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- PDB-5b46: 2-Oxoacid:Ferredoxin Oxidoreductase 2 from Sulfolobus tokodai - l... -

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Basic information

Entry
Database: PDB / ID: 5b46
Title2-Oxoacid:Ferredoxin Oxidoreductase 2 from Sulfolobus tokodai - ligand free form
Components(2-oxoacid--ferredoxin oxidoreductase ...) x 2
KeywordsOXIDOREDUCTASE / thiamin pyrophosphate / iron-sulfur cluster / ferredoxin
Function / homology
Function and homology information


2-oxoglutarate synthase activity / 2-oxoacid oxidoreductase (ferredoxin) / 2-oxobutyrate synthase activity / 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:ferredoxin oxidoreductase, core domain II / Pyruvate:ferredoxin oxidoreductase core domain II / Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain ...: / : / 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:ferredoxin oxidoreductase, core domain II / Pyruvate:ferredoxin oxidoreductase core domain II / 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 / THIAMINE DIPHOSPHATE / 2-oxoacid:ferredoxin oxidoreductase 2, subunit alpha / 2-oxoacid:ferredoxin oxidoreductase 2, subunit beta
Similarity search - Component
Biological speciesSulfolobus tokodaii str. 7 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9545
Polymers104,1522
Non-polymers8013
Water4,738263
1
A: 2-oxoacid--ferredoxin oxidoreductase alpha subunit
B: 2-oxoacid--ferredoxin oxidoreductase beta subunit
hetero molecules

A: 2-oxoacid--ferredoxin oxidoreductase alpha subunit
B: 2-oxoacid--ferredoxin oxidoreductase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,90710
Polymers208,3054
Non-polymers1,6036
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area27700 Å2
ΔGint-204 kcal/mol
Surface area56500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.889, 205.048, 126.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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2-oxoacid--ferredoxin oxidoreductase ... , 2 types, 2 molecules AB

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


Mass: 70297.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii str. 7 (archaea) / Strain: 7 / Gene: STK_24350 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3)
References: UniProt: Q96XT2, 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: 33855.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii str. 7 (archaea) / Strain: 7 / Gene: STK_24330 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3)
References: UniProt: Q96XT4, 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, 266 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-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#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.: 263 / 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: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.7 M ammonium tartrate dibasic, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2013
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 76707 / % possible obs: 98.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 30.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 3.1 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→33.93 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.457 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.152 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21922 3866 5 %RANDOM
Rwork0.17456 ---
obs0.17679 72834 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.717 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→33.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7294 0 35 263 7592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197482
X-RAY DIFFRACTIONr_bond_other_d0.0030.027260
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.96810125
X-RAY DIFFRACTIONr_angle_other_deg1.233316721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5435926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69524.465327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.092151329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3191539
X-RAY DIFFRACTIONr_chiral_restr0.1380.21122
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218386
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021662
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_it3.6463.9383710
X-RAY DIFFRACTIONr_mcbond_other3.6453.9383709
X-RAY DIFFRACTIONr_mcangle_it4.7385.8844634
X-RAY DIFFRACTIONr_mcangle_other4.7385.8844635
X-RAY DIFFRACTIONr_scbond_it4.9184.4943772
X-RAY DIFFRACTIONr_scbond_other4.9184.4943773
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0666.4985480
X-RAY DIFFRACTIONr_long_range_B_refined8.32631.6238442
X-RAY DIFFRACTIONr_long_range_B_other8.32931.5778387
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 278 -
Rwork0.255 5281 -
obs--97.61 %

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