7ODG | pdb_00007odg

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 (Depositor), 0.196 (DCC)
R-Value Work:
0.162 (Depositor), 0.171 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 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
Modeled Residue Count: 868
Deposited Residue Count: 931
Unique protein chains: 2

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31891
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 F [auth S] SDF format, chain E [auth S] MOL2 format, chain F [auth S] MOL2 format, chain E [auth S] mmCIF format, chain F [auth S] mmCIF format, chain E [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] mmCIF 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] mmCIF 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] mmCIF 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] mmCIF 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]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.188 (Depositor), 0.196 (DCC)
R-Value Work: 0.162 (Depositor), 0.171 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.467	α = 90
b = 95.76	β = 90
c = 120.633	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-07

Deposition Author(s):

Schmidt, A.

Kalms, J.

Scheerer, P.

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

Revision History (Full details and data files)

Version 1.0: 2021-07-07
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary