9K05 | pdb_00009k05

Crystal structure of Pyrococcus abyssi AIR synthetase N186A mutant bound to FGAR and AMP

• PDB DOI: https://doi.org/10.2210/pdb9K05/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus abyssi GE5
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-10-15 Released: 2025-10-15 
• Deposition Author(s): Chen, Y.H., Chen, C.J.
• Funding Organization(s): National Science Council (NSC, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.193 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Pyrococcus abyssi AIR synthetase N186A mutant bound to FGAR and AMP

Chen, Y.H., Chen, C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 74.69 kDa 
• Atom Count: 5,828 
• Modeled Residue Count: 668 
• Deposited Residue Count: 668 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylformylglycinamidine cyclo-ligase	A, B	334	Pyrococcus abyssi GE5	Mutation(s): 1  Gene Names: purM, PYRAB16520, PAB1083 EC: 6.3.3.1
UniProt
Find proteins for Q9UY56 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9UY56  Go to UniProtKB:  Q9UY56

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	D [auth A], E [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
FGR (Subject of Investigation/LOI)	C [auth A], F [auth B]	N-(N-FORMYLGLYCYL)-5-O-PHOSPHONO-BETA-D-RIBOFURANOSYLAMINE C8 H15 N2 O9 P VDXLUNDMVKSKHO-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.193 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.854	α = 90
b = 112.294	β = 106.329
c = 71.343	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Chen, Y.H., Chen, C.J.

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Funding Organization	Location	Grant Number
National Science Council (NSC, Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release