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- PDB-5b48: 2-Oxoacid:Ferredoxin Oxidoreductase 1 from Sulfolobus tokodai -

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Basic information

Entry
Database: PDB / ID: 5b48
Title2-Oxoacid:Ferredoxin Oxidoreductase 1 from Sulfolobus tokodai
Components(2-oxoacid--ferredoxin oxidoreductase ...) x 2
KeywordsOXIDOREDUCTASE / thiamin pyrophosphate / iron-sulfur cluster / ferredoxin
Function / homology
Function and homology information


2-oxobutyrate synthase activity / 2-oxoglutarate synthase activity / 2-oxoacid oxidoreductase (ferredoxin) / pyruvate synthase activity / thiamine pyrophosphate binding / 4 iron, 4 sulfur cluster binding / magnesium ion binding
Similarity search - Function
2-oxoacid:acceptor oxidoreductase, beta subunit / Pyruvate ferredoxin oxidoreductase beta subunit, C-terminal / Pyruvate ferredoxin oxidoreductase beta subunit C terminal / 2-oxoacid:acceptor oxidoreductase, alpha subunit / Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain / Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg / Pyruvate-flavodoxin oxidoreductase, central domain / Pyruvate/ketoisovalerate oxidoreductase, catalytic domain / Pyruvate ferredoxin/flavodoxin oxidoreductase / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II ...2-oxoacid:acceptor oxidoreductase, beta subunit / Pyruvate ferredoxin oxidoreductase beta subunit, C-terminal / Pyruvate ferredoxin oxidoreductase beta subunit C terminal / 2-oxoacid:acceptor oxidoreductase, alpha subunit / Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain / Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg / Pyruvate-flavodoxin oxidoreductase, central domain / Pyruvate/ketoisovalerate oxidoreductase, catalytic domain / Pyruvate ferredoxin/flavodoxin oxidoreductase / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Chem-TDN / 2-oxoacid:ferredoxin oxidoreductase 1, subunit alpha / 2-oxoacid:ferredoxin oxidoreductase 1, subunit beta
Similarity search - Component
Biological speciesSulfolobus tokodaii str. 7 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYan, Z. / Maruyama, A. / Arakawa, T. / Fushinobu, S. / Wakagi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS KAKENHI24580136 Japan
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structures of archaeal 2-oxoacid:ferredoxin oxidoreductases from Sulfolobus tokodaii
Authors: Yan, Z. / Maruyama, A. / Arakawa, T. / Fushinobu, S. / Wakagi, T.
History
DepositionApr 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: 2-oxoacid--ferredoxin oxidoreductase alpha subunit
B: 2-oxoacid--ferredoxin oxidoreductase beta subunit
C: 2-oxoacid--ferredoxin oxidoreductase alpha subunit
D: 2-oxoacid--ferredoxin oxidoreductase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,8267
Polymers207,9674
Non-polymers8583
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21990 Å2
ΔGint-146 kcal/mol
Surface area55720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.150, 145.878, 170.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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2-oxoacid--ferredoxin oxidoreductase ... , 2 types, 4 molecules ACBD

#1: Protein 2-oxoacid--ferredoxin oxidoreductase alpha subunit


Mass: 70331.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii str. 7 (archaea) / Strain: 7 / Gene: STK_23000 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3)
References: UniProt: Q96Y66, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With an iron-sulfur protein as acceptor
#2: Protein 2-oxoacid--ferredoxin oxidoreductase beta subunit


Mass: 33652.621 Da / Num. of mol.: 2 / Mutation: K5T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii str. 7 (archaea) / Strain: 7 / Gene: STK_22980 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3)
References: UniProt: Q96Y68, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With an iron-sulfur protein as acceptor

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Non-polymers , 4 types, 64 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-TDN / 2-[(2E)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-(1-oxidanylpropylidene)-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate


Mass: 482.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N4O8P2S
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 15% PEG3350, 0.1 M Tris-HCl, 0.1 M NaBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 24, 2005
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 65171 / % possible obs: 99.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 27
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 1.72 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B46

5b46


Resolution: 2.5→36.47 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 11.974 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.651 / ESU R Free: 0.328 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27799 3274 5.1 %RANDOM
Rwork0.21121 ---
obs0.21466 61283 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.549 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12972 0 39 61 13072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01913249
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212906
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.96917918
X-RAY DIFFRACTIONr_angle_other_deg1.106329690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.33751623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25824.346573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.755152330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.321572
X-RAY DIFFRACTIONr_chiral_restr0.1010.22041
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114660
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022881
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.756.4236582
X-RAY DIFFRACTIONr_mcbond_other4.756.4236581
X-RAY DIFFRACTIONr_mcangle_it7.0479.6158175
X-RAY DIFFRACTIONr_mcangle_other7.0469.6158176
X-RAY DIFFRACTIONr_scbond_it5.2367.0626667
X-RAY DIFFRACTIONr_scbond_other5.2367.0626668
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.06110.3539732
X-RAY DIFFRACTIONr_long_range_B_refined10.91451.59614525
X-RAY DIFFRACTIONr_long_range_B_other10.91451.59714525
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 192 -
Rwork0.297 4013 -
obs--88.88 %

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