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- PDB-6qgr: The F420-reducing [NiFe] hydrogenase complex from Methanosarcina ... -

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Basic information

Entry
Database: PDB / ID: 6qgr
TitleThe F420-reducing [NiFe] hydrogenase complex from Methanosarcina barkeri at the Nia-S state
Components(Coenzyme F420 hydrogenase subunit ...) x 3
KeywordsOXIDOREDUCTASE / [NiFe] containing hydrogenase / reversible oxidation of dihydrogen / oxygen sensitive / methanogenic acetoclastic Archaea / METAL BINDING PROTEIN
Function / homology
Function and homology information


coenzyme F420 hydrogenase / coenzyme F420 hydrogenase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / ferredoxin hydrogenase activity / nickel cation binding / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding
Similarity search - Function
Nuclear Transport Factor 2; Chain: A, - #750 / Coenzyme F420 hydrogenase subunit beta, archaea / Coenzyme F420 hydrogenase, subunit gamma / 4Fe-4S dicluster domain / : / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus ...Nuclear Transport Factor 2; Chain: A, - #750 / Coenzyme F420 hydrogenase subunit beta, archaea / Coenzyme F420 hydrogenase, subunit gamma / 4Fe-4S dicluster domain / : / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Nickel-dependent hydrogenases large subunit signature 2. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / Alpha-Beta Plaits - #20 / 4Fe-4S binding domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Nuclear Transport Factor 2; Chain: A, / 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 / Alpha-Beta Plaits / Roll / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / (R,R)-2,3-BUTANEDIOL / FLAVIN-ADENINE DINUCLEOTIDE / : / FE2/S2 (INORGANIC) CLUSTER / Chem-NFU / IRON/SULFUR CLUSTER / Coenzyme F420 hydrogenase subunit gamma / Coenzyme F420 hydrogenase subunit beta / Coenzyme F420 hydrogenase subunit alpha
Similarity search - Component
Biological speciesMethanosarcina barkeri MS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.839 Å
AuthorsIlina, Y. / Lorent, C. / Katz, S. / Jeoung, J.H. / Shima, S. / Horch, M. / Zebger, I. / Dobbek, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSPP 1927 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: X-ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] Hydrogenases.
Authors: Ilina, Y. / Lorent, C. / Katz, S. / Jeoung, J.H. / Shima, S. / Horch, M. / Zebger, I. / Dobbek, H.
History
DepositionJan 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Coenzyme F420 hydrogenase subunit gamma
A: Coenzyme F420 hydrogenase subunit alpha
B: Coenzyme F420 hydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,71828
Polymers108,4283
Non-polymers4,29025
Water11,620645
1
G: Coenzyme F420 hydrogenase subunit gamma
A: Coenzyme F420 hydrogenase subunit alpha
B: Coenzyme F420 hydrogenase subunit beta
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)1,352,612336
Polymers1,301,13336
Non-polymers51,479300
Water64936
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation17_545z,x-1/2,y+1/21
crystal symmetry operation18_544z,-x-1/2,-y-1/21
crystal symmetry operation19_545-z,-x-1/2,y+1/21
crystal symmetry operation20_544-z,x-1/2,-y-1/21
crystal symmetry operation45_545y+1/2,z-1/2,x1
crystal symmetry operation46_445-y-1/2,z-1/2,-x1
crystal symmetry operation47_545y+1/2,-z-1/2,-x1
crystal symmetry operation48_445-y-1/2,-z-1/2,x1
Buried area264600 Å2
ΔGint-2620 kcal/mol
Surface area326010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.826, 235.826, 235.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11G-304-

FES

21G-304-

FES

31A-503-

MG

41A-505-

144

51A-505-

144

61A-798-

HOH

71A-920-

HOH

81A-938-

HOH

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Components

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Coenzyme F420 hydrogenase subunit ... , 3 types, 3 molecules GAB

#1: Protein Coenzyme F420 hydrogenase subunit gamma


Mass: 27598.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina barkeri MS (archaea) / References: UniProt: A0A0E3LP72, coenzyme F420 hydrogenase
#2: Protein Coenzyme F420 hydrogenase subunit alpha


Mass: 48531.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: FRH-A harbours an active site for the dihydrogen catalysis
Source: (natural) Methanosarcina barkeri MS (archaea) / References: UniProt: A0A0E3QYL7*PLUS
#3: Protein Coenzyme F420 hydrogenase subunit beta


Mass: 32297.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina barkeri MS (archaea) / References: UniProt: A0A0E3QWH3, coenzyme F420 hydrogenase

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Non-polymers , 10 types, 670 molecules

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


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#6: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3
#7: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O2
#8: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: Chemical ChemComp-NFU / formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / NI-FE REDUCED ACTIVE CENTER


Mass: 195.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3HFeN2NiO
#10: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#11: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#12: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Tris, MPD, PEG1000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.981 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 1.839→50 Å / Num. obs: 183344 / % possible obs: 99.57 % / Redundancy: 4 % / Rrim(I) all: 0.211 / Net I/σ(I): 6.62
Reflection shellResolution: 1.8395→1.8823 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
MxCuBEdata collection
XDSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OMF

4omf


Resolution: 1.839→48.138 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.78 / Phase error: 28.01
RfactorNum. reflection% reflection
Rfree0.2206 2086 1.14 %
Rwork0.1753 --
obs0.1758 183258 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.839→48.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7578 0 208 645 8431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0178027
X-RAY DIFFRACTIONf_angle_d1.33710917
X-RAY DIFFRACTIONf_dihedral_angle_d21.9143004
X-RAY DIFFRACTIONf_chiral_restr0.0921229
X-RAY DIFFRACTIONf_plane_restr0.0081377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8395-1.88230.44241370.400312056X-RAY DIFFRACTION99
1.8823-1.92930.38061400.397811970X-RAY DIFFRACTION100
1.9293-1.98150.40371370.360912137X-RAY DIFFRACTION99
1.9815-2.03980.40591390.341511946X-RAY DIFFRACTION99
2.0398-2.10570.3621410.311812048X-RAY DIFFRACTION99
2.1057-2.18090.35471380.298912051X-RAY DIFFRACTION100
2.1809-2.26820.31171400.285212132X-RAY DIFFRACTION100
2.2682-2.37150.31351390.255512114X-RAY DIFFRACTION100
2.3715-2.49650.25091390.210212059X-RAY DIFFRACTION100
2.4965-2.65290.25541420.186512128X-RAY DIFFRACTION100
2.6529-2.85770.20251390.167312078X-RAY DIFFRACTION100
2.8577-3.14520.21941390.15112136X-RAY DIFFRACTION100
3.1452-3.60020.19181390.13112111X-RAY DIFFRACTION100
3.6002-4.53540.16391340.11112081X-RAY DIFFRACTION100
4.5354-48.15420.14811430.129512125X-RAY DIFFRACTION100

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