9K06 | pdb_00009k06

Crystal structure of Pyrococcus abyssi AIR synthetase with residues 51-54 replaced by Neisseria gonorrhoeae residues 49-56

• PDB DOI: https://doi.org/10.2210/pdb9K06/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: 1.70 Å
• R-Value Free: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Pyrococcus abyssi AIR synthetase with residues 51-54 replaced by Neisseria gonorrhoeae residues 49-56

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: 72.08 kDa 
• Atom Count: 5,393 
• Modeled Residue Count: 650 
• Deposited Residue Count: 650 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylformylglycinamidine cyclo-ligase	A, B	325	Pyrococcus abyssi GE5	Mutation(s): 2  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
FLC (Subject of Investigation/LOI)	D [auth A], F [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.905	α = 90
b = 112.79	β = 107.074
c = 70.906	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