524648→35.9348943832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4734 0 151 265 5150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004284427307485002
X-RAY DIFFRACTIONf_angle_d0.9449045970176828
X-RAY DIFFRACTIONf_chiral_restr0.0516200228914747
X-RAY DIFFRACTIONf_plane_restr0.00461086688891875
X-RAY DIFFRACTIONf_dihedral_angle_d18.50251636363000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0203-2.06730.288527860788920.250707673241940X-RAY DIFFRACTION70.2142363511
2.0673-2.1190.2799097492061030.2587083414332116X-RAY DIFFRACTION76.4908652189
2.119-2.17620.2974915138511240.2402392837712197X-RAY DIFFRACTION80.3670360111
2.1762-2.24030.2632520107491220.2475718073092430X-RAY DIFFRACTION87.45716244
2.2403-2.31260.324907737431380.2384258968072564X-RAY DIFFRACTION94.5747287364
2.3126-2.39520.279998523881500.2405374901072712X-RAY DIFFRACTION98.3843245101
2.3952-2.49110.2823592209831250.2386134755422770X-RAY DIFFRACTION99.4845360825
2.4911-2.60440.2637916072311560.2457630567622753X-RAY DIFFRACTION99.7941680961
2.6044-2.74170.2856856781521510.2476850340132739X-RAY DIFFRACTION99.9654098928
2.7417-2.91340.31389557251190.2502999363762818X-RAY DIFFRACTION100
2.9134-3.13820.2708950514511680.2453025002832761X-RAY DIFFRACTION99.9317639031
3.1382-3.45380.2666148678761540.2198832618212785X-RAY DIFFRACTION99.8640842678
3.4538-3.9530.2043264058151520.1894716304922790X-RAY DIFFRACTION99.4927291173
3.953-4.97830.1870360345321430.1734140437792848X-RAY DIFFRACTION99.5672436751
4.9783-35.930.2013139519341610.1881986086072944X-RAY DIFFRACTION99.1379310345
Refinement TLS params.Method: refined / Origin x: -3.71340669681 Å / Origin y: 16.5125369526 Å / Origin z: 134.01268667 Å
111213212223313233
T0.164399922764 Å2-0.0163060700726 Å2-0.0119717922179 Å2-0.133487805294 Å2-0.015344461292 Å2--0.19784784113 Å2
L0.36078256161 °2-0.040165725629 °2-0.446900298849 °2-0.211159393395 °20.350631554261 °2--1.88508511906 °2
S-0.00118486182555 Å °-0.00122744094303 Å °-0.00398528483561 Å °0.0501700068887 Å °-0.0553746227611 Å °0.0527106650477 Å °0.153877446398 Å °-0.140544467517 Å °0.041677103729 Å °
Refinement TLS groupSelection details: all

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