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- PDB-9sq3: Crystal structure of the Molybdenum-containing nitrogenase from M... -

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Basic information

Entry
Database: PDB / ID: 9sq3
TitleCrystal structure of the Molybdenum-containing nitrogenase from Methanocaldococcus infernus refined to 1.21 A resolution - crystalline form B.
Components
  • Nitrogenase
  • Nitrogenase protein alpha chain
KeywordsOXIDOREDUCTASE / Nitrogenase / N2-fixation / FeMo-cofactor / hyperthermophile / extremophile / metallo-cofactor / metalloenzyme / P-cluster / archaea / methanogen / marine / hydrogenotrophic / Methanococcales.
Function / homology
Function and homology information


nitrogenase / nitrogenase activity / iron-sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase alpha chain / Nitrogenase component 1, alpha chain / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / : / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase
Similarity search - Domain/homology
: / : / HYDROSULFURIC ACID / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICE / Chem-ICS / Nitrogenase / Nitrogenase protein alpha chain
Similarity search - Component
Biological speciesMethanocaldococcus infernus ME (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsMaslac, N. / Torer, M.R. / Bolte, P. / Wagner, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Molecular basis of N2-fixation in a hyperthermophilic archaeon
Authors: Maslac, N. / Torer, M.R. / Bolte, P. / Wagner, T.
History
DepositionSep 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 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: Nitrogenase protein alpha chain
B: Nitrogenase
C: Nitrogenase protein alpha chain
D: Nitrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,48746
Polymers213,1234
Non-polymers8,36342
Water36,4082021
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30240 Å2
ΔGint-232 kcal/mol
Surface area56890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.504, 80.243, 105.744
Angle α, β, γ (deg.)74.49, 82.25, 65.02
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Nitrogenase protein alpha chain


Mass: 54738.129 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanocaldococcus infernus ME (archaea) / Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: ME / Tissue: / / References: UniProt: D5VU98, nitrogenase
#2: Protein Nitrogenase


Mass: 51823.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanocaldococcus infernus ME (archaea) / Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: ME / Tissue: / / References: UniProt: D5VU97, nitrogenase

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Non-polymers , 13 types, 2063 molecules

#3: Chemical ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS9 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ICE / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 755.386 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS8
#8: Chemical ChemComp-A1JPX / FE(8)-S(7) CLUSTER, P1+ state conformer B


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-UNX / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#11: Chemical ChemComp-A1JPW / FE(8)-S(7) CLUSTER, P1+ state conformer A


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#14: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2021 / 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: 2.4 Å3/Da / Density % sol: 48.76 % / Description: Orthorhombic brown rods
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Samples were centrifuged at 13,000 x g for 3 min to remove macro-aggregates and dust, and crystallised inside an anaerobic chamber (N2/H2 (97:3%) atmosphere, 20 degree Celsius). ...Details: Samples were centrifuged at 13,000 x g for 3 min to remove macro-aggregates and dust, and crystallised inside an anaerobic chamber (N2/H2 (97:3%) atmosphere, 20 degree Celsius). Crystallisation was done by the sitting drop method in 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) containing 90 uL of crystallisation solution in the reservoir. Crystals were obtained by mixing 0.7 uL of crystallisation solution with 0.7 uL of protein sample at 22.4 mg.ml-1. The crystallisation solution contained the following: 30 % v/v 2-methyl-2,4-pentanediol, 100 mM Tris pH 8.5, 500 mM Sodium chloride and 8 % w/v Polyethylene glycol 8,000 (Crystallisation solution of the JBScreen Wizard form Jena Bioscience, Germany).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.21→101.86 Å / Num. obs: 371908 / % possible obs: 92 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Rrim(I) all: 0.079 / Net I/σ(I): 12.9
Reflection shellResolution: 1.21→1.35 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.071 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 18595 / CC1/2: 0.669 / Rpim(I) all: 0.425 / Rrim(I) all: 1.154 / % possible all: 74.5

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→33.62 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.22 / Stereochemistry target values: ML
Details: The model was manually built via Coot and refined with phenix.refine. The refinement steps were performed by considering all atoms as anisotropic with hydrogens in the riding position. The ...Details: The model was manually built via Coot and refined with phenix.refine. The refinement steps were performed by considering all atoms as anisotropic with hydrogens in the riding position. The model was validated by the MolProbity server
RfactorNum. reflection% reflection
Rfree0.146 18775 5.06 %
Rwork0.1208 --
obs0.1221 371077 61.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.71 Å2
Refinement stepCycle: LAST / Resolution: 1.21→33.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14906 0 291 2023 17220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01316175
X-RAY DIFFRACTIONf_angle_d1.47222099
X-RAY DIFFRACTIONf_dihedral_angle_d14.8776099
X-RAY DIFFRACTIONf_chiral_restr0.1112292
X-RAY DIFFRACTIONf_plane_restr0.0212810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.220.2024170.2118304X-RAY DIFFRACTION2
1.22-1.240.3087190.2186543X-RAY DIFFRACTION3
1.24-1.250.2495430.2186814X-RAY DIFFRACTION4
1.25-1.270.2467710.21181223X-RAY DIFFRACTION6
1.27-1.290.27011030.22532031X-RAY DIFFRACTION11
1.29-1.30.23331460.21942847X-RAY DIFFRACTION15
1.3-1.320.25791710.2113475X-RAY DIFFRACTION18
1.32-1.340.22082150.21574163X-RAY DIFFRACTION22
1.34-1.360.23872630.2125005X-RAY DIFFRACTION26
1.36-1.390.22583200.19755965X-RAY DIFFRACTION32
1.39-1.410.23553900.19887124X-RAY DIFFRACTION38
1.41-1.440.22664340.1998193X-RAY DIFFRACTION43
1.44-1.460.2185690.184610477X-RAY DIFFRACTION55
1.46-1.490.22826340.171912497X-RAY DIFFRACTION66
1.49-1.530.21498100.168314466X-RAY DIFFRACTION77
1.53-1.560.21339260.159316711X-RAY DIFFRACTION88
1.56-1.60.19989910.145918049X-RAY DIFFRACTION95
1.6-1.640.18999420.14818135X-RAY DIFFRACTION96
1.64-1.690.18229610.139417590X-RAY DIFFRACTION93
1.69-1.750.15769480.127618419X-RAY DIFFRACTION97
1.75-1.810.14569970.114918398X-RAY DIFFRACTION97
1.81-1.880.13849680.105218435X-RAY DIFFRACTION97
1.88-1.970.14119790.108118511X-RAY DIFFRACTION97
1.97-2.070.13279450.097518399X-RAY DIFFRACTION97
2.07-2.20.11619360.096817998X-RAY DIFFRACTION95
2.2-2.370.130510400.101218495X-RAY DIFFRACTION98
2.37-2.610.127710060.106418581X-RAY DIFFRACTION98
2.61-2.990.13329590.114118604X-RAY DIFFRACTION98
2.99-3.760.12089910.109218353X-RAY DIFFRACTION97
3.76-33.620.13769810.125718497X-RAY DIFFRACTION97

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