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

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Basic information

Entry
Database: PDB / ID: 5odc
TitleHeterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus at 2.3 A resolution
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
Similarity search - Function
4Fe-4S dicluster domain / : / 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 ...4Fe-4S dicluster domain / : / 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 / 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 / Alpha-helical ferredoxin / Nickel-dependent hydrogenase, large subunit, nickel binding site / 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 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
Similarity search - Domain/homology
Non-cubane [4Fe-4S]-cluster / ACETATE ION / 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 ...Non-cubane [4Fe-4S]-cluster / ACETATE ION / 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 / SAD / Resolution: 2.3 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

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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)465,76372
Polymers451,69812
Non-polymers14,06560
Water14,988832
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area79310 Å2
ΔGint-905 kcal/mol
Surface area124180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)378.047, 98.446, 137.884
Angle α, β, γ (deg.)90.00, 110.70, 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 / Source method: isolated from a natural source / Details: GB ref WP_018154264.1
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Tissue: /
References: UniProt: A0A2D0TCB9*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase
#2: Protein Heterodisulfide reductase, subunit B


Mass: 32075.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: GB ref WP_018154154.1, This subunit contains two pentacoordinated non cubane [4Fe-4S] cluster
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Tissue: /
References: UniProt: A0A2D0TCB4*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase
#3: Protein Heterodisulfide reductase, subunit C


Mass: 20483.650 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: GB ref WP_018154153.1, The C-terminus is too flexible to be modeled in the electron density
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Tissue: /
References: UniProt: A0A2D0TC97*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase

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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 / Source method: isolated from a natural source / Details: GB ref WP_018154260.1
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Tissue: /
References: UniProt: A0A2D0TC98*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase
#5: Protein Methyl-viologen reducing hydrogenase subunit G


Mass: 32511.432 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GB ref WP_018154261.1
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Tissue: /
References: UniProt: A0A2D0TC99*PLUS, hydrogenase (acceptor)
#6: Protein Methyl-viologen reducing hydrogenase subunit A


Mass: 53129.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: GB ref WP_018154262.1, The C-terminus has been post-translationally cleaved
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Tissue: /
References: UniProt: A0A2D0TCA6*PLUS, hydrogenase (acceptor)

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Non-polymers , 13 types, 892 molecules

#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#10: 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
#11: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#13: Chemical
ChemComp-9S8 / Non-cubane [4Fe-4S]-cluster


Mass: 351.640 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Fe4S4
#14: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#15: 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
#16: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#17: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#18: 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
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / 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: 2.67 Å3/Da / Density % sol: 53.86 % / Description: Black thick plate square shape.
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. The best-diffracting crystals were obtained using the sitting drop method in a crystallization ...Details: Crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution. The best-diffracting crystals were obtained using the sitting drop method in a crystallization plate (96-well 2-drop MRC Crystallization Plates in polystyrene, Molecular Dimensions, Suffolk, UK); the crystallization reservoir contained 100 mM Tris/HCl, pH 8.5, 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 appear after 1-2 weeks and are cryoprotected in the crystallization solution supplemented with 30% glycerol.
PH range: 8-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.733 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.733 Å / Relative weight: 1
ReflectionResolution: 2.3→49.22 Å / Num. obs: 204479 / % possible obs: 97.4 % / Redundancy: 8.5 % / Biso Wilson estimate: 38.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.053 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 25173 / CC1/2: 0.5 / Rpim(I) all: 0.282 / % possible all: 83

