7ODH

Crystal structure of the O2-tolerant MBH-P242C from Ralstonia eutropha in its as-isolated state

• PDB DOI: https://doi.org/10.2210/pdb7ODH/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Cupriavidus necator H16
• Expression System: Cupriavidus necator H16
• Mutation(s): Yes 


• Deposited: 2021-04-29 Released: 2021-07-07 
• Deposition Author(s): Schmidt, A., Kalms, J., Scheerer, P.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.133 
• R-Value Work: 0.112 
• R-Value Observed: 0.113 

Literature

Resonance Raman spectroscopic analysis of the iron-sulfur cluster redox chain of the Ralstonia eutropha membrane-bound [NiFe]-hydrogenase

Siebert, E., Schmidt, A., Frielingsdorf, S., Kalms, J., Kuhlmann, U., Lenz, O., Scheerer, P., Zebger, I., Hildebrandt, P.

(2021) J Raman Spectrosc 

• DOI: https://doi.org/10.1002/jrs.6163

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 104.8 kDa 
• Atom Count: 7,984 
• Modelled Residue Count: 865 
• Deposited Residue Count: 931 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uptake hydrogenase large subunit	A [auth L]	603	Cupriavidus necator H16	Mutation(s): 0  Gene Names: hoxG, PHG002 EC: 1.12.99.6
UniProt
Find proteins for P31891 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337)) Explore P31891  Go to UniProtKB:  P31891

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uptake hydrogenase small subunit	B [auth S]	328	Cupriavidus necator H16	Mutation(s): 1  Gene Names: hoxK, PHG001 EC: 1.12.99.6
UniProt
Find proteins for P31892 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337)) Explore P31892  Go to UniProtKB:  P31892

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4 (Subject of Investigation/LOI)	I [auth S], J [auth S]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F4S	M [auth S]	FE4-S3 CLUSTER Fe4 S3 QQACTBFBZNWJMV-UHFFFAOYSA-N
NFV (Subject of Investigation/LOI)	C [auth L]	NI-FE OXIDIZED ACTIVE CENTER C3 Fe N2 Ni O2 MPQMGFDSXFFIQL-UHFFFAOYSA-N
CL	D [auth L], E [auth L], F [auth L], G [auth L], L [auth S]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	H [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
O	K [auth S], N [auth S]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	B [auth S]	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.133 
• R-Value Work: 0.112 
• R-Value Observed: 0.113 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.606	α = 90
b = 95.676	β = 90
c = 120.824	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Schmidt, A., Kalms, J., Scheerer, P.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	UniSysCat
German Research Foundation (DFG)	Germany	UniCat

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Advisory, Data collection, Database references, Refinement description