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

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Basic information

Entry
Database: PDB / ID: 9spz
TitleCrystal structure of the Molybdenum-containing nitrogenase from Methanocaldococcus infernus refined to 1.37 A resolution - crystalline form A
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
FE(8)-S(7) CLUSTER, OXIDIZED / FE(8)-S(7) CLUSTER / FE4-S3 CLUSTER / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / IRON/SULFUR CLUSTER / Nitrogenase / Nitrogenase protein alpha chain
Similarity search - Component
Biological speciesMethanocaldococcus infernus ME (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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 18, 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)219,58339
Polymers213,1234
Non-polymers6,46035
Water26,1941454
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.433, 117.180, 106.627
Angle α, β, γ (deg.)90.00, 91.48, 90.00
Int Tables number4
Space group name H-MP1211

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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 , 12 types, 1489 molecules

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


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-1CL / FE(8)-S(7) CLUSTER, OXIDIZED


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#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-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C7H10O7 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-F4S / FE4-S3 CLUSTER / T-CLUSTER


Mass: 319.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S3 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#13: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1454 / 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: 2.32 Å3/Da / Density % sol: 46.91 % / Description: Thick brown plate
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 degrees 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 degrees Celsius). Crystallisation was done by the sitting drop method in 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) plate containing 90 uL of crystallisation solution in the reservoir in all cases. Crystals were obtained by mixing 0.7 uL of crystallisation solution with 0.7 uL of protein sample at a concentration of 2.95 mg/mL. 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: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→78.85 Å / Num. obs: 273586 / % possible obs: 95.3 % / Redundancy: 10.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.029 / Rrim(I) all: 0.096 / Net I/σ(I): 12.3
Reflection shellResolution: 1.37→1.515 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.198 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 13675 / CC1/2: 0.658 / Rpim(I) all: 0.404 / Rrim(I) all: 1.266 / % possible all: 68.2

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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: 1.37→21.91 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.51 / 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
Rfree0.1556 13619 4.98 %
Rwork0.1233 --
obs0.1249 273457 67.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.37→21.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14915 0 233 1454 16602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01115810
X-RAY DIFFRACTIONf_angle_d1.26221509
X-RAY DIFFRACTIONf_dihedral_angle_d15.3945927
X-RAY DIFFRACTIONf_chiral_restr0.8772258
X-RAY DIFFRACTIONf_plane_restr0.0132738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.468840.2272144X-RAY DIFFRACTION1
1.39-1.40.1781280.2484461X-RAY DIFFRACTION4
1.4-1.420.3009520.2138744X-RAY DIFFRACTION6
1.42-1.440.2207680.2341014X-RAY DIFFRACTION8
1.44-1.460.2663640.21561496X-RAY DIFFRACTION12
1.46-1.480.20151100.19452265X-RAY DIFFRACTION18
1.48-1.50.2281590.19543273X-RAY DIFFRACTION26
1.5-1.520.23782460.19154371X-RAY DIFFRACTION35
1.52-1.540.23772550.18695516X-RAY DIFFRACTION43
1.54-1.570.2143010.17916382X-RAY DIFFRACTION50
1.57-1.60.22133780.17587215X-RAY DIFFRACTION57
1.6-1.620.20654120.16988025X-RAY DIFFRACTION63
1.62-1.660.20144550.16229033X-RAY DIFFRACTION71
1.66-1.690.20025210.15569886X-RAY DIFFRACTION78
1.69-1.730.19485970.156810832X-RAY DIFFRACTION85
1.73-1.770.185930.151511518X-RAY DIFFRACTION90
1.77-1.810.19536050.143212102X-RAY DIFFRACTION95
1.81-1.860.17586590.134112611X-RAY DIFFRACTION99
1.86-1.910.16736810.125512756X-RAY DIFFRACTION100
1.91-1.980.15537080.121912653X-RAY DIFFRACTION100
1.98-2.050.17226690.111412782X-RAY DIFFRACTION100
2.05-2.130.15186910.108512713X-RAY DIFFRACTION100
2.13-2.220.14496940.10312744X-RAY DIFFRACTION100
2.22-2.340.14576810.104312656X-RAY DIFFRACTION99
2.34-2.490.14686790.107112627X-RAY DIFFRACTION99
2.49-2.680.14686130.115212860X-RAY DIFFRACTION100
2.68-2.950.14836780.117212736X-RAY DIFFRACTION100
2.95-3.370.14097090.11712791X-RAY DIFFRACTION100
3.37-4.250.13436320.107112830X-RAY DIFFRACTION100
4.25-21.910.14796770.136412802X-RAY DIFFRACTION99

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