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- PDB-9bt4: Pyruvate:Ferredoxin Oxidoreductase from Methanosarcina acetivorans -

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Basic information

Entry
Database: PDB / ID: 9bt4
TitlePyruvate:Ferredoxin Oxidoreductase from Methanosarcina acetivorans
Components(Pyruvate:Ferredoxin Oxidoreductase, subunit ...) x 4
KeywordsELECTRON TRANSPORT / Oxidoreductase
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / pyruvate synthase / organic acid metabolic process / sulfur compound biosynthetic process / thiamine pyrophosphate binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / metal ion binding
Similarity search - Function
: / : / 2-oxoacid:acceptor oxidoreductase, gamma subunit, pyruvate/2-ketoisovalerate / : / : / 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate / : / Pyruvate:ferredoxin oxidoreductase, core domain II / Pyruvate:ferredoxin oxidoreductase core domain II / Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain ...: / : / 2-oxoacid:acceptor oxidoreductase, gamma subunit, pyruvate/2-ketoisovalerate / : / : / 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate / : / 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 / 4Fe-4S binding domain / 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 / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / THIAMINE DIPHOSPHATE / Pyruvate synthase subunit PorC / Pyruvate synthase subunit PorD / Pyruvate synthase subunit PorA / Pyruvate synthase, subunit beta
Similarity search - Component
Biological speciesMethanosarcina acetivorans C2A (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsCatlin, D. / Nair, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-02ER15296 United States
CitationJournal: Structure / Year: 2024
Title: Structural organization of pyruvate: ferredoxin oxidoreductase from the methanogenic archaeon Methanosarcina acetivorans.
Authors: Cossu, M. / Catlin, D. / Elliott, S.J. / Metcalf, W.W. / Nair, S.K.
History
DepositionMay 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Pyruvate:Ferredoxin Oxidoreductase, subunit alpha
A: Pyruvate:Ferredoxin Oxidoreductase, subunit alpha
C: Pyruvate:Ferredoxin Oxidoreductase, subunit beta
D: Pyruvate:Ferredoxin Oxidoreductase, subunit beta
G: Pyruvate:Ferredoxin Oxidoreductase, subunit delta
H: Pyruvate:Ferredoxin Oxidoreductase, subunit delta
E: Pyruvate:Ferredoxin Oxidoreductase, subunit gamma
F: Pyruvate:Ferredoxin Oxidoreductase, subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,72818
Polymers210,7198
Non-polymers3,00910
Water14,520806
1
B: Pyruvate:Ferredoxin Oxidoreductase, subunit alpha
D: Pyruvate:Ferredoxin Oxidoreductase, subunit beta
H: Pyruvate:Ferredoxin Oxidoreductase, subunit delta
F: Pyruvate:Ferredoxin Oxidoreductase, subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8649
Polymers105,3604
Non-polymers1,5055
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-129 kcal/mol
Surface area36720 Å2
MethodPISA
2
A: Pyruvate:Ferredoxin Oxidoreductase, subunit alpha
C: Pyruvate:Ferredoxin Oxidoreductase, subunit beta
G: Pyruvate:Ferredoxin Oxidoreductase, subunit delta
E: Pyruvate:Ferredoxin Oxidoreductase, subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8649
Polymers105,3604
Non-polymers1,5055
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9910 Å2
ΔGint-129 kcal/mol
Surface area36800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.121, 79.121, 496.524
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Pyruvate:Ferredoxin Oxidoreductase, subunit ... , 4 types, 8 molecules BACDGHEF

#1: Protein Pyruvate:Ferredoxin Oxidoreductase, subunit alpha


Mass: 44348.641 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans C2A (archaea) / References: UniProt: Q8TUN4
#2: Protein Pyruvate:Ferredoxin Oxidoreductase, subunit beta


Mass: 31973.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans C2A (archaea) / References: UniProt: Q8TUN5
#3: Protein Pyruvate:Ferredoxin Oxidoreductase, subunit delta


Mass: 9405.790 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans C2A (archaea) / References: UniProt: Q8TUN3
#4: Protein Pyruvate:Ferredoxin Oxidoreductase, subunit gamma


Mass: 19631.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans C2A (archaea) / References: UniProt: Q8TUN2, pyruvate synthase

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Non-polymers , 4 types, 816 molecules

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


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / 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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 10-15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.92→67.9 Å / Num. obs: 726473 / % possible obs: 99.7 % / Redundancy: 5.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.091 / Net I/σ(I): 8.8
Reflection shellResolution: 1.92→1.925 Å / Rmerge(I) obs: 0.745 / Num. unique obs: 7657 / CC1/2: 0.705 / Rpim(I) all: 0.343

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→25.001 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.382 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.136
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2002 6491 4.888 %
Rwork0.1732 126291 -
all0.175 --
obs-132782 99.691 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 22.107 Å2
Baniso -1Baniso -2Baniso -3
1-0.296 Å20.148 Å20 Å2
2--0.296 Å2-0 Å2
3----0.959 Å2
Refinement stepCycle: LAST / Resolution: 1.92→25.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14456 0 102 806 15364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01214900
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.82220210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0551884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.696578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.699102495
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.36910610
X-RAY DIFFRACTIONr_chiral_restr0.0830.22282
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211107
X-RAY DIFFRACTIONr_nbd_refined0.1940.27641
X-RAY DIFFRACTIONr_nbtor_refined0.30.210282
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.21074
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1780.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1240.216
X-RAY DIFFRACTIONr_mcbond_it0.8882.0947566
X-RAY DIFFRACTIONr_mcangle_it1.5413.7579440
X-RAY DIFFRACTIONr_scbond_it1.2822.2567334
X-RAY DIFFRACTIONr_scangle_it2.1564.09310698
X-RAY DIFFRACTIONr_lrange_it4.10123.18723550
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.92-1.970.2244070.2293550.2297790.9670.96799.82620.217
1.97-2.0230.2434520.20890940.20995600.960.97199.85360.205
2.023-2.0810.2254710.288270.20193250.9650.97499.71050.196
2.081-2.1450.2354560.19385060.19589920.9630.97699.66640.188
2.145-2.2150.1994110.18382520.18486920.9750.97999.66640.177
2.215-2.2920.2044290.17480010.17584540.9740.98199.71610.167
2.292-2.3780.2173560.17478150.17681960.9670.98199.6950.166
2.378-2.4740.2174030.16974390.17178650.9690.98299.70760.161
2.474-2.5830.2124090.16770560.16975120.9740.98399.37430.157
2.583-2.7070.2033380.17168590.17272080.9730.98399.84740.162
2.707-2.8520.2053790.18165060.18268860.9740.98199.98550.176
2.852-3.0220.2063270.1861510.18164790.9760.98199.98460.176
3.022-3.2280.1973040.17257780.17360850.9760.98399.95070.172
3.228-3.4820.1952770.17154320.17257130.9750.98299.930.173
3.482-3.8060.1912730.15749990.15952740.9770.98699.96210.164
3.806-4.2430.1642220.14545120.14647380.9860.98899.91560.157
4.243-4.8770.1632410.14639320.14742240.9850.98898.79260.165
4.877-5.9170.211460.17534130.17735740.9780.98499.58030.197
5.917-8.1420.1721190.1726980.1728240.9840.98499.75210.197
8.142-25.0010.165690.1616170.1616990.9870.98799.23480.199

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