9R51 | pdb_00009r51

Dimeric state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus in crystalline form 1

PDB DOI: https://doi.org/10.2210/pdb9R51/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanothermococcus thermolithotrophicus DSM 2095
Mutation(s): No

Deposited: 2025-05-08 Released: 2025-10-22
Deposition Author(s): Jespersen, M., Lemaire, O.N., Wagner, T.
Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.207 (Depositor), 0.207 (DCC)
R-Value Work:
0.180 (Depositor), 0.179 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural and Spectroscopic Insights into Catalytic Intermediates of a [NiFe]-hydrogenase from Group 3.

Jespersen, M., Lorent, C., Lemaire, O.N., Zebger, I., Wagner, T.

(2025) Chembiochem 26: e202500692-e202500692

PubMed: 41078086 Search on PubMed
DOI: https://doi.org/10.1002/cbic.202500692
Primary Citation of Related Structures:
9R51, 9R52, 9R5I, 9R6Z

PubMed Abstract:
Hydrogenases catalyze reversible H ₂ production and are potential models for renewable energy catalysts. Here, the full redox landscape of a group 3 [NiFe]-hydrogenase from methanothermococcus thermolithotrophicus is elucidated, resembling group 1 enzymes. Structural and spectroscopic analyses reveal a catalytic-ready state with nickel seesaw coordination, enabling intermediate trapping and advancing mechanistic understanding of oxygen-sensitive [NiFe] enzymes.

Organizational Affiliation

Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.

