9K00 | pdb_00009k00

Crystal structure of Pyrococcus abyssi AIR synthetase

PDB DOI: https://doi.org/10.2210/pdb9K00/pdb

Classification: LIGASE
Organism(s): Pyrococcus abyssi GE5
Expression System: Escherichia coli
Mutation(s): No

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.213 (Depositor), 0.214 (DCC)
R-Value Work:
0.169 (Depositor), 0.171 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Pyrococcus abyssi AIR synthetase

Chen, Y.H., Chen, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 