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

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Basic information

Entry
Database: PDB / ID: 5odh
TitleHeterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus soaked with heterodisulfide for 3.5 minutes
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
Function / homology
Function and homology information


dihydromethanophenazine:CoB-CoM heterodisulfide reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / CoB--CoM heterodisulfide reductase activity / hydrogenase (acceptor) / Oxidoreductases; Acting on a sulfur group of donors / 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 / hydrogenase (acceptor) / Oxidoreductases; Acting on a sulfur group of donors / 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 / plasma membrane
Similarity search - Function
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #140 / 4Fe-4S dicluster domain / : / F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : ...Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #140 / 4Fe-4S dicluster domain / : / F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / Cysteine-rich domain / Cysteine-rich domain / 4Fe-4S dicluster domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenases large subunit signature 2. / FAD-dependent oxidoreductase 2, FAD binding domain / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / FAD binding domain / Alpha-helical ferredoxin / Alpha-Beta Plaits - #20 / Pyridine nucleotide-disulphide oxidoreductase / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster 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 / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
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 / Coenzyme B ...Non-cubane [4Fe-4S]-cluster / ACETATE ION / 1-THIOETHANESULFONIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / : / FE2/S2 (INORGANIC) CLUSTER / Chem-NFU / Chem-PE3 / IRON/SULFUR CLUSTER / Coenzyme B / 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: 2.2 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)467,28263
Polymers451,69812
Non-polymers15,58451
Water10,989610
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area76940 Å2
ΔGint-941 kcal/mol
Surface area123700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)366.381, 97.104, 133.974
Angle α, β, γ (deg.)90.00, 108.43, 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 [4Fe-4S] 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 already 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 , 13 types, 661 molecules

#7: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#9: 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.: 4 / Source method: obtained synthetically / Formula: C28H58O15
#10: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Comment: FAD*YM
#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.: 3 / Source method: obtained synthetically / Formula: Fe
#17: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#18: Chemical ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


Mass: 343.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H22NO7PS
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.5 %
Description: Black thick plate square shape of about 0.2-0.4 mm
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: All 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, ...Details: All 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, 3% (v/v) DMSO, 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 and 1 ul of precipitant. The crystals appeared after 1-2 weeks in this condition. The cryo-cool trapping experiment was performed as following: crystals were soaked for 3min30sec in the crystallization solution supplemented with 66 mM CoM-S-S-CoB. The crystal was cryo-protected by a soak in the crystallization solution supplemented by 30% glycerol and 10 mM CoM-S-S-CoB.

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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: 2.2→48.552 Å / Num. obs: 225651 / % possible obs: 99.8 % / Redundancy: 4.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.073 / Net I/σ(I): 8.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.435 / Num. unique obs: 32668 / CC1/2: 0.451 / Rpim(I) all: 0.237 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ODC

5odc


Resolution: 2.2→48.552 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.47
RfactorNum. reflection% reflection
Rfree0.2447 11273 5 %
Rwork0.2138 --
obs0.2154 225648 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31029 0 469 610 32108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632161
X-RAY DIFFRACTIONf_angle_d1.52743609
X-RAY DIFFRACTIONf_dihedral_angle_d18.04319636
X-RAY DIFFRACTIONf_chiral_restr0.1484885
X-RAY DIFFRACTIONf_plane_restr0.0055569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.37423610.32797058X-RAY DIFFRACTION99
2.225-2.25120.33423400.31997113X-RAY DIFFRACTION99
2.2512-2.27860.35453350.31217082X-RAY DIFFRACTION99
2.2786-2.30750.34043700.29867133X-RAY DIFFRACTION100
2.3075-2.33780.31833890.28947088X-RAY DIFFRACTION100
2.3378-2.36990.33864080.28617130X-RAY DIFFRACTION100
2.3699-2.40370.30373650.28377060X-RAY DIFFRACTION100
2.4037-2.43960.33463740.28167181X-RAY DIFFRACTION100
2.4396-2.47770.3043480.27567130X-RAY DIFFRACTION100
2.4777-2.51830.30823840.27277086X-RAY DIFFRACTION100
2.5183-2.56180.30724210.2647088X-RAY DIFFRACTION100
2.5618-2.60830.30553700.26387095X-RAY DIFFRACTION100
2.6083-2.65850.30653800.25257122X-RAY DIFFRACTION100
2.6585-2.71280.29963800.25617170X-RAY DIFFRACTION100
2.7128-2.77170.28953630.25837093X-RAY DIFFRACTION100
2.7717-2.83620.28113760.24947131X-RAY DIFFRACTION100
2.8362-2.90710.28833970.24627105X-RAY DIFFRACTION100
2.9071-2.98570.29593800.23957127X-RAY DIFFRACTION100
2.9857-3.07360.29943760.23377160X-RAY DIFFRACTION100
3.0736-3.17280.26113900.21757154X-RAY DIFFRACTION100
3.1728-3.28610.26213730.2157146X-RAY DIFFRACTION100
3.2861-3.41770.24233900.20657168X-RAY DIFFRACTION100
3.4177-3.57320.2393600.19777177X-RAY DIFFRACTION100
3.5732-3.76150.2283440.18587201X-RAY DIFFRACTION100
3.7615-3.9970.19884030.17357121X-RAY DIFFRACTION100
3.997-4.30550.18323750.15967188X-RAY DIFFRACTION100
4.3055-4.73840.17033700.15217221X-RAY DIFFRACTION100
4.7384-5.42330.18083550.16287244X-RAY DIFFRACTION100
5.4233-6.82980.18713860.17167219X-RAY DIFFRACTION100
6.8298-48.56380.16564100.16197384X-RAY DIFFRACTION100

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