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- PDB-9r5i: Dimeric state of the F420-reducing hydrogenase from Methanothermo... -

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Basic information

Entry
Database: PDB / ID: 9r5i
TitleDimeric state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus in crystalline form 3
Components(F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit ...) x 3
KeywordsOXIDOREDUCTASE / [NiFe]-hydrogenase / redox cycle / catalysis / [4Fe-4S]-cluster / F420 cofactor / FAD / hydrogen activation / thermophilic methanogen
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / : / FE2/S2 (INORGANIC) CLUSTER / Chem-NFU / IRON/SULFUR CLUSTER
Function and homology information
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsJespersen, M. / Lemaire, O.N. / Wagner, T.
Funding support Germany, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)WA 4053/1-1 Germany
German Research Foundation (DFG)ZE 510/2-2 Germany
CitationJournal: Chembiochem / Year: 2025
Title: Structural and Spectroscopic Insights into Catalytic Intermediates of a [NiFe]-hydrogenase from Group 3.
Authors: Jespersen, M. / Lorent, C. / Lemaire, O.N. / Zebger, I. / Wagner, T.
History
DepositionMay 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit alpha
B: F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit beta
C: F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit gamma
D: F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit alpha
E: F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit gamma
F: F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,30157
Polymers206,0026
Non-polymers8,29951
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39560 Å2
ΔGint-408 kcal/mol
Surface area57650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.606, 196.606, 192.072
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit ... , 3 types, 6 molecules ADBFCE

#1: Protein F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit alpha


Mass: 45839.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The C-terminal extension has been cleaved off during maturation.
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: DSM 2095 / Tissue: / / References: coenzyme F420 hydrogenase
#2: Protein F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit beta


Mass: 31091.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: DSM 2095 / Tissue: / / References: coenzyme F420 hydrogenase
#3: Protein F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit gamma


Mass: 26070.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: DSM 2095 / Tissue: / / References: coenzyme F420 hydrogenase

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Non-polymers , 10 types, 51 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: 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 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#13: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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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: 5.34 Å3/Da / Density % sol: 76.97 % / Description: Brown hexagonal plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: The enzyme was crystallized at a concentration of 38.8 mg.ml-1 in 25 mM Tris/HCl pH 7.6, 10% (v/v) glycerol, and 2 mM dithiothreitol. Crystals were obtained anaerobically in a Coy tent ...Details: The enzyme was crystallized at a concentration of 38.8 mg.ml-1 in 25 mM Tris/HCl pH 7.6, 10% (v/v) glycerol, and 2 mM dithiothreitol. Crystals were obtained anaerobically in a Coy tent filled with a N2/H2 (97:3 %) atmosphere by initial screening at 20 degrees Celsius using the sitting-drop method on 96-well MRC two-drop crystallisation plates in polystyrene (SWISSCI). The reservoir contained 90 ul of the following crystallization solution: 30 % (v/v) Polyethylene glycol 400, 100 mM MES pH 6.5, and 200 mM LiSO4. 0.7 ul of protein and 0.7 ul of the crystallization solution were spotted.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.73891 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73891 Å / Relative weight: 1
ReflectionResolution: 3.13→127.41 Å / Num. obs: 52281 / % possible obs: 95.1 % / Redundancy: 20.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.304 / Rpim(I) all: 0.069 / Rrim(I) all: 0.312 / Net I/σ(I): 10
Reflection shellResolution: 3.13→3.35 Å / Redundancy: 21.1 % / Rmerge(I) obs: 2.449 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2616 / CC1/2: 0.62 / Rpim(I) all: 0.545 / Rrim(I) all: 2.51 / % possible all: 67.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.13→77.83 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.06 / Stereochemistry target values: ML
Details: Model correction was performed in coot, and refinement with Phenix. The model was refined with Translation libration Screw.
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 2614 5 %Random selection
Rwork0.1744 ---
obs0.176 52264 69.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.44 Å2
Refinement stepCycle: LAST / Resolution: 3.13→77.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14094 0 389 0 14483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614754
X-RAY DIFFRACTIONf_angle_d0.93519987
X-RAY DIFFRACTIONf_dihedral_angle_d15.6135482
X-RAY DIFFRACTIONf_chiral_restr0.0772277
X-RAY DIFFRACTIONf_plane_restr0.0052492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.13-3.190.2907110.2775152X-RAY DIFFRACTION4
3.19-3.250.2714340.2658568X-RAY DIFFRACTION15
3.25-3.320.3769450.27761091X-RAY DIFFRACTION29
3.32-3.390.3017630.26821355X-RAY DIFFRACTION36
3.39-3.470.3372720.26441540X-RAY DIFFRACTION41
3.47-3.550.31231090.25951784X-RAY DIFFRACTION48
3.55-3.650.25331240.21752042X-RAY DIFFRACTION55
3.65-3.760.29241130.21162268X-RAY DIFFRACTION60
3.76-3.880.22781170.19662663X-RAY DIFFRACTION70
3.88-4.020.25481480.19612824X-RAY DIFFRACTION75
4.02-4.180.20321630.1823106X-RAY DIFFRACTION82
4.18-4.370.1891720.17463499X-RAY DIFFRACTION92
4.37-4.60.18671980.15333723X-RAY DIFFRACTION99
4.6-4.890.18742190.15143759X-RAY DIFFRACTION100
4.89-5.260.19811840.15663804X-RAY DIFFRACTION100
5.26-5.790.22072020.1743804X-RAY DIFFRACTION100
5.79-6.630.19822100.17193833X-RAY DIFFRACTION100
6.63-8.350.18042270.16313840X-RAY DIFFRACTION100
8.35-77.830.17822030.15813995X-RAY DIFFRACTION100
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)
