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- PDB-9tn7: F420-nitrite reductase from Methanocaldococcus infernus at 1.58 A... -

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Basic information

Entry
Database: PDB / ID: 9tn7
TitleF420-nitrite reductase from Methanocaldococcus infernus at 1.58 A resolution
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 / nitrogen-assimilation / NO3-metabolism
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
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: 1.58 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 1.0Jun 24, 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)75,19425
Polymers69,8191
Non-polymers5,37524
Water11,115617
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)300,777100
Polymers279,2774
Non-polymers21,49996
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 area51600 Å2
ΔGint-928 kcal/mol
Surface area88380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.200, 114.110, 136.710
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-1104-

HOH

21A-1204-

HOH

31A-1252-

HOH

41A-1295-

HOH

51A-1367-

HOH

61A-1370-

HOH

71A-1414-

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 , 11 types, 641 molecules

#2: 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
#3: Chemical ChemComp-SRM / SIROHEME


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


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3 / 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: Chemical ChemComp-NA / SODIUM ION


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


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


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.86 Å3/Da / Density % sol: 57.07 % / Description: Brown polygonal plates slightly twinned
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
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, 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 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 MES pH 6.5, and 400 mM Potassium chloride. The crystals appeared in 7 to 12 days.

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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: 1.58→87.6 Å / Num. obs: 89629 / % possible obs: 94.8 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.035 / Rrim(I) all: 0.129 / Net I/σ(I): 11.4
Reflection shellResolution: 1.58→1.71 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.957 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4481 / CC1/2: 0.558 / Rpim(I) all: 0.544 / Rrim(I) all: 2.032 / % possible all: 52.6

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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: 1.58→42.32 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.62 / Stereochemistry target values: ML
Details: The refinement has been performed in phenix.refine with all atoms except water considered anisotropic. Hydrogens were refined (in riding positions) and removed from the deposited model.
RfactorNum. reflection% reflection
Rfree0.1672 4514 5.04 %
Rwork0.138 --
obs0.1394 89621 81.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.15 Å2
Refinement stepCycle: LAST / Resolution: 1.58→42.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4894 0 233 617 5744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115387
X-RAY DIFFRACTIONf_angle_d1.3147299
X-RAY DIFFRACTIONf_dihedral_angle_d15.422141
X-RAY DIFFRACTIONf_chiral_restr0.071776
X-RAY DIFFRACTIONf_plane_restr0.014902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.391120.244137X-RAY DIFFRACTION1
1.6-1.610.282990.262779X-RAY DIFFRACTION2
1.61-1.630.3733140.2223220X-RAY DIFFRACTION6
1.63-1.650.2611250.2211552X-RAY DIFFRACTION16
1.65-1.680.3171600.22591068X-RAY DIFFRACTION31
1.68-1.70.2685720.22651546X-RAY DIFFRACTION45
1.7-1.720.24061130.2192211X-RAY DIFFRACTION64
1.72-1.750.24371500.21932933X-RAY DIFFRACTION85
1.75-1.780.21141740.20923373X-RAY DIFFRACTION98
1.78-1.810.22921760.19393455X-RAY DIFFRACTION100
1.81-1.840.20911810.18253453X-RAY DIFFRACTION100
1.84-1.870.24662000.17053428X-RAY DIFFRACTION100
1.87-1.910.20681930.1523432X-RAY DIFFRACTION100
1.91-1.950.20191680.14183442X-RAY DIFFRACTION100
1.95-1.990.19511720.13223462X-RAY DIFFRACTION100
1.99-2.030.16611870.12393461X-RAY DIFFRACTION100
2.03-2.080.17221890.12123465X-RAY DIFFRACTION100
2.08-2.140.1561830.11763451X-RAY DIFFRACTION100
2.14-2.20.14261940.11523424X-RAY DIFFRACTION100
2.2-2.280.1511780.10943502X-RAY DIFFRACTION100
2.28-2.360.14581850.1123437X-RAY DIFFRACTION100
2.36-2.450.16341700.11273496X-RAY DIFFRACTION100
2.45-2.560.14421930.123466X-RAY DIFFRACTION100
2.56-2.70.16271810.12633488X-RAY DIFFRACTION100
2.7-2.870.17311960.13213461X-RAY DIFFRACTION100
2.87-3.090.17191850.14083508X-RAY DIFFRACTION100
3.09-3.40.15291920.14023487X-RAY DIFFRACTION100
3.4-3.890.15151950.1343516X-RAY DIFFRACTION100
3.89-4.90.15641840.12133569X-RAY DIFFRACTION100
4.9-42.320.16841930.16173685X-RAY DIFFRACTION100

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