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- PDB-9r52: Dimeric state of the F420-reducing hydrogenase from Methanothermo... -

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Basic information

Entry
Database: PDB / ID: 9r52
TitleDimeric state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus in crystalline form 2
Components(F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus ...) x 3
KeywordsOXIDOREDUCTASE / [NiFe]-hydrogenase / redox cycle / catalysis / [4Fe-4S]-cluster / F420 cofactor / FAD / hydrogen activation / thermophilic methanogen
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / : / Chem-NFU / IRON/SULFUR CLUSTER
Function and homology information
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,42121
Polymers103,0013
Non-polymers3,42018
Water13,061725
1
A: F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus alpha subunit
B: F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus beta subunit
C: F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus gamma subunit
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)212,84342
Polymers206,0026
Non-polymers6,84136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area35350 Å2
ΔGint-361 kcal/mol
Surface area59800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.028, 163.482, 128.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-837-

HOH

21A-915-

HOH

31A-922-

HOH

41A-933-

HOH

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Components

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F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus ... , 3 types, 3 molecules ABC

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


Mass: 45839.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The C-terminal extension has been cleaved off during the hydrogenase 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 beta subunit


Mass: 31091.084 Da / Num. of mol.: 1 / 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 gamma subunit


Mass: 26070.508 Da / Num. of mol.: 1 / 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 , 6 types, 743 molecules

#4: 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: 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
#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.9 % / Description: Black rod
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystals were obtained anaerobically in a Coy tent filled with a N2/H2 (97:3%) atmosphere at 20 degree Celsius using the sitting/drop method in CombiClover crystallisation plates. The enzyme ...Details: Crystals were obtained anaerobically in a Coy tent filled with a N2/H2 (97:3%) atmosphere at 20 degree Celsius using the sitting/drop method in CombiClover crystallisation plates. The enzyme was used at a concentration of 6.1 mg/ml in 25 mM Tris/HCl pH 7.6, 10% (v/v) glycerol, 2 mM dithiothreitol and 2 mM flavin adenine dinucleotide (FAD). 2 ul of the protein sample was mixed with 2 ul of the following crystallisation solution made of 45 % (w/v) Pentaerythritol propoxylate (17/8 PO/OH) and 100 mM Tris pH 8.5.
PH range: / / Temp details: /

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.65→69.27 Å / Num. obs: 92187 / % possible obs: 94.1 % / Redundancy: 20.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.026 / Rrim(I) all: 0.115 / Net I/σ(I): 16.1
Reflection shellResolution: 1.65→1.79 Å / Redundancy: 18.4 % / Rmerge(I) obs: 2.354 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4460 / CC1/2: 0.588 / Rpim(I) all: 0.56 / Rrim(I) all: 2.421 / % possible all: 59.9

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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: 1.65→64.41 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.03 / Stereochemistry target values: ML
Details: The model was manually optimized with coot and refined with Phenix. Refinement was performed with translation-libration screw and by adding hydrogens in riding positions.
RfactorNum. reflection% reflection
Rfree0.1826 4605 5 %
Rwork0.1411 --
obs0.1432 92177 77.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.11 Å2
Refinement stepCycle: LAST / Resolution: 1.65→64.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7015 0 155 725 7895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087350
X-RAY DIFFRACTIONf_angle_d1.1899970
X-RAY DIFFRACTIONf_dihedral_angle_d15.2822741
X-RAY DIFFRACTIONf_chiral_restr0.1021138
X-RAY DIFFRACTIONf_plane_restr0.0091251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.301250.2569149X-RAY DIFFRACTION4
1.67-1.690.199150.2583240X-RAY DIFFRACTION6
1.69-1.710.2308140.2548404X-RAY DIFFRACTION11
1.71-1.740.3307410.266583X-RAY DIFFRACTION16
1.74-1.760.2513560.2429966X-RAY DIFFRACTION26
1.76-1.780.2988770.22911524X-RAY DIFFRACTION41
1.78-1.810.25541250.21261892X-RAY DIFFRACTION52
1.81-1.830.24071050.19682312X-RAY DIFFRACTION61
1.83-1.860.24061440.18872540X-RAY DIFFRACTION68
1.86-1.890.24411590.17682917X-RAY DIFFRACTION78
1.89-1.930.20321600.17933173X-RAY DIFFRACTION84
1.93-1.960.22341980.17053463X-RAY DIFFRACTION93
1.96-20.22852060.15923690X-RAY DIFFRACTION98
2-2.040.21192030.14983727X-RAY DIFFRACTION100
2.04-2.080.21161790.13913784X-RAY DIFFRACTION100
2.08-2.130.18192070.13383759X-RAY DIFFRACTION100
2.13-2.190.1762150.12823752X-RAY DIFFRACTION100
2.19-2.240.16871850.12343259X-RAY DIFFRACTION99
2.25-2.310.17451710.11743391X-RAY DIFFRACTION97
2.31-2.390.16261810.11113787X-RAY DIFFRACTION100
2.39-2.470.15532030.11643751X-RAY DIFFRACTION100
2.47-2.570.16371980.11493792X-RAY DIFFRACTION100
2.57-2.690.16131890.12523774X-RAY DIFFRACTION100
2.69-2.830.16242180.13683765X-RAY DIFFRACTION100
2.83-3.010.18531830.14853804X-RAY DIFFRACTION100
3.01-3.240.1931540.14033860X-RAY DIFFRACTION100
3.24-3.560.19191920.13893830X-RAY DIFFRACTION100
3.56-4.080.15111980.12593832X-RAY DIFFRACTION100
4.08-5.140.15342020.12243862X-RAY DIFFRACTION100
5.14-64.410.21462220.18043990X-RAY DIFFRACTION100

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