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- PDB-9tn9: F420-nitrite reductase from Methanocaldococcus infernus soaked wi... -

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Basic information

Entry
Database: PDB / ID: 9tn9
TitleF420-nitrite reductase from Methanocaldococcus infernus soaked with 50 mM nitrite
ComponentsCoenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein
KeywordsOXIDOREDUCTASE / F420H2-oxidase / iron-sulfur cluster / archaea / hyperthermophile / marine / methanogen / sulfite / nitrite / F420 / siroheme / FAD / ferredoxin / sulfite-reductase / nitrite-reductase / Fsr / Fnr
Function / homology
Function and homology information


oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / 4 iron, 4 sulfur cluster binding / heme binding / metal ion binding
Similarity search - Function
Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily ...Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily / Nitrite and sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like half domain / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / 4Fe-4S binding 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
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / : / NITRITE ION / Chem-PXN / IRON/SULFUR CLUSTER / SULFITE ION / SIROHEME / Coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein
Similarity search - Component
Biological speciesMethanocaldococcus infernus ME (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHeidenreich, A. / Wagner, T.
Funding support Germany, France, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
Agence Nationale de la Recherche (ANR)ANR-24-CE93-0004-01 France
CitationJournal: To Be Published
Title: NO3 reduction salvage pathway in a deep-sea hyperthermophilic methanogen
Authors: Heidenreich, A. / Gouveia, A.G. / Wagner, T.
History
DepositionDec 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,96321
Polymers69,8191
Non-polymers5,14320
Water14,214789
1
A: Coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein
hetero molecules

A: Coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein
hetero molecules

A: Coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein
hetero molecules

A: Coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,85184
Polymers279,2774
Non-polymers20,57380
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area49440 Å2
ΔGint-798 kcal/mol
Surface area87690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.760, 113.000, 135.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1157-

HOH

21A-1293-

HOH

31A-1337-

HOH

41A-1406-

HOH

51A-1424-

HOH

61A-1500-

HOH

71A-1563-

HOH

81A-1587-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein


Mass: 69819.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanocaldococcus infernus ME (archaea) / Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: ME / Tissue: / / References: UniProt: D5VTU8

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Non-polymers , 12 types, 809 molecules

#2: 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
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SRM / SIROHEME


Mass: 916.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H44FeN4O16 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PXN / (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol / PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH)


Mass: 368.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H36O8
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#11: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#12: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / 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: 2.8 Å3/Da / Density % sol: 56.17 % / Description: Dark brown trapezoidal thick plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Prior to crystallisation, fresh sample was centrifuged at 13 000 g for 3 min to remove macro-aggregates and dust. The sample was crystallised in an anaerobic chamber filled with a N2/H2 (97: ...Details: Prior to crystallisation, fresh sample was centrifuged at 13 000 g for 3 min to remove macro-aggregates and dust. The sample was crystallised in an anaerobic chamber filled with a N2/H2 (97:3%) atmosphere, at 20 degrees Celsius. The crystallisation was done in 96-Well MRC 2-Drop polystyrene plates (SWISSCI) containing 90 uL of crystallisation solution in the reservoir. 0.7 uL of enzyme at 6.5 mg/ml + 1 mM FAD was mixed with 0.7 uL of the crystallisation solution. The crystallisation solution contained 45 % w/v pentaerythritol propoxylate (5/4 PO/OH), 100 mM sodium acetate pH 4.6, and 400 mM potassium chloride. Prior to flash-freezing in liquid nitrogen, crystals were soaked in the crystallisation solution supplemented with 50 mM sodium nitrite for 5 min.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.2→86.86 Å / Num. obs: 175298 / % possible obs: 95.1 % / Redundancy: 5.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.031 / Rrim(I) all: 0.074 / Net I/σ(I): 11.9
Reflection shellResolution: 1.205→1.326 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.938 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8765 / CC1/2: 0.47 / Rpim(I) all: 0.513 / Rrim(I) all: 1.074 / % possible all: 56.9

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→42.02 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.49 / Stereochemistry target values: ML
Details: The refinement has been performed with phenix.refine considering all atoms anisotropic. The refinement has been done with hydrogens in riding position.
RfactorNum. reflection% reflection
Rfree0.1427 8740 4.99 %
Rwork0.1157 --
obs0.117 175289 73.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.51 Å2
Refinement stepCycle: LAST / Resolution: 1.2→42.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4894 0 222 789 5905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135384
X-RAY DIFFRACTIONf_angle_d1.4817296
X-RAY DIFFRACTIONf_dihedral_angle_d15.8142147
X-RAY DIFFRACTIONf_chiral_restr0.106778
X-RAY DIFFRACTIONf_plane_restr0.017900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.112420.238776X-RAY DIFFRACTION1
1.22-1.230.2894140.2527259X-RAY DIFFRACTION3
1.23-1.250.2284290.2528490X-RAY DIFFRACTION7
1.25-1.260.2578470.2454712X-RAY DIFFRACTION10
1.26-1.280.2477630.23921084X-RAY DIFFRACTION14
1.28-1.30.2648720.24121630X-RAY DIFFRACTION22
1.3-1.320.25621370.22792361X-RAY DIFFRACTION32
1.32-1.340.24651970.22313549X-RAY DIFFRACTION47
1.34-1.360.2452810.21434600X-RAY DIFFRACTION61
1.36-1.380.23322940.19385197X-RAY DIFFRACTION69
1.38-1.40.20042890.18725649X-RAY DIFFRACTION75
1.4-1.430.20973220.17436106X-RAY DIFFRACTION81
1.43-1.460.19683140.16126757X-RAY DIFFRACTION89
1.46-1.490.19523480.15357026X-RAY DIFFRACTION93
1.49-1.520.17423900.1467286X-RAY DIFFRACTION96
1.52-1.550.15323850.13157449X-RAY DIFFRACTION99
1.55-1.590.1523950.12647586X-RAY DIFFRACTION100
1.59-1.630.13833920.11567549X-RAY DIFFRACTION100
1.63-1.680.13883910.10327561X-RAY DIFFRACTION100
1.68-1.740.12423760.09897595X-RAY DIFFRACTION100
1.74-1.80.1314260.09687520X-RAY DIFFRACTION100
1.8-1.870.11443750.09677587X-RAY DIFFRACTION100
1.87-1.960.11524110.09397599X-RAY DIFFRACTION100
1.96-2.060.12513960.09337526X-RAY DIFFRACTION99
2.06-2.190.12554190.09267546X-RAY DIFFRACTION100
2.19-2.360.12054100.09547598X-RAY DIFFRACTION99
2.36-2.590.13073760.10247606X-RAY DIFFRACTION99
2.59-2.970.13313910.11347594X-RAY DIFFRACTION99
2.97-3.740.14214050.11587622X-RAY DIFFRACTION99
3.74-42.020.15093930.1247829X-RAY DIFFRACTION98

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