7ODG

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

PDB DOI: https://doi.org/10.2210/pdb7ODG/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.188
R-Value Work: 0.162
R-Value Observed: 0.164

wwPDB Validation 3D Report Full Report

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

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

Macromolecule Content

Total Structure Weight: 104.57 kDa
Atom Count: 7,361
Modelled Residue Count: 868
Deposited Residue Count: 931
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31891
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31892
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain E [auth S] SDF format, chain F [auth S] MOL2 format, chain E [auth S] MOL2 format, chain F [auth S]	E [auth S], F [auth S]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth S] Focus chain F [auth S] Interactions & Density Focus chain E [auth S] Focus chain F [auth S]
F4S (Subject of Investigation/LOI) Query on F4S Download Ideal Coordinates CCD File SDF format, chain G [auth S] MOL2 format, chain G [auth S]	G [auth S]	FE4-S3 CLUSTER Fe₄ S₃ QQACTBFBZNWJMV-UHFFFAOYSA-N		Interactions Focus chain G [auth S] Interactions & Density Focus chain G [auth S]
NFU (Subject of Investigation/LOI) Query on NFU Download Ideal Coordinates CCD File SDF format, chain C [auth L] MOL2 format, chain C [auth L]	C [auth L]	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C₃ H Fe N₂ Ni O QCZROEOIPZWDEO-UHFFFAOYSA-N		Interactions Focus chain C [auth L] Interactions & Density Focus chain C [auth L]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth S] MOL2 format, chain H [auth S]	H [auth S]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth S] Interactions & Density Focus chain H [auth S]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth L] MOL2 format, chain D [auth L]	D [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth L] Interactions & Density Focus chain D [auth L]