15.58233.54380.70376.60060.52162.1818-0.80490.46270.0347-1.22940.8434-0.4166-0.06010.3699-0.00230.633-0.1170.12550.4981-0.01080.5081-40.986949.8613-0.2715
22.3601-1.02170.67850.78170.3670.83730.0056-0.1801-0.2040.1278-0.1003-0.11880.15960.0010.05530.6336-0.12030.10350.44940.05210.45-58.737229.037211.28
32.86763.4967-1.23324.6785-1.45621.80890.1039-1.1084-1.07520.2974-0.4257-0.25940.44670.36910.41080.78570.03210.01420.62840.18270.816-44.961121.18620.9505
42.9479-0.171-1.04112.58131.38272.30310.1759-0.56240.03610.04180.1635-0.5558-0.14010.4002-0.24760.6373-0.0981-0.01910.51320.16870.5327-42.370443.140317.2671
52.9470.0732-0.36723.5694-1.51195.08030.19030.02940.6108-0.00670.3125-0.0726-0.7131-0.16580.09910.753-0.15340.07910.4699-0.03170.4998-59.172553.40579.5995
62.4314-0.7340.63323.4968-1.36653.7668-0.0819-0.48480.14190.4366-0.0679-0.2757-0.3490.09750.08070.6725-0.16680.00080.51980.04280.5496-51.164446.174919.5217
74.51841.34120.62414.7196-0.54633.1370.3928-0.524-0.86570.9811-0.6273-0.83450.23690.0419-0.15060.7282-0.0152-0.12380.52820.08530.4189-49.149729.432823.2446
83.7923-0.47380.07484.3211-1.60161.90830.1056-0.5061-0.12560.5084-0.19540.3160.2142-0.35460.05490.6752-0.18890.12860.5546-0.03790.3177-70.944634.44118.2268
98.86762.1430.19610.8526-0.47420.66730.450.37560.2587-0.0371-0.24570.17790.127-0.0068-0.26470.6108-0.09340.06770.4364-0.04690.4399-53.793144.35327.8922
102.1334-1.11980.98932.01751.01872.8606-0.1356-0.42-0.90670.36860.1650.35540.2551-0.21040.0760.8868-0.02630.22550.54210.20760.9047-72.0739-4.44888.8097
113.84220.5950.69010.50640.33760.7964-0.044-0.3446-1.0717-0.1720.1006-0.41810.1978-0.1273-0.08130.7461-0.02120.13640.4318-0.00070.7982-77.0593-6.9714-3.1787
123.68970.83652.45826.0084-2.5768.577-0.0021-0.1369-0.2789-1.1966-0.0254-1.14430.4170.42090.02020.6217-0.09990.12840.38610.00290.4389-48.307623.5414-2.4068
136.08315.1124-1.97785.3417-2.46011.29370.06550.76910.345-0.89980.20420.2708-0.3260.3269-0.15910.9541-0.15750.30310.67980.00690.5172-39.146940.6018-8.5167
143.4060.50021.96367.977-2.45713.1388-0.2983-0.3103-0.2531-0.63910.5302-0.3344-0.14340.7533-0.05040.9411-0.24240.270.6209-0.07660.3732-52.104332.9986-13.0775
154.5724-5.136-2.77215.89463.73024.67490.0520.13970.8617-0.24810.0799-0.6331-0.71170.2677-0.331.2021-0.32790.32060.7330.03110.6514-52.264737.645-16.9653
162.2042-1.59290.00573.0984-0.3122.4246-0.09310.4164-0.4528-0.6309-0.1208-0.18870.1662-0.07020.2490.7135-0.2110.1110.5026-0.04060.496-59.73825.869-10.7565
172.48170.30322.13096.31351.87552.2545-0.09050.1059-0.4237-0.2334-0.1552-0.40770.05330.15530.31090.8151-0.14830.23990.4565-0.00670.544-73.27114.3522-6.2203
181.02590.81520.19011.37320.10.9966-0.1921-0.12350.0909-0.15290.11980.3557-0.15630.0760.07250.7168-0.03650.01780.4542-0.10680.4022-107.753919.8262-7.0088
191.52920.50410.13621.0143-0.08951.4027-0.13330.18880.7612-0.3424-0.10040.1814-0.19280.06410.21750.89690.0267-0.08960.3674-0.13030.6752-110.176836.0315-11.8114
202.91991.8741.41472.46011.34511.5679-0.2353-0.22480.9496-0.2623-0.26730.7605-0.7161-0.16380.25211.05070.0425-0.150.5942-0.02060.9437-122.311538.4873-10.7422
211.64110.76040.71781.5174-0.16333.00450.0978-0.23690.00650.19310.07080.13240.1096-0.3927-0.09860.66490.06190.02250.5251-0.17440.6642-122.818817.2523-3.7907
223.96960.79940.16634.38630.25693.1033-0.05570.0301-0.537-0.00160.0901-0.33520.2574-0.16640.01870.6825-0.02810.0560.4564-0.05870.4761-107.6834.309-0.8025
233.55960.21060.06244.92150.10110.79-0.2221-0.5870.2562-0.04320.10260.6689-0.0556-0.55540.04340.8069-0.11150.05180.514-0.1490.659-123.370117.91641.1997
245.04883.10431.33536.73131.29412.2295-0.3436-0.17061.2588-0.4162-0.12941.3897-0.8407-0.139-0.01370.79310.06740.11130.5582-0.0740.7669-121.404132.6314-3.3956
