4TTT

Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form - oxidized state 3

PDB DOI: https://doi.org/10.2210/pdb4TTT/pdb

Classification: OXIDOREDUCTASE
Organism(s): Cupriavidus necator H16
Expression System: Cupriavidus necator H16
Mutation(s): No

Deposited: 2014-06-23 Released: 2015-01-28
Deposition Author(s): Schmidt, A., Kalms, J., Scheerer, P.
Funding Organization(s): UNICAT

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.165
R-Value Work: 0.134
R-Value Observed: 0.136

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase

Kalms, J., Schmidt, A., Frielingsdorf, S., Utesch, T., Gotthard, G., von Stetten, D., van der Linden, P., Royant, A., Mroginski, M., Carpentier, P., Lenz, O., Scheerer, P.

(2018) Proc Natl Acad Sci U S A

DOI: https://doi.org/10.1073/pnas.1712267115

Macromolecule Content

Total Structure Weight: 106.06 kDa
Atom Count: 7,560
Modelled Residue Count: 867
Deposited Residue Count: 942
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uptake hydrogenase large subunit hoxG	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 hoxK	B [auth S]	339	Cupriavidus necator H16	Mutation(s): 0 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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain H [auth S] MOL2 format, chain H [auth S]	H [auth S]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain H [auth S] Interactions & Density Focus chain H [auth S]
F4S Query on F4S Download Ideal Coordinates CCD File SDF format, chain J [auth S] MOL2 format, chain J [auth S]	J [auth S]	FE4-S3 CLUSTER Fe₄ S₃ QQACTBFBZNWJMV-UHFFFAOYSA-N		Interactions Focus chain J [auth S] Interactions & Density Focus chain J [auth S]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain I [auth S] MOL2 format, chain I [auth S]	I [auth S]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain I [auth S] Interactions & Density Focus chain I [auth S]
NFV Query on NFV Download Ideal Coordinates CCD File SDF format, chain C [auth L] MOL2 format, chain C [auth L]	C [auth L]	NI-FE OXIDIZED ACTIVE CENTER C₃ Fe N₂ Ni O₂ MPQMGFDSXFFIQL-UHFFFAOYSA-N		Interactions Focus chain C [auth L] Interactions & Density Focus chain C [auth L]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth L] MOL2 format, chain D [auth L]	D [auth L]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth L] Interactions & Density Focus chain D [auth L]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain K [auth S] SDF format, chain L [auth S] MOL2 format, chain F [auth L] MOL2 format, chain K [auth S] MOL2 format, chain L [auth S]	F [auth L], K [auth S], L [auth S]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth L] Focus chain K [auth S] Focus chain L [auth S] Interactions & Density Focus chain F [auth L] Focus chain K [auth S] Focus chain L [auth S]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth L] MOL2 format, chain E [auth L]	E [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth L] Interactions & Density Focus chain E [auth L]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth L] MOL2 format, chain G [auth L]	G [auth L]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth L] Interactions & Density Focus chain G [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.165
R-Value Work: 0.134
R-Value Observed: 0.136
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.774	α = 90
b = 95.57	β = 90
c = 119.228	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2015-01-28

Deposition Author(s):

Schmidt, A.

Kalms, J.

Scheerer, P.

Funding Organization	Location	Grant Number
UNICAT	Germany	--

Revision History (Full details and data files)

Version 1.0: 2015-01-28
Type: Initial release
Version 1.1: 2018-02-21
Changes: Database references, Derived calculations, Other, Source and taxonomy, Structure summary
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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4TTT

Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form - oxidized state 3

Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2