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- PDB-4omf: The F420-reducing [NiFe]-hydrogenase complex from Methanothermoba... -

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Basic information

Entry
Database: PDB / ID: 4omf
TitleThe F420-reducing [NiFe]-hydrogenase complex from Methanothermobacter marburgensis, the first X-ray structure of a group 3 family member
Components(F420-reducing hydrogenase, subunit ...) x 3
KeywordsOXIDOREDUCTASE / [NiFe]-center / 3[4Fe-4S] cluster / ferredoxin fold / FAD binding / potential F420 binding / anaerobic enzyme
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 / iron-sulfur cluster binding / nickel cation 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 alpha / Coenzyme F420 hydrogenase subunit beta, archaea / Coenzyme F420 hydrogenase, subunit gamma / 4Fe-4S dicluster domain / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / 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 alpha / Coenzyme F420 hydrogenase subunit beta, archaea / Coenzyme F420 hydrogenase, subunit gamma / 4Fe-4S dicluster domain / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / 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
zinc(II)hydrogensulfide / FLAVIN-ADENINE DINUCLEOTIDE / N,N-dimethylmethanamine / Chem-NFU / IRON/SULFUR CLUSTER / UNKNOWN / Unknown ligand / F420-reducing hydrogenase, subunit beta / F420-reducing hydrogenase, subunit gamma / F420-reducing hydrogenase, subunit alpha
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / cryo-EM model of FrhABG complex, calculated SAD phases were combined / Resolution: 1.71 Å
AuthorsVitt, S. / Ma, K. / Warkentin, E. / Moll, J. / Pierik, A. / Shima, S. / Ermler, U.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: The F420-Reducing [NiFe]-Hydrogenase Complex from Methanothermobacter marburgensis, the First X-ray Structure of a Group 3 Family Member.
Authors: Vitt, S. / Ma, K. / Warkentin, E. / Moll, J. / Pierik, A.J. / Shima, S. / Ermler, U.
History
DepositionJan 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Jun 20, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_ptnr2_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: F420-reducing hydrogenase, subunit gamma
A: F420-reducing hydrogenase, subunit alpha
B: F420-reducing hydrogenase, subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,73418
Polymers105,9203
Non-polymers2,81415
Water13,709761
1
G: F420-reducing hydrogenase, subunit gamma
A: F420-reducing hydrogenase, subunit alpha
B: F420-reducing hydrogenase, subunit beta
hetero molecules

G: F420-reducing hydrogenase, subunit gamma
A: F420-reducing hydrogenase, subunit alpha
B: F420-reducing hydrogenase, subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,46836
Polymers211,8406
Non-polymers5,62830
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555x,-y+1/2,-z+1/21
Buried area32540 Å2
ΔGint-420 kcal/mol
Surface area55210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.160, 233.160, 233.160
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-533-

HOH

21A-763-

HOH

31A-779-

HOH

41A-791-

HOH

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Components

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F420-reducing hydrogenase, subunit ... , 3 types, 3 molecules GAB

#1: Protein F420-reducing hydrogenase, subunit gamma


Mass: 30267.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg / References: UniProt: D9PYF7, coenzyme F420 hydrogenase
#2: Protein F420-reducing hydrogenase, subunit alpha


Mass: 44873.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg / References: UniProt: D9PYF9, coenzyme F420 hydrogenase
#3: Protein F420-reducing hydrogenase, subunit beta


Mass: 30778.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg / References: UniProt: D9PYF6, coenzyme F420 hydrogenase

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Non-polymers , 10 types, 776 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-DTZ / zinc(II)hydrogensulfide


Mass: 131.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S2Zn
#6: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: 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
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-KEN / N,N-dimethylmethanamine


Mass: 59.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9N
#11: Chemical ChemComp-UNK / UNKNOWN


