4TTT | pdb_00004ttt

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.165 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.134 (Depositor) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

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

Biological Assembly 1  

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

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

Macromolecule Content 

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

Macromolecules

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 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

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	H [auth S]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F4S	J [auth S]	FE4-S3 CLUSTER Fe4 S3 QQACTBFBZNWJMV-UHFFFAOYSA-N
F3S	I [auth S]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
NFV	C [auth L]	NI-FE OXIDIZED ACTIVE CENTER C3 Fe N2 Ni O2 MPQMGFDSXFFIQL-UHFFFAOYSA-N
PO4	D [auth L]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	F [auth L], K [auth S], L [auth S]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	G [auth L]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.165 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.134 (Depositor) 
• R-Value Observed: 0.136 (Depositor) 

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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Schmidt, A., Kalms, J., Scheerer, P.

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Funding Organization	Location	Grant Number
UNICAT	Germany	--

Revision History  

• 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