8IFX

Aquifex aeolicus TsaD-TsaB in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb8IFX/pdb

• Classification: TRANSFERASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-02-20 Released: 2024-03-20 
• Deposition Author(s): Lu, S.Z., Zhang, W.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.253 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Starting Model: experimental

Literature

Crystal structure of Aquifex aeolicus TsaD-TsaB in complex with ADP

Lu, S.Z., Zhang, W.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 61.31 kDa 
• Atom Count: 4,479 
• Modelled Residue Count: 523 
• Deposited Residue Count: 535 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA N6-adenosine threonylcarbamoyltransferase	A	335	Aquifex aeolicus	Mutation(s): 0  Gene Names: tsaD, gcp, aq_801 EC: 2.3.1.234
UniProt
Find proteins for O66986 (Aquifex aeolicus (strain VF5)) Explore O66986  Go to UniProtKB:  O66986

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gcp-like domain-containing protein	B	200	Aquifex aeolicus	Mutation(s): 0  Gene Names: aq_082
UniProt
Find proteins for O66494 (Aquifex aeolicus (strain VF5)) Explore O66494  Go to UniProtKB:  O66494

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	D [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
PEG	E [auth A], F [auth A], G [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.253 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.017	α = 90
b = 98.017	β = 90
c = 131.432	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
Aimless	data scaling
Coot	model building
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-20 
Deposition Author(s): Lu, S.Z., Zhang, W.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32000847

Revision History  

• Version 1.0: 2024-03-20
  Type: Initial release