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- PDB-5odi: Heterodisulfide reductase / [NiFe]-hydrogenase complex from Metha... -

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Basic information

Entry
Database: PDB / ID: 5odi
TitleHeterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus cocrystallized with CoM-SH
Components
  • (Heterodisulfide reductase, subunit ...) x 3
  • (Methyl-viologen reducing hydrogenase, subunit ...) x 3
KeywordsOXIDOREDUCTASE / Heterodisulfide reductase / [NiFe]-hydrogenase / FeS cluster / ferredoxin / CCG motif / methanogenesis / flavoprotein / flavin-based electron bifurcation / [2Fe-2S] cluster / macromolecular complex / anaerobic / thioredoxin / metabolism / oxydoreductase.
Function / homology
Function and homology information


dihydromethanophenazine:CoB-CoM heterodisulfide reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / CoB--CoM heterodisulfide reductase activity / Oxidoreductases; Acting on a sulfur group of donors / hydrogenase (acceptor) / methanogenesis / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / nickel cation binding ...dihydromethanophenazine:CoB-CoM heterodisulfide reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / CoB--CoM heterodisulfide reductase activity / Oxidoreductases; Acting on a sulfur group of donors / hydrogenase (acceptor) / methanogenesis / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / nickel cation binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
F420-non-reducing hydrogenase iron-sulfur subunit D / Cysteine-rich domain / CoB--CoM heterodisulphide reductase, subunit B / CoB--CoM heterodisulphide reductase, subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / Nickel-dependent hydrogenases large subunit signature 2. ...F420-non-reducing hydrogenase iron-sulfur subunit D / Cysteine-rich domain / CoB--CoM heterodisulphide reductase, subunit B / CoB--CoM heterodisulphide reductase, subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / FAD-dependent oxidoreductase 2, FAD binding domain / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Alpha-helical ferredoxin / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / FAD binding domain / Pyridine nucleotide-disulphide oxidoreductase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 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 / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Non-cubane [4Fe-4S]-cluster / ACETATE ION / 1-THIOETHANESULFONIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / : / FE2/S2 (INORGANIC) CLUSTER / Chem-NFU / Chem-PE3 / IRON/SULFUR CLUSTER / Heterodisulfide reductase, subunit C ...Non-cubane [4Fe-4S]-cluster / ACETATE ION / 1-THIOETHANESULFONIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / : / FE2/S2 (INORGANIC) CLUSTER / Chem-NFU / Chem-PE3 / IRON/SULFUR CLUSTER / Heterodisulfide reductase, subunit C / Methyl-viologen reducing hydrogenase subunit D / Methyl-viologen reducing hydrogenase subunit G / Methyl-viologen reducing hydrogenase subunit A / Heterodisulfide reductase, subunit B / CoB--CoM heterodisulfide reductase iron-sulfur subunit A
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWagner, T. / Koch, J. / Ermler, U. / Shima, S.
CitationJournal: Science / Year: 2017
Title: Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.
Authors: Wagner, T. / Koch, J. / Ermler, U. / Shima, S.
History
DepositionJul 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heterodisulfide reductase, subunit A
B: Heterodisulfide reductase, subunit B
C: Heterodisulfide reductase, subunit C
D: Methyl-viologen reducing hydrogenase, subunit D
E: Methyl-viologen reducing hydrogenase, subunit G
F: Methyl-viologen reducing hydrogenase, subunit A
G: Heterodisulfide reductase, subunit A
H: Heterodisulfide reductase, subunit B
I: Heterodisulfide reductase, subunit C
J: Methyl-viologen reducing hydrogenase, subunit D
K: Methyl-viologen reducing hydrogenase, subunit G
L: Methyl-viologen reducing hydrogenase, subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,94558
Polymers451,69812
Non-polymers13,24746
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area76530 Å2
ΔGint-886 kcal/mol
Surface area126510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)370.528, 97.077, 135.149
Angle α, β, γ (deg.)90.00, 109.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Heterodisulfide reductase, subunit ... , 3 types, 6 molecules AGBHCI

#1: Protein Heterodisulfide reductase, subunit A


Mass: 71591.672 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: / / References: UniProt: A0A2D0TCB9*PLUS
#2: Protein Heterodisulfide reductase, subunit B


Mass: 32075.318 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Details: This subunit contains two pentacoordinated non cubane [4Fe4S] clusters
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: /
References: UniProt: A0A2D0TCB4*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase
#3: Protein Heterodisulfide reductase, subunit C


Mass: 20483.650 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: / / References: UniProt: A0A2D0TC97*PLUS

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Methyl-viologen reducing hydrogenase, subunit ... , 3 types, 6 molecules DJEKFL

#4: Protein Methyl-viologen reducing hydrogenase, subunit D


Mass: 16057.495 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: / / References: UniProt: A0A2D0TC98*PLUS
#5: Protein Methyl-viologen reducing hydrogenase, subunit G


Mass: 32511.432 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: /
References: UniProt: A0A2D0TC99*PLUS, hydrogen dehydrogenase
#6: Protein Methyl-viologen reducing hydrogenase, subunit A


Mass: 53129.602 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Details: The C-terminus has been post-translationally cleaved
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: /
References: UniProt: A0A2D0TCA6*PLUS, hydrogen dehydrogenase

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Non-polymers , 12 types, 600 molecules

#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#9: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical
ChemComp-9S8 / Non-cubane [4Fe-4S]-cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#12: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O3S2
#13: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#14: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#15: Chemical ChemComp-NFU / formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / NI-FE REDUCED ACTIVE CENTER


Mass: 195.591 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3HFeN2NiO
#16: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#17: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Description: Black thick plate, square shape of about 0.2-0.4 mm length
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution using the sitting drop method (96-well 2-drop MRC Crystallization Plates in polystyrene, Molecular ...Details: Crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution using the sitting drop method (96-well 2-drop MRC Crystallization Plates in polystyrene, Molecular Dimensions, Suffolk, UK). The crystallization reservoir contained 100 mM Tris/HCl, pH 8.5, 1% (w/v) polyethylene glycol 3350, 30% (w/v) polyethylene glycol 4000, and 200 mM Na acetate trihydrate. Crystallization drop contained 1 ul HdrABC-MvhAGD at 25 mg/ml premixed with 2 mM FAD, 10 mM CoM-SH and 1 ul of precipitant. The crystals appear after 1-2 weeks and are cryoprotected in the crystallization solution supplemented with 30% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97916 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.4→48.54 Å / Num. obs: 176807 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 30.54 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.071 / Net I/σ(I): 7.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 25737 / CC1/2: 0.332 / Rpim(I) all: 0.188 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ODC

5odc


Resolution: 2.4→48.54 Å / Cor.coef. Fo:Fc: 0.9146 / Cor.coef. Fo:Fc free: 0.8865 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.363 / SU Rfree Blow DPI: 0.237
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 8805 4.98 %RANDOM
Rwork0.2015 ---
obs0.2035 176789 99.94 %-
Displacement parametersBiso mean: 64.65 Å2
Baniso -1Baniso -2Baniso -3
1-4.2309 Å20 Å23.2754 Å2
2---1.1058 Å20 Å2
3----3.1251 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å
Refinement stepCycle: 1 / Resolution: 2.4→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms61987 0 1111 554 63652
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00663200HARMONIC8
X-RAY DIFFRACTIONt_angle_deg1.05114891HARMONIC8
X-RAY DIFFRACTIONt_dihedral_angle_d14257SINUSOIDAL6
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes820HARMONIC6
X-RAY DIFFRACTIONt_gen_planes9024HARMONIC40
X-RAY DIFFRACTIONt_it63200HARMONIC20
X-RAY DIFFRACTIONt_nbd39SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.29
X-RAY DIFFRACTIONt_other_torsion15.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4130SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact70328SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2942 682 5.23 %
Rwork0.2497 12357 -
all0.252 13039 -
obs--99.94 %
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)
10.43040.21110.46080.04080.25031.3599-0.18650.00390.2635-0.00610.03580.0602-0.0067-0.01020.15060.14190.0911-0.1614-0.15660.0320.058232.26578.431565.872
2-0.44182.39172.42532.32581.85641.766-0.00830.0004-0.0998-0.00740.0150.08460.072-0.0139-0.00670.12560.008-0.1593-0.0612-0.07930.036519.4158-39.364518.6808
3-0.317-0.31360.46131.93831.0212.12290.03110.0475-0.0834-0.0206-0.0276-0.01330.00340.0435-0.00350.12860.029-0.10170.0871-0.0424-0.102432.5597-24.397515.0932
4-0.0893-0.46011.45591.91131.09892.75310.00240.0452-0.03020.0192-0.0196-0.0294-0.00080.0380.01720.20870.1521-0.08-0.019-0.0016-0.071749.0119-1.8187.5342
50.63650.12990.88610-0.26472.20230.0046-0.03630.04760.0062-0.00930.07330.0135-0.02380.00470.19530.138-0.1134-0.0932-0.104-0.007654.45058.6261117.0241
60.62550.02790.77930.33940.09520.7858-0.0052-0.10940.09850.0733-0.0016-0.0661-0.05230.18570.00680.1280.0059-0.07330.1958-0.1547-0.163972.917914.6389133.0774
70.11070.05240.857900.51420.6658-0.1802-0.02810.06530.0224-0.1409-0.02070.2245-0.26780.32110.20.0534-0.05150.1138-0.0189-0.156510.273-3.249552.9836
80.89560.45790.10240.9118-0.46331.5476-0.0395-0.00240.1491-0.00580.0662-0.1087-0.01890.0337-0.02660.0210.0541-0.13850.2169-0.1015-0.119678.2183-4.317450.8114
91.6723-0.41910.28040.0201-0.39050.82420.0060.0179-0.02140.00240.02470.0134-0.01320.0627-0.03070.1450.1568-0.09430.1027-0.0804-0.105467.8326-21.532352.5198
101.6722-1.37010.586100.432.3842-0.0042-0.0021-0.01690.02220.0030.01640.00660.0360.00120.03560.158-0.15480.1383-0.0116-0.0647-0.87133.079226.3172
110.7833-0.31892.85170.31060.21312.95830.00090.02570.01360.11440.01150.00510.08070.0022-0.01250.04040.1706-0.16210.041-0.0339-0.0418-28.824513.738417.2336
120.52630.40732.10440.94180.68081.881-0.00290.1475-0.0590.1234-0.06440.15150.2127-0.12820.06730.0130.1451-0.17170.0848-0.11-0.0452-48.15039.58971.7863
130.1063-0.30330.79310.1557-0.04991.2567-0.0152-0.00250.00590.0187-0.00760.00340.0292-0.02650.02280.03720.0302-0.03470.00490.0059-0.018823.35690.534757.5937
140.4790.61210.52440.09070.35930.6012-0.0125-0.01740.0836-0.2714-0.04780.0860.0091-0.07960.06020.09260.1580.121-0.04730.0089-0.111920.47143.533960.1605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }
11X-RAY DIFFRACTION11{ K|* }
12X-RAY DIFFRACTION12{ L|* }
13X-RAY DIFFRACTION13{ S|* }
14X-RAY DIFFRACTION14{ W|* }

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