Macromolecule Content

Total Structure Weight: 427.53 kDa
Atom Count: 30,819
Modeled Residue Count: 3,656
Deposited Residue Count: 3,732
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit alpha	A, D, G, J	410	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0 EC: 1.12.98.1
UniProt
Find proteins for Q60338 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q60338 Go to UniProtKB: Q60338
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q60338
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit beta	B, F, I, L	282	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0 EC: 1.12.98.1
UniProt
Find proteins for Q60341 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q60341 Go to UniProtKB: Q60341
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q60341
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit gamma	C, E, H, K	241	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0 EC: 1.12.98.1
UniProt
Find proteins for Q60340 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q60340 Go to UniProtKB: Q60340
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q60340
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain EB [auth F] SDF format, chain UC [auth L] SDF format, chain Y [auth B] SDF format, chain ZB [auth I] MOL2 format, chain EB [auth F] MOL2 format, chain UC [auth L] MOL2 format, chain Y [auth B] MOL2 format, chain ZB [auth I] mmCIF format, chain EB [auth F] mmCIF format, chain UC [auth L] mmCIF format, chain Y [auth B] mmCIF format, chain ZB [auth I]	EB [auth F], UC [auth L], Y [auth B], ZB [auth I]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain EB [auth F] Focus chain UC [auth L] Focus chain Y [auth B] Focus chain ZB [auth I] Interactions & Density Focus chain EB [auth F] Focus chain UC [auth L] Focus chain Y [auth B] Focus chain ZB [auth I]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain DB [auth F] SDF format, chain EA [auth C] SDF format, chain NC [auth K] SDF format, chain OC [auth K] SDF format, chain PC [auth K] SDF format, chain RB [auth H] SDF format, chain SB [auth H] SDF format, chain TB [auth H] SDF format, chain TC [auth L] SDF format, chain VA [auth E] SDF format, chain WA [auth E] SDF format, chain X [auth B] SDF format, chain XA [auth E] SDF format, chain YB [auth I] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain NC [auth K] MOL2 format, chain OC [auth K] MOL2 format, chain PC [auth K] MOL2 format, chain RB [auth H] MOL2 format, chain SB [auth H] MOL2 format, chain TB [auth H] MOL2 format, chain TC [auth L] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain YB [auth I] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain EA [auth C] mmCIF format, chain NC [auth K] mmCIF format, chain OC [auth K] mmCIF format, chain PC [auth K] mmCIF format, chain RB [auth H] mmCIF format, chain SB [auth H] mmCIF format, chain TB [auth H] mmCIF format, chain TC [auth L] mmCIF format, chain VA [auth E] mmCIF format, chain WA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain YB [auth I]	CA [auth C] DA [auth C] DB [auth F] EA [auth C] NC [auth K] CA [auth C], DA [auth C], DB [auth F], EA [auth C], NC [auth K], OC [auth K], PC [auth K], RB [auth H], SB [auth H], TB [auth H], TC [auth L], VA [auth E], WA [auth E], X [auth B], XA [auth E], YB [auth I]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain NC [auth K] Focus chain OC [auth K] Focus chain PC [auth K] Focus chain RB [auth H] Focus chain SB [auth H] Focus chain TB [auth H] Focus chain TC [auth L] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain YB [auth I] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain NC [auth K] Focus chain OC [auth K] Focus chain PC [auth K] Focus chain RB [auth H] Focus chain SB [auth H] Focus chain TB [auth H] Focus chain TC [auth L] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain YB [auth I]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain GC [auth J] SDF format, chain LB [auth G] MOL2 format, chain GC [auth J] MOL2 format, chain LB [auth G] mmCIF format, chain GC [auth J] mmCIF format, chain LB [auth G]	GC [auth J], LB [auth G]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain GC [auth J] Focus chain LB [auth G] Interactions & Density Focus chain GC [auth J] Focus chain LB [auth G]
NFU (Subject of Investigation/LOI) Query on NFU Download Ideal Coordinates CCD File SDF format, chain DC [auth J] SDF format, chain JA [auth D] SDF format, chain JB [auth G] SDF format, chain M [auth A] MOL2 format, chain DC [auth J] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth G] MOL2 format, chain M [auth A] mmCIF format, chain DC [auth J] mmCIF format, chain JA [auth D] mmCIF format, chain JB [auth G] mmCIF format, chain M [auth A]	DC [auth J], JA [auth D], JB [auth G], M [auth A]	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C₃ H Fe N₂ Ni O QCZROEOIPZWDEO-UHFFFAOYSA-N		Interactions Focus chain DC [auth J] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain M [auth A] Interactions & Density Focus chain DC [auth J] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain M [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EC [auth J] SDF format, chain FB [auth F] SDF format, chain FC [auth J] SDF format, chain GB [auth F] SDF format, chain KA [auth D] SDF format, chain KB [auth G] SDF format, chain LA [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain YA [auth E] MOL2 format, chain EC [auth J] MOL2 format, chain FB [auth F] MOL2 format, chain FC [auth J] MOL2 format, chain GB [auth F] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth G] MOL2 format, chain LA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain YA [auth E] mmCIF format, chain EC [auth J] mmCIF format, chain FB [auth F] mmCIF format, chain FC [auth J] mmCIF format, chain GB [auth F] mmCIF format, chain KA [auth D] mmCIF format, chain KB [auth G] mmCIF format, chain LA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain YA [auth E]	EC [auth J] FB [auth F] FC [auth J] GB [auth F] KA [auth D] EC [auth J], FB [auth F], FC [auth J], GB [auth F], KA [auth D], KB [auth G], LA [auth D], O [auth A], P [auth A], YA [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EC [auth J] Focus chain FB [auth F] Focus chain FC [auth J] Focus chain GB [auth F] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain LA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain YA [auth E] Interactions & Density Focus chain EC [auth J] Focus chain FB [auth F] Focus chain FC [auth J] Focus chain GB [auth F] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain LA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain YA [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth E] SDF format, chain AC [auth I] SDF format, chain BA [auth B] SDF format, chain BB [auth E] SDF format, chain BC [auth I] SDF format, chain CB [auth E] SDF format, chain CC [auth I] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain HB [auth F] SDF format, chain HC [auth J] SDF format, chain IA [auth C] SDF format, chain IB [auth F] SDF format, chain IC [auth J] SDF format, chain JC [auth J] SDF format, chain KC [auth J] SDF format, chain LC [auth J] SDF format, chain MA [auth D] SDF format, chain MB [auth G] SDF format, chain NA [auth D] SDF format, chain NB [auth G] SDF format, chain OA [auth D] SDF format, chain OB [auth G] SDF format, chain PA [auth D] SDF format, chain PB [auth G] SDF format, chain Q [auth A] SDF format, chain QA [auth D] SDF format, chain QC [auth K] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain RC [auth K] SDF format, chain S [auth A] SDF format, chain SA [auth D] SDF format, chain SC [auth K] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain UB [auth H] SDF format, chain V [auth A] SDF format, chain VB [auth H] SDF format, chain VC [auth L] SDF format, chain WB [auth H] SDF format, chain WC [auth L] SDF format, chain XB [auth H] SDF format, chain ZA [auth E] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth E] MOL2 format, chain AC [auth I] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth E] MOL2 format, chain BC [auth I] MOL2 format, chain CB [auth E] MOL2 format, chain CC [auth I] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth F] MOL2 format, chain HC [auth J] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth F] MOL2 format, chain IC [auth J] MOL2 format, chain JC [auth J] MOL2 format, chain KC [auth J] MOL2 format, chain LC [auth J] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth G] MOL2 format, chain NA [auth D] MOL2 format, chain NB [auth G] MOL2 format, chain OA [auth D] MOL2 format, chain OB [auth G] MOL2 format, chain PA [auth D] MOL2 format, chain PB [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain QC [auth K] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain RC [auth K] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain SC [auth K] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UB [auth H] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth H] MOL2 format, chain VC [auth L] MOL2 format, chain WB [auth H] MOL2 format, chain WC [auth L] MOL2 format, chain XB [auth H] MOL2 format, chain ZA [auth E] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth E] mmCIF format, chain AC [auth I] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth E] mmCIF format, chain BC [auth I] mmCIF format, chain CB [auth E] mmCIF format, chain CC [auth I] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain HB [auth F] mmCIF format, chain HC [auth J] mmCIF format, chain IA [auth C] mmCIF format, chain IB [auth F] mmCIF format, chain IC [auth J] mmCIF format, chain JC [auth J] mmCIF format, chain KC [auth J] mmCIF format, chain LC [auth J] mmCIF format, chain MA [auth D] mmCIF format, chain MB [auth G] mmCIF format, chain NA [auth D] mmCIF format, chain NB [auth G] mmCIF format, chain OA [auth D] mmCIF format, chain OB [auth G] mmCIF format, chain PA [auth D] mmCIF format, chain PB [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain QC [auth K] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain RC [auth K] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain SC [auth K] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain UB [auth H] mmCIF format, chain V [auth A] mmCIF format, chain VB [auth H] mmCIF format, chain VC [auth L] mmCIF format, chain WB [auth H] mmCIF format, chain WC [auth L] mmCIF format, chain XB [auth H] mmCIF format, chain ZA [auth E]	AA [auth B] AB [auth E] AC [auth I] BA [auth B] BB [auth E] AA [auth B], AB [auth E], AC [auth I], BA [auth B], BB [auth E], BC [auth I], CB [auth E], CC [auth I], FA [auth C], GA [auth C], HA [auth C], HB [auth F], HC [auth J], IA [auth C], IB [auth F], IC [auth J], JC [auth J], KC [auth J], LC [auth J], MA [auth D], MB [auth G], NA [auth D], NB [auth G], OA [auth D], OB [auth G], PA [auth D], PB [auth G], Q [auth A], QA [auth D], QC [auth K], R [auth A], RA [auth D], RC [auth K], S [auth A], SA [auth D], SC [auth K], T [auth A], U [auth A], UB [auth H], V [auth A], VB [auth H], VC [auth L], WB [auth H], WC [auth L], XB [auth H], ZA [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth E] Focus chain AC [auth I] Focus chain BA [auth B] Focus chain BB [auth E] Focus chain BC [auth I] Focus chain CB [auth E] Focus chain CC [auth I] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain HB [auth F] Focus chain HC [auth J] Focus chain IA [auth C] Focus chain IB [auth F] Focus chain IC [auth J] Focus chain JC [auth J] Focus chain KC [auth J] Focus chain LC [auth J] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain NA [auth D] Focus chain NB [auth G] Focus chain OA [auth D] Focus chain OB [auth G] Focus chain PA [auth D] Focus chain PB [auth G] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain QC [auth K] Focus chain R [auth A] Focus chain RA [auth D] Focus chain RC [auth K] Focus chain S [auth A] Focus chain SA [auth D] Focus chain SC [auth K] Focus chain T [auth A] Focus chain U [auth A] Focus chain UB [auth H] Focus chain V [auth A] Focus chain VB [auth H] Focus chain VC [auth L] Focus chain WB [auth H] Focus chain WC [auth L] Focus chain XB [auth H] Focus chain ZA [auth E] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth E] Focus chain AC [auth I] Focus chain BA [auth B] Focus chain BB [auth E] Focus chain BC [auth I] Focus chain CB [auth E] Focus chain CC [auth I] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain HB [auth F] Focus chain HC [auth J] Focus chain IA [auth C] Focus chain IB [auth F] Focus chain IC [auth J] Focus chain JC [auth J] Focus chain KC [auth J] Focus chain LC [auth J] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain NA [auth D] Focus chain NB [auth G] Focus chain OA [auth D] Focus chain OB [auth G] Focus chain PA [auth D] Focus chain PB [auth G] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain QC [auth K] Focus chain R [auth A] Focus chain RA [auth D] Focus chain RC [auth K] Focus chain S [auth A] Focus chain SA [auth D] Focus chain SC [auth K] Focus chain T [auth A] Focus chain U [auth A] Focus chain UB [auth H] Focus chain V [auth A] Focus chain VB [auth H] Focus chain VC [auth L] Focus chain WB [auth H] Focus chain WC [auth L] Focus chain XB [auth H] Focus chain ZA [auth E]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain MC [auth J] SDF format, chain QB [auth G] SDF format, chain TA [auth D] SDF format, chain W [auth A] MOL2 format, chain MC [auth J] MOL2 format, chain QB [auth G] MOL2 format, chain TA [auth D] MOL2 format, chain W [auth A] mmCIF format, chain MC [auth J] mmCIF format, chain QB [auth G] mmCIF format, chain TA [auth D] mmCIF format, chain W [auth A]	MC [auth J], QB [auth G], TA [auth D], W [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain MC [auth J] Focus chain QB [auth G] Focus chain TA [auth D] Focus chain W [auth A] Interactions & Density Focus chain MC [auth J] Focus chain QB [auth G] Focus chain TA [auth D] Focus chain W [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain UA [auth D] MOL2 format, chain UA [auth D] mmCIF format, chain UA [auth D]	UA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain UA [auth D] Interactions & Density Focus chain UA [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain Z [auth B] MOL2 format, chain N [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain N [auth A] mmCIF format, chain Z [auth B]	N [auth A], Z [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain Z [auth B] Interactions & Density Focus chain N [auth A] Focus chain Z [auth B]