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- PDB-9pzj: Benzylsuccinate synthase alpha-beta-gamma complex with bound tolu... -

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Basic information

Entry
Database: PDB / ID: 9pzj
TitleBenzylsuccinate synthase alpha-beta-gamma complex with bound toluene and fumarate
Components(benzylsuccinate synthase ...) x 3
KeywordsLYASE / Benzylsuccinate Synthase / Glycyl Radical Enzyme / FeS cluster / toluene / fumarate
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / lyase activity / metal ion binding / cytosol
Similarity search - Function
Benzylsuccinate synthase beta subunit / : / Benzylsuccinate synthase beta subunit / Benzylsuccinate synthase gamma subunit / Benzylsuccinate synthase gamma subunit superfamily / BssC/TutF protein / : / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain ...Benzylsuccinate synthase beta subunit / : / Benzylsuccinate synthase beta subunit / Benzylsuccinate synthase gamma subunit / Benzylsuccinate synthase gamma subunit superfamily / BssC/TutF protein / : / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile.
Similarity search - Domain/homology
FUMARIC ACID / TOLUENE / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / TutF / TutD / TutG
Similarity search - Component
Biological speciesThauera aromatica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLiu, J. / Andorfer, M.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145910 United States
CitationJournal: Biochemistry / Year: 2025
Title: Accessory Subunit Regulates Thiyl Radical Formation in Benzylsuccinate Synthase.
Authors: Anas, S. / Liu, J. / Vats, A. / Gainadi, R. / Sharif, S. / Piriyatamwong, A. / Andorfer, M.C.
History
DepositionAug 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: benzylsuccinate synthase alpha chain
B: benzylsuccinate synthase beta chain
C: benzylsuccinate synthase gamma chain
D: benzylsuccinate synthase alpha chain
E: benzylsuccinate synthase beta chain
F: benzylsuccinate synthase gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,46216
Polymers235,4276
Non-polymers2,03510
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16900 Å2
ΔGint-117 kcal/mol
Surface area61690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.396, 118.535, 124.929
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Benzylsuccinate synthase ... , 3 types, 6 molecules ADBECF

#1: Protein benzylsuccinate synthase alpha chain / TutD


Mass: 99117.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: has a SGTGSGSS linker and Histag at the C-terminus of protein
Source: (gene. exp.) Thauera aromatica (bacteria) / Gene: tutD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O68395, benzylsuccinate synthase
#2: Protein benzylsuccinate synthase beta chain / TutG


Mass: 11730.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Has a Histag and TEV site at the N-terminus / Source: (gene. exp.) Thauera aromatica (bacteria) / Gene: tutG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O68396
#3: Protein benzylsuccinate synthase gamma chain / TutF


Mass: 6865.687 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thauera aromatica (bacteria) / Gene: tutF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O68394

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Non-polymers , 5 types, 23 molecules

#4: Chemical ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MBN / TOLUENE


Mass: 92.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 29% (w/v) PEG3350, 100 mM Tris pH 8.5, 60 mM KCl, 5 mM fumarate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.9→33.68 Å / Num. obs: 48786 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.992 / Net I/σ(I): 9.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4793 / CC1/2: 0.735 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→33.68 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 1464 3 %
Rwork0.2118 --
obs0.2128 48770 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→33.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15611 0 76 13 15700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316063
X-RAY DIFFRACTIONf_angle_d0.56921716
X-RAY DIFFRACTIONf_dihedral_angle_d15.6642179
X-RAY DIFFRACTIONf_chiral_restr0.042255
X-RAY DIFFRACTIONf_plane_restr0.0062846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-30.37741470.31864644X-RAY DIFFRACTION100
3-3.120.35031400.30094687X-RAY DIFFRACTION100
3.12-3.270.30531540.27284664X-RAY DIFFRACTION100
3.27-3.440.27341490.25574676X-RAY DIFFRACTION100
3.44-3.650.24451370.22784700X-RAY DIFFRACTION100
3.65-3.930.27231470.20314705X-RAY DIFFRACTION100
3.93-4.330.21581460.18084722X-RAY DIFFRACTION100
4.33-4.950.20351480.16664738X-RAY DIFFRACTION100
4.95-6.240.22591470.18144797X-RAY DIFFRACTION100
6.24-33.680.17241490.16794973X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -3.4093 Å / Origin y: 35.3578 Å / Origin z: -30.461 Å
111213212223313233
T0.3324 Å20.0429 Å20.0231 Å2-0.1938 Å2-0.0046 Å2--0.2875 Å2
L0.7077 °2-0.1677 °20.2271 °2-0.2945 °2-0.0218 °2--0.6222 °2
S0.0221 Å °-0.0798 Å °-0.0149 Å °-0.0071 Å °0.0302 Å °0.0109 Å °0.1838 Å °0.0201 Å °-0.0507 Å °
Refinement TLS groupSelection details: all

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