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 9SPZ | pdb_00009spz

Crystal structure of the Molybdenum-containing nitrogenase from Methanocaldococcus infernus refined to 1.37 A resolution - crystalline form A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 
    0.156 (Depositor), 0.156 (DCC) 
  • R-Value Work: 
    0.123 (Depositor), 0.124 (DCC) 
  • R-Value Observed: 
    0.125 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Molecular basis of N 2 fixation in a hyperthermophilic archaeon.

Maslac, N., Torer, M.R., Bolte, P., Wagner, T.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-77173-0
  • Primary Citation Related Structures: 
    9SPZ, 9SQ3

  • PubMed Abstract: 

    Exploring the natural diversity of phylogenetically distant nitrogenases is crucial for gaining new insights into the mechanism of atmospheric N 2 fixation and unlocking biotechnological developments in sustainable ammonia production. Here, we investigated the N 2 -fixing system of Methanocaldococcus infernus, a deep-sea hyperthermophilic archaeon growing diazotrophically at 92 °C. This natively isolated nitrogenase has a melting temperature close to the water boiling point, with an extrapolated specific activity superior to mesophilic homologues. The crystal structures obtained at near-atomic resolution present the most simplified known nitrogenase, harbouring strategic hot spots for thermostability. It combines the structural traits of all three known nitrogenase isoforms, reinforcing the proposal that ancestral nitrogenases were more similar to the archaeal enzyme than to the bacterial homologues. In contrast to structural homologues, the electron-transferring metallocofactor "P-cluster" is trapped in a rare state awaiting electron delivery, providing a detailed picture of the physiological state. The active site, harbouring the FeMo-cofactor catalyst, exhibits a mixture of the resting and "turnover" states, previously described solely in the bacterial vanadium and iron-only nitrogenases. Therefore, these results unify a mechanistic principle of all nitrogenases and highlight the advantages of the hyperthermostable nature of the archaeal enzyme, opening new avenues for further understanding of how nature splits the N 2 triple bond.


  • Organizational Affiliation: 
    • Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, Germany.

Macromolecule Content 

  • Total Structure Weight: 219.58 kDa 
  • Atom Count: 16,851 
  • Modeled Residue Count: 1,869 
  • Deposited Residue Count: 1,878 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrogenase protein alpha chain
A, C
477Methanocaldococcus infernus MEMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for D5VU98 (Methanocaldococcus infernus (strain DSM 11812 / JCM 15783 / ME))
Explore D5VU98 
Go to UniProtKB:  D5VU98
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5VU98
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrogenase
B, D
462Methanocaldococcus infernus MEMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for D5VU97 (Methanocaldococcus infernus (strain DSM 11812 / JCM 15783 / ME))
Explore D5VU97 
Go to UniProtKB:  D5VU97
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5VU97
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ICS
(Subject of Investigation/LOI)

Query on ICS



Download:Ideal Coordinates CCD File
IA [auth C],
L [auth A]
iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
CLF
(Subject of Investigation/LOI)

Query on CLF



Download:Ideal Coordinates CCD File
Q [auth B]FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
1CL
(Subject of Investigation/LOI)

Query on 1CL



Download:Ideal Coordinates CCD File
HA [auth C],
K [auth A]
FE(8)-S(7) CLUSTER, OXIDIZED
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
SF4
(Subject of Investigation/LOI)

Query on SF4



Download:Ideal Coordinates CCD File
M [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F4S
(Subject of Investigation/LOI)

Query on F4S



Download:Ideal Coordinates CCD File
R [auth B]FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-UHFFFAOYSA-N
HCA
(Subject of Investigation/LOI)

Query on HCA



Download:Ideal Coordinates CCD File
KA [auth C],
P [auth A]
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
MPD

Query on MPD



Download:Ideal Coordinates CCD File
S [auth B],
Y [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
GA [auth C]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
GA [auth C],
I [auth A],
J [auth A],
LA [auth D],
T [auth B],
X [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
DA [auth C]
EA [auth C]
FA [auth C]
H [auth A]
N [auth A]
DA [auth C],
EA [auth C],
FA [auth C],
H [auth A],
N [auth A],
U [auth B],
V [auth B],
W [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
BA [auth B],
CA [auth B],
JA [auth C],
MA [auth D],
O [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
AA [auth B],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free:  0.156 (Depositor), 0.156 (DCC) 
  • R-Value Work:  0.123 (Depositor), 0.124 (DCC) 
  • R-Value Observed: 0.125 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.433α = 90
b = 117.18β = 91.48
c = 106.627γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-29
    Type: Initial release
  • Version 1.1: 2026-09-02
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Derived calculations, Structure summary
  • Version 1.2: 2026-09-23
    Changes: Database references, Structure summary