7E0L | pdb_00007e0l

Class III hybrid cluster protein (HCP) from Methanothermobacter marburgensis

• PDB DOI: https://doi.org/10.2210/pdb7E0L/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanothermobacter marburgensis str. Marburg
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-01-28 Released: 2022-02-02 
• Deposition Author(s): Fujishiro, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.82 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Class III hybrid cluster protein homodimeric architecture shows evolutionary relationship with Ni, Fe-carbon monoxide dehydrogenases

Fujishiro, T., Takaoka, K.

(2023) Nat Commun 

• DOI: https://doi.org/10.1038/s41467-023-41289-4

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 228.85 kDa 
• Atom Count: 15,353 
• Modeled Residue Count: 1,953 
• Deposited Residue Count: 2,024 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxylamine reductase	A, B, C [auth K], D [auth M]	506	Methanothermobacter marburgensis str. Marburg	Mutation(s): 0  Gene Names: hcp, MTBMA_c00390 EC: 1.7.99.1
UniProt
Find proteins for D9PYV4 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore D9PYV4  Go to UniProtKB:  D9PYV4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	F [auth A], I [auth B], L [auth K], O [auth M]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
FS2 (Subject of Investigation/LOI)	E [auth A], H [auth B], K, N [auth M]	FE-S-O HYBRID CLUSTER Fe4 O3 S2 DEAINXNPDRNZAH-UHFFFAOYSA-N
FE	G [auth A], J [auth B], M [auth K], P [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A, B, C [auth K], D [auth M]	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.82 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.95	α = 90
b = 67.95	β = 90
c = 469.26	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Fujishiro, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	17K14510

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 2.0: 2022-10-19
  Type: Coordinate replacement
  Reason: Polymer geometry
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references
• Version 2.2: 2023-11-15
  Changes: Data collection
• Version 2.3: 2023-11-29
  Changes: Refinement description
• Version 2.4: 2024-10-16
  Changes: Structure summary