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- PDB-4pkf: Benzylsuccinate synthase alpha-beta-gamma complex -

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Basic information

Entry
Database: PDB / ID: 4pkf
TitleBenzylsuccinate synthase alpha-beta-gamma complex
Components
  • TutD
  • TutF
  • TutG
KeywordsLYASE / radical / complex
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / lyase activity / metal ion binding
Similarity search - Function
High-Potential Iron-Sulfur Protein; Chain A - #20 / Benzylsuccinate synthase beta subunit / Benzylsuccinate synthase beta subunit / Benzylsuccinate synthase gamma subunit / Benzylsuccinate synthase gamma subunit superfamily / BssC/TutF protein / High-Potential Iron-Sulfur Protein; Chain A / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain ...High-Potential Iron-Sulfur Protein; Chain A - #20 / Benzylsuccinate synthase beta subunit / Benzylsuccinate synthase beta subunit / Benzylsuccinate synthase gamma subunit / Benzylsuccinate synthase gamma subunit superfamily / BssC/TutF protein / High-Potential Iron-Sulfur Protein; Chain A / 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. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / TutF / TutD / TutG
Similarity search - Component
Biological speciesThauera aromatica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.002 Å
AuthorsFunk, M.A. / Drennan, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)0645960 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structures of benzylsuccinate synthase elucidate roles of accessory subunits in glycyl radical enzyme activation and activity.
Authors: Funk, M.A. / Judd, E.T. / Marsh, E.N. / Elliott, S.J. / Drennan, C.L.
History
DepositionMay 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TutD
B: TutG
C: TutF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9498
Polymers115,2863
Non-polymers6635
Water15,061836
1
A: TutD
B: TutG
C: TutF
hetero molecules

A: TutD
B: TutG
C: TutF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,89916
Polymers230,5726
Non-polymers1,32710
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area15840 Å2
ΔGint-126 kcal/mol
Surface area60380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.424, 120.421, 136.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1003-

HOH

21A-1097-

HOH

31A-1115-

HOH

41A-1149-

HOH

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein TutD / benzylsuccinate synthase alpha chain


Mass: 99117.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thauera aromatica (bacteria) / Strain: T1 / Gene: tutD / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: O68395, benzylsuccinate synthase
#2: Protein TutG / benzylsuccinate synthase beta chain


Mass: 9303.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thauera aromatica (bacteria) / Strain: T1 / Gene: tutG / Plasmid: pRSFDuet / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: O68396, benzylsuccinate synthase
#3: Protein TutF / benzylsuccinate synthase gamma chain


Mass: 6865.687 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thauera aromatica (bacteria) / Strain: T1 / Gene: tutF / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: O68394, benzylsuccinate synthase

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Non-polymers , 4 types, 841 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 836 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.8 % / Description: yellow-brown rods
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 2:1 protein (~8 mg/mL in 50 mM Tris, pH 7.6, 15% glycerol, 200 mM sodium chloride) to well solution (25% PEG3350, 100 mM Tris, pH 8.5, 200 mM NH4 ammonium acetate, diffraction-quality ...Details: 2:1 protein (~8 mg/mL in 50 mM Tris, pH 7.6, 15% glycerol, 200 mM sodium chloride) to well solution (25% PEG3350, 100 mM Tris, pH 8.5, 200 mM NH4 ammonium acetate, diffraction-quality crystals typically appeared after 1-2 weeks

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 62251 / Num. obs: 62251 / % possible obs: 99.2 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 21.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 11 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 9.6 / % possible all: 87.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1678) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.002→49.532 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.177 3111 5 %random
Rwork0.1288 ---
obs0.1313 62244 98.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.002→49.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7675 0 27 836 8538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137935
X-RAY DIFFRACTIONf_angle_d1.31810724
X-RAY DIFFRACTIONf_dihedral_angle_d15.3552993
X-RAY DIFFRACTIONf_chiral_restr0.0641113
X-RAY DIFFRACTIONf_plane_restr0.0071406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.002-2.03320.23971220.16142262X-RAY DIFFRACTION84
2.0332-2.06650.20451450.13982548X-RAY DIFFRACTION95
2.0665-2.10210.19261470.12472655X-RAY DIFFRACTION99
2.1021-2.14030.20451370.12942703X-RAY DIFFRACTION100
2.1403-2.18150.21061570.12852658X-RAY DIFFRACTION100
2.1815-2.2260.1991480.12872672X-RAY DIFFRACTION100
2.226-2.27440.19191430.12552705X-RAY DIFFRACTION100
2.2744-2.32740.19821230.12342697X-RAY DIFFRACTION100
2.3274-2.38560.18911320.12692676X-RAY DIFFRACTION100
2.3856-2.450.18391350.12752702X-RAY DIFFRACTION100
2.45-2.52210.21581400.13212718X-RAY DIFFRACTION100
2.5221-2.60350.19481440.14392678X-RAY DIFFRACTION100
2.6035-2.69660.21671000.13952750X-RAY DIFFRACTION100
2.6966-2.80460.19191370.14112708X-RAY DIFFRACTION100
2.8046-2.93220.19051570.13732700X-RAY DIFFRACTION100
2.9322-3.08670.20121470.14112714X-RAY DIFFRACTION100
3.0867-3.28010.17351500.13352710X-RAY DIFFRACTION100
3.2801-3.53330.16891740.12992709X-RAY DIFFRACTION100
3.5333-3.88870.16391480.12132730X-RAY DIFFRACTION100
3.8887-4.45110.13611380.10852762X-RAY DIFFRACTION100
4.4511-5.60670.14171330.11852789X-RAY DIFFRACTION100
5.6067-49.5470.16341540.13512887X-RAY DIFFRACTION100

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