Type: L-peptide linking / Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2
#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.: 761 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 17-20 % PEE797, 100 mM MES/NaOH, 400 mM MgCl2, 5% glycerol, 100 mM trimethylamine oxide, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 281.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0, 1.71
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 5, 2011
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.711
ReflectionResolution: 1.7→50 Å / Num. obs: 112689 / % possible obs: 86.1 % / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
XDSdata scaling
SADABSdata scaling
SHARPphasing
SHELXDphasing
Cootmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
RefinementMethod to determine structure: cryo-EM model of FrhABG complex, calculated SAD phases were combined
Resolution: 1.71→19.99 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 17.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.181 5898 5.23 %
Rwork0.15 --
obs0.152 112689 99.6 %
all-113130 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6885 0 113 761 7759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117216
X-RAY DIFFRACTIONf_angle_d1.3179815
X-RAY DIFFRACTIONf_dihedral_angle_d14.4782742
X-RAY DIFFRACTIONf_chiral_restr0.0641113
X-RAY DIFFRACTIONf_plane_restr0.0091257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.72590.37181930.363415X-RAY DIFFRACTION96
1.7259-1.74620.31082130.28133478X-RAY DIFFRACTION100
1.7462-1.76750.28192050.24383554X-RAY DIFFRACTION100
1.7675-1.78990.26151920.24433600X-RAY DIFFRACTION100
1.7899-1.81340.27963040.22993440X-RAY DIFFRACTION100
1.8134-1.83820.24562030.21263527X-RAY DIFFRACTION100
1.8382-1.86450.26721820.20313564X-RAY DIFFRACTION100
1.8645-1.89230.21521910.19433555X-RAY DIFFRACTION100
1.8923-1.92180.25441780.18213605X-RAY DIFFRACTION100
1.9218-1.95330.2271870.17153547X-RAY DIFFRACTION100
1.9533-1.9870.20472200.17123550X-RAY DIFFRACTION100
1.987-2.0230.21661880.15883556X-RAY DIFFRACTION100
2.023-2.06190.18461630.15773590X-RAY DIFFRACTION100
2.0619-2.1040.1892020.15073512X-RAY DIFFRACTION100
2.104-2.14970.17521950.14573567X-RAY DIFFRACTION100
2.1497-2.19960.16642130.14013569X-RAY DIFFRACTION100
2.1996-2.25450.17271790.13643568X-RAY DIFFRACTION100
2.2545-2.31540.18262010.14013536X-RAY DIFFRACTION100
2.3154-2.38340.17941800.14293638X-RAY DIFFRACTION100
2.3834-2.46020.18211940.14393550X-RAY DIFFRACTION100
2.4602-2.5480.16861820.13833550X-RAY DIFFRACTION100
2.548-2.64980.18812140.14253554X-RAY DIFFRACTION100
2.6498-2.77010.16672260.14233530X-RAY DIFFRACTION100
2.7701-2.91570.17421750.14113621X-RAY DIFFRACTION100
2.9157-3.09780.17771710.14393608X-RAY DIFFRACTION100
3.0978-3.3360.16852190.14383509X-RAY DIFFRACTION99
3.336-3.66980.1591730.13463636X-RAY DIFFRACTION100
3.6698-4.19650.14851890.12653575X-RAY DIFFRACTION99
4.1965-5.27110.13781940.1233587X-RAY DIFFRACTION99
5.2711-19.99470.15741720.14593700X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1602-0.073-0.02420.7902-0.13850.2710.02050.0431-0.0095-0.0550.00130.17060.0104-0.1042-0.02310.12570.0009-0.02450.21330.00760.1959-9.894763.002841.2187
20.27-0.0218-0.0970.4775-0.01460.35280.01340.03430.0217-0.0371-0.01050.048-0.0379-0.039-0.00360.12260.0095-0.01710.15360.00890.1499.893477.444734.0318
30.34240.02610.04130.8928-0.2460.77840.00920.0132-0.0809-0.11240.00270.01710.16-0.0398-0.00390.1802-0.0326-0.02550.1904-0.01990.1975-0.35730.440938.5358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 46 through 303 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2 through 386 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 281 )

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