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- EMDB-10495: Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate ... -

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Basic information

Entry
Database: EMDB / ID: EMD-10495
TitleCryo-EM Structure of NADH reduced form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus
Map data
Sample
  • Complex: Formate dehydrogenase, NADH reduced
    • Protein or peptide: x 4 types
  • Ligand: x 7 types
Function / homology
Function and homology information


formate dehydrogenase complex / formate dehydrogenase / formate metabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / molybdopterin cofactor binding / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding ...formate dehydrogenase complex / formate dehydrogenase / formate metabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / molybdopterin cofactor binding / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / metal ion binding
Similarity search - Function
Formate dehydrogenase, delta subunit / NADH-dependant formate dehydrogenase delta subunit FdsD / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain ...Formate dehydrogenase, delta subunit / NADH-dependant formate dehydrogenase delta subunit FdsD / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / Aspartate decarboxylase-like domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
Formate dehydrogenase subunit beta / NAD-dependent formate dehydrogenase subunit delta / Formate dehydrogenase / Formate dehydrogenase subunit gamma / NAD-dependent formate dehydrogenase, delta subunit / formate dehydrogenase / NAD-dependent formate dehydrogenase, beta subunit / NAD-dependent formate dehydrogenase, gamma subunit
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsWendler P / Radon C / Mittelstaedt G
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research FoundationEXC 314/2 Germany
European UnioniNext-4008 Germany
German Research FoundationEXC 2008/1 Germany
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase.
Authors: Christin Radon / Gerd Mittelstädt / Benjamin R Duffus / Jörg Bürger / Tobias Hartmann / Thorsten Mielke / Christian Teutloff / Silke Leimkühler / Petra Wendler /
Abstract: Metal-containing formate dehydrogenases (FDH) catalyse the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active site. They display a diverse subunit and cofactor ...Metal-containing formate dehydrogenases (FDH) catalyse the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active site. They display a diverse subunit and cofactor composition, but structural information on these enzymes is limited. Here we report the cryo-electron microscopic structures of the soluble Rhodobacter capsulatus FDH (RcFDH) as isolated and in the presence of reduced nicotinamide adenine dinucleotide (NADH). RcFDH assembles into a 360 kDa dimer of heterotetramers revealing a putative interconnection of electron pathway chains. In the presence of NADH, the RcFDH structure shows charging of cofactors, indicative of an increased electron load.
History
DepositionNov 15, 2019-
Header (metadata) releaseApr 22, 2020-
Map releaseApr 22, 2020-
UpdateApr 29, 2020-
Current statusApr 29, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tg9
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10495.png

Downloads & links

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Map

FileDownload / File: emd_10495.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.0223 / Movie #1: 0.03
Minimum - Maximum-0.15199098 - 0.347558
Average (Standard dev.)0.00069495675 (±0.0073885787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 239.68001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z239.680239.680239.680
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.1520.3480.001

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Supplemental data

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Sample components

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Entire : Formate dehydrogenase, NADH reduced

EntireName: Formate dehydrogenase, NADH reduced
Components
  • Complex: Formate dehydrogenase, NADH reduced
    • Protein or peptide: Formate dehydrogenase subunit alpha
    • Protein or peptide: Formate dehydrogenase subunit beta
    • Protein or peptide: Formate dehydrogenase subunit gamma
    • Protein or peptide: NAD-dependent formate dehydrogenase subunit delta
  • Ligand: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
  • Ligand: MOLYBDENUM(VI) ION
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: HYDROSULFURIC ACIDHydrogen sulfide
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

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Supramolecule #1: Formate dehydrogenase, NADH reduced

SupramoleculeName: Formate dehydrogenase, NADH reduced / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Recombinant expressionOrganism: Rhodobacter capsulatus (bacteria)
Molecular weightExperimental: 360 KDa

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Macromolecule #1: Formate dehydrogenase subunit alpha

MacromoleculeName: Formate dehydrogenase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 104.589211 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus (bacteria)
SequenceString: MKDLIIPPLD WTQDMGTPKR EGAPVHLTID GVEVTVPAGT SVLRAAAEAG ISIPKLCATD NVEPVGSCRL CMVEIEGMRG TPTSCTTPV APGMRVHTQT PQLQKLRRGV MELYISDHPL DCLTCAANGD CELQDMAGAV GLREVRYQAK DTHFARRDAT G PNPRYIPK ...String:
MKDLIIPPLD WTQDMGTPKR EGAPVHLTID GVEVTVPAGT SVLRAAAEAG ISIPKLCATD NVEPVGSCRL CMVEIEGMRG TPTSCTTPV APGMRVHTQT PQLQKLRRGV MELYISDHPL DCLTCAANGD CELQDMAGAV GLREVRYQAK DTHFARRDAT G PNPRYIPK DNSNPYFSYD PAKCIVCMRC VRACEEVQGT FALTVMGRGF DARISPAAPD FLSSDCVSCG ACVQACPTAT LV EKSVERI GTPERKVVTT CAYCGVGCSF EAHMLGDQLV RMVPWKGGAA NRGHSCVKGR FAYGYATHQD RILKPMIRDK ITD PWREVN WTEALDFTAT RLRALRDSHG ADALGVITSS RCTNEETYLV QKLARAVFGT NNTDTCARVC HSPTGYGLKQ TFGT SAGTQ DFDSVEETDL ALVIGANPTD GHPVFASRLR KRLRAGAKLI VVDPRRIDLL NTPHRGEAWH LQLKPGTNVA VMTAM AHVI VTEQIFDKRF IGDRCDWDEW ADYAEFVANP EYAPEAVESL TGVPAGLLRQ AARAYAAAPN AAIYYGLGVT EHSQGS TTV IAIANLAMMT GNIGRPGVGV NPLRGQNNVQ GSCDMGSFPH EFPGYRHVSD DATRGLFERT WGVTLSSEPG LRIPNML DA AVEGRFKALY VQGEDILQSD PDTRHVSAGL AAMDLVIVHD LFLNETANYA HVFLPGSTFL EKDGTFTNAE RRINRVRR V MAPKAGFADW EVTQMLANAL GAGWHYTHPS EIMAEIAATT PGFAAVTYEM LDARGSVQWP CNEKAPEGSP IMHVEGFVR GKGRFIRTAY LPTDEKTGPR FPLLLTTGRI LSQYNVGAQT RRTENTVWHG EDRLEIHPTD AETRGIRDGD WVRLASRAGE TTLRATVTD RVSPGVVYTT FHHPDTQANV VTTDTSDWAT NCPEYKVTAV QVAASNGPSD WQQDYAAQAA AARRIEAAE

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Macromolecule #2: Formate dehydrogenase subunit beta

MacromoleculeName: Formate dehydrogenase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 52.75577 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus (bacteria)
SequenceString: MKIWLPCDAA AKACGAEAVL AALRLEAEKR GGALDIARNG SRGMIWLEPL LEVETPAGRI GFGPMTPADV PALFDALESH PKALGLVEE IPFFKRQTRL TFARCGRIEP LSLAQFAAAE GWAGLRKALK MTPAEVVEEV LASGLRGRGG AGFPTGIKWR T VAAAQADQ ...String:
MKIWLPCDAA AKACGAEAVL AALRLEAEKR GGALDIARNG SRGMIWLEPL LEVETPAGRI GFGPMTPADV PALFDALESH PKALGLVEE IPFFKRQTRL TFARCGRIEP LSLAQFAAAE GWAGLRKALK MTPAEVVEEV LASGLRGRGG AGFPTGIKWR T VAAAQADQ KYIVCNVDEG DSGSFADRML IEGDPFCLVE GMAIAGHAVG ATRGYVYIRS EYPDAIAVMR AAIAMAKPFL AE AGFEMEV RVGAGAYVCG EETSLLNSLE GKRGTVRAKP PLPALKGLFG KPTVVNNLLS LAAVPWIIAH GAKAYESFGM DRS RGTIPL QIGGNVKRGG LFETGFGITL GELVEDICGG TASGRPVKAV QVGGPLGAYH PVSDYHLPFC YEQFAGQGGL VGHA GLVVH DDTADMLKLA RFAMEFCAIE SCGTCTPCRI GAVRGVEVID RIAAGDASAM PLLDDLCQTM KLGSLCALGG FTPYP VQSA IRHFPADFPC AREAAE

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Macromolecule #3: Formate dehydrogenase subunit gamma

MacromoleculeName: Formate dehydrogenase subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: formate dehydrogenase
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 15.60305 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus (bacteria)
SequenceString:
MTDTARLRAI LAAHRGREGA LLPILHDVQA AFGFIPEDAY APIAADLGLT RAEVAGVVGF YHDFRKAPAG RHVIKLCRAE ACQAMGMDA VQARLESALG LRLGDSSEAV TLEAVYCLGL CACAPAAMVD DRLVGRLDAA AVAGIVAELG A

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Macromolecule #4: NAD-dependent formate dehydrogenase subunit delta

MacromoleculeName: NAD-dependent formate dehydrogenase subunit delta / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 7.388531 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus (bacteria)
SequenceString:
MSDDKIIRMA NQIAAFFAVQ PGDRAGPVAA HISENWSAPM RAALLAHVAA QSPGLDPLVI AAAPQIRPVP A

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Macromolecule #5: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,1...

MacromoleculeName: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
type: ligand / ID: 5 / Number of copies: 4 / Formula: MGD
Molecular weightTheoretical: 740.557 Da
Chemical component information

ChemComp-MGD:
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE

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Macromolecule #6: MOLYBDENUM(VI) ION

MacromoleculeName: MOLYBDENUM(VI) ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: 6MO
Molecular weightTheoretical: 95.94 Da

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Macromolecule #7: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 7 / Number of copies: 4 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

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Macromolecule #8: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 8 / Number of copies: 10 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #9: HYDROSULFURIC ACID

MacromoleculeName: HYDROSULFURIC ACID / type: ligand / ID: 9 / Number of copies: 2 / Formula: H2S
Molecular weightTheoretical: 34.081 Da
Chemical component information

ChemComp-H2S:
HYDROSULFURIC ACID / Hydrogen sulfide

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Macromolecule #10: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 10 / Number of copies: 2 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

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Macromolecule #11: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

MacromoleculeName: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / type: ligand / ID: 11 / Number of copies: 2 / Formula: NAI
Molecular weightTheoretical: 665.441 Da
Chemical component information

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Nicotinamide adenine dinucleotide

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
75.0 mMpotassium phosphate
10.0 mMsodium azide
GridModel: Quantifoil R2/4 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy #1

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageCooling holder cryogen: NITROGEN
Microscopy ID1
Image recordingImage recording ID: 1 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Electron microscopy #1~

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Microscopy ID1
Image recordingImage recording ID: 2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.10)
Details: CTFFIND4 was used to estimate contrast transfer function parameters. CTF correction was done in Relion 3.0.
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 199229
Image recording ID1
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

1fdo

,

3iam

,

5xf9

)
RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-6tg9:
Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus

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