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- PDB-8zqd: Anaerobically isolated active [FeFe]-hydrogenase CbA5H -

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Basic information

Entry
Database: PDB / ID: 8zqd
TitleAnaerobically isolated active [FeFe]-hydrogenase CbA5H
Components[FeFe]-hydrogenase
KeywordsOXIDOREDUCTASE / [FeFe]-hydrogenases / homodimer / Zn-binding
Function / homology
Function and homology information


ferredoxin hydrogenase activity / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain ...Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Soluble ligand binding domain / SLBB domain / 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
Chem-402 / IRON/SULFUR CLUSTER / [FeFe]-hydrogenase
Similarity search - Component
Biological speciesClostridium beijerinckii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.21 Å
AuthorsKawamoto, A. / Kurisu, G.
Funding support Germany, Japan, 6items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC2033-390677874-RESOLV Germany
Japan Science and TechnologyJPMJSC21C2 Japan
German Research Foundation (DFG)HA2555/10-1 Germany
German Research Foundation (DFG)AP242/12-1 Germany
Japan Society for the Promotion of Science (JSPS)21H02417 Japan
German Research Foundation (DFG)461338801 Germany
CitationJournal: To Be Published
Title: Anaerobically isolated active [FeFe]-hydrogenase CbA5H
Authors: Duan, J. / Rutz, A. / Kawamoto, A. / Naskar, S. / Edenharter, K. / Leimkuhler, S. / Hofmann, E. / Happe, T. / Kurisu, G.
History
DepositionJun 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: [FeFe]-hydrogenase
B: [FeFe]-hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,95412
Polymers150,0042
Non-polymers2,95110
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein [FeFe]-hydrogenase


Mass: 75001.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium beijerinckii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1I9RYV3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-402 / dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)


Mass: 354.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5Fe2N3O3S2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: homodimeric structure of the active [FeFe]-hydrogenase CbA5H
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Clostridium beijerinckii (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8 / Details: 100 mM Tris-HCl, 2mM NaDT
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMTris HydrochlorideTris-HCl1
22 mMsodium dithioniteNaDT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 50 % / Chamber temperature: 278 K / Details: Vitrification carried out in anaerobic condition

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9994
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Spherical aberration corrector: Microscope was modified with a Cs corrector

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2SerialEMimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 7759751
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175586 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6TTL

6ttl


Accession code: 6TTL / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310078
ELECTRON MICROSCOPYf_angle_d0.67113590
ELECTRON MICROSCOPYf_dihedral_angle_d9.1991430
ELECTRON MICROSCOPYf_chiral_restr0.041520
ELECTRON MICROSCOPYf_plane_restr0.0031740

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