251.90940.74080.41061.79860.33110.7539-0.0628-0.29920.29120.13130.02120.0334-0.20470.10090.02940.7417-0.03260.10020.4671-0.13020.3873-106.966919.8492-0.1581
266.75521.849-2.54563.80221.12887.4061-0.1910.59790.6653-1.32750.1050.3476-0.8989-0.5375-0.00610.872-0.0534-0.110.2977-0.00510.5184-105.450328.3157-24.105
273.7884.7593-0.15416.61011.00443.6960.05190.3323-0.344-0.2443-0.3383-0.06950.19030.61680.28370.8652-0.08940.01570.5187-0.13280.4701-110.88289.0633-27.7827
282.39840.28931.17750.0803-0.08461.94380.15690.1563-0.5754-0.82220.283-0.17710.8195-0.1869-0.32091.2319-0.22970.10920.6671-0.22540.2544-97.169616.3088-25.7923
293.51370.84750.37834.0846-5.59818.6436-0.5458-0.0063-0.3828-1.06980.1282-0.71781.5946-0.46640.49941.3839-0.08480.09780.4933-0.09270.6169-95.240310.6329-26.7285
301.1265-0.6162-0.00342.7962-1.11092.8628-0.13810.21560.1732-0.57990.1961-0.1823-0.04290.3175-0.07510.7362-0.17780.01130.4121-0.0970.418-92.742422.312-19.5738
316.651-4.28442.8268.1726-3.11978.22810.3950.99810.6907-0.8641-0.6334-0.377-0.92370.78250.29931.0476-0.2220.04670.64910.10040.5818-88.156633.6697-31.4151
326.7394-0.1324-0.65883.9281-0.60683.78540.0859-0.50380.139-0.0468-0.20220.0938-0.31070.23220.10780.9153-0.16880.03830.3948-0.01690.3769-81.691536.8176-10.3996
332.01540.0119-2.4721.51160.52724.5584-0.15270.67750.0607-0.79920.175-0.0073-0.2444-1.1153-0.00411.4926-0.4358-0.32660.9157-0.16620.2408-84.659643.4921-25.3033
342.7304-0.2184-0.65222.4099-0.77661.376-0.4589-0.08880.8520.52990.1263-0.2084-0.6995-0.01750.37841.4147-0.0637-0.2670.5734-0.09210.7744-90.193561.4091-11.7316
353.49270.05611.20380.25260.39611.2892-0.58990.24030.8435-0.63950.25030.1244-0.53320.18820.25811.1224-0.234-0.12870.5310.07350.6872-78.62160.0458-18.0793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 195 )
4X-RAY DIFFRACTION4chain 'A' and (resid 196 through 224 )
5X-RAY DIFFRACTION5chain 'A' and (resid 225 through 249 )
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 280 )
7X-RAY DIFFRACTION7chain 'A' and (resid 281 through 305 )
8X-RAY DIFFRACTION8chain 'A' and (resid 306 through 343 )
9X-RAY DIFFRACTION9chain 'A' and (resid 344 through 393 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 96 )
11X-RAY DIFFRACTION11chain 'B' and (resid 97 through 282 )
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 32 )
13X-RAY DIFFRACTION13chain 'C' and (resid 33 through 60 )
14X-RAY DIFFRACTION14chain 'C' and (resid 61 through 78 )
15X-RAY DIFFRACTION15chain 'C' and (resid 79 through 91 )
16X-RAY DIFFRACTION16chain 'C' and (resid 92 through 170 )
17X-RAY DIFFRACTION17chain 'C' and (resid 171 through 241 )
18X-RAY DIFFRACTION18chain 'D' and (resid 2 through 117 )
19X-RAY DIFFRACTION19chain 'D' and (resid 118 through 164 )
20X-RAY DIFFRACTION20chain 'D' and (resid 165 through 195 )
21X-RAY DIFFRACTION21chain 'D' and (resid 196 through 229 )
22X-RAY DIFFRACTION22chain 'D' and (resid 230 through 257 )
23X-RAY DIFFRACTION23chain 'D' and (resid 258 through 281 )
24X-RAY DIFFRACTION24chain 'D' and (resid 282 through 305 )
25X-RAY DIFFRACTION25chain 'D' and (resid 306 through 393 )
26X-RAY DIFFRACTION26chain 'E' and (resid 2 through 32 )
27X-RAY DIFFRACTION27chain 'E' and (resid 33 through 60 )
28X-RAY DIFFRACTION28chain 'E' and (resid 61 through 78 )
29X-RAY DIFFRACTION29chain 'E' and (resid 79 through 91 )
30X-RAY DIFFRACTION30chain 'E' and (resid 92 through 155 )
31X-RAY DIFFRACTION31chain 'E' and (resid 156 through 170 )
32X-RAY DIFFRACTION32chain 'E' and (resid 171 through 222 )
33X-RAY DIFFRACTION33chain 'E' and (resid 223 through 241 )
34X-RAY DIFFRACTION34chain 'F' and (resid 1 through 96 )
35X-RAY DIFFRACTION35chain 'F' and (resid 97 through 282 )

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