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→49.22 Å / Cor.coef. Fo:Fc: 0.9452 / Cor.coef. Fo:Fc free: 0.9336 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.256 / SU Rfree Blow DPI: 0.179
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 10353 5.06 %RANDOM
Rwork0.1778 ---
obs0.1789 204471 97.28 %-
Displacement parametersBiso mean: 49.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.6268 Å20 Å20.5811 Å2
2--1.8038 Å20 Å2
3----4.4305 Å2
Refine analyzeLuzzati coordinate error obs: 0.296 Å
Refinement stepCycle: 1 / Resolution: 2.3→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms61847 0 1504 832 64183
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00563156HARMONIC5
X-RAY DIFFRACTIONt_angle_deg1114761HARMONIC5
X-RAY DIFFRACTIONt_dihedral_angle_d14270SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes819HARMONIC2
X-RAY DIFFRACTIONt_gen_planes9008HARMONIC20
X-RAY DIFFRACTIONt_it63156HARMONIC20
X-RAY DIFFRACTIONt_nbd31SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.79
X-RAY DIFFRACTIONt_other_torsion14.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4127SEMIHARMONIC5
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_contact70649SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2708 578 4.91 %
Rwork0.2487 11192 -
all0.2498 11770 -
obs--97.28 %
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)
10.50230.1359-0.12880.0755-0.03410.0483-0.0206-0.0272-0.15130.02330.0386-0.0423-0.0241-0.0008-0.018-0.11460.03030.0071-0.1088-0.00710.2362120.681673.117927.5581
20.92360.3029-0.07241.59390.26290.00170.00580.040.02910.04380.0075-0.0147-0.0750.085-0.0133-0.0306-0.03630.0435-0.14650.0270.1175161.0633121.5161.8766
30.91040.2703-0.17980.8357-0.39320.21020.00340.05330.0028-0.0434-0.00810.0075-0.02770.02110.0047-0.054-0.06380.0647-0.0248-0.02630.0755154.6765106.821-9.9618
41.80670.2295-0.03360.895-0.12430.0116-0.00920.06320.03640.01140.02830.0067-0.0118-0.013-0.0191-0.0780.00330.0253-0.00170.02010.081193.573783.330232.5709
51.14190.1253-0.37460.00290.00620.3468-0.0121-0.00420.00360.06760.0328-0.0270.0234-0.0301-0.0208-0.06480.03240.0243-0.01570.04680.050469.974773.086651.0503
60.79830.154-0.14630.426-0.13410.176-0.02260.0878-0.06260.0320.09850.07840.0932-0.2075-0.0759-0.1363-0.0270.02890.08030.11260.062745.495267.059151.0458
70.338-0.184-0.07570-0.00290.125-0.0082-0.1140.027-0.0180.0424-0.0254-0.04490.0341-0.0341-0.13680.0104-0.0121-0.0852-0.03150.2461145.472985.048432.5376
81.85010.29810.896101.11530.413-0.0222-0.0292-0.0305-0.09010.01220.01170.0654-0.1230.0099-0.0727-0.0635-0.03370.09690.0119-0.026897.18585.227-15.4215
91.2984-0.23310.09920.2244-0.0779-0.11050.00450.0235-0.0048-0.02420.0059-0.0341-0.0196-0.0672-0.0105-0.04630.1056-0.00660.03420.05530.0353104.2105101.765-6.843
100.973-0.20310.24430.5081-0.3870.0926-0.02360.0280.0433-0.02340.01150.0237-0.00560.02940.0121-0.1571-0.0093-0.0014-0.0290.02380.1897171.888678.898220.6573
111.8805-0.10740.39890.0017-0.0960.033-0.05540.00970.04390.0197-0.03290.02760.03940.04030.0882-0.17530.0027-0.0177-0.05710.09230.1469198.656768.146133.0624
121.1509-0.1130.09230.4790.16870.3277-0.06550.02690.14090.0432-0.0142-0.0409-0.04240.20810.0796-0.2578-0.0608-0.05380.07090.13740.1307223.538671.846834.3337
130.2569-0.1768-0.1340.1189-0.0713-0.03990.00060.00330.0108-0.00280.00320.0033-0.00540.0063-0.00380.01110.00390.003-0.00650.00860.0115132.744781.08827.0564
140.7406-0.0550.04250.153-0.0024-0.00430.0111-0.0659-0.0287-0.0116-0.0118-0.0720.01130.04620.0007-0.1090.03820.0262-0.0566-0.03110.0731133.22778.081231.3789
152.2271-0.1224-0.54130.4553-0.46680.7489-0.0039-0.0294-0.00450.0231-0.00120.0060.0077-0.00310.00510.0133-0.0027-0.00590.00790.00640.0069139.765483.457326.4581
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{ P|* }
14X-RAY DIFFRACTION14{ W|* }
15X-RAY DIFFRACTION15{ Z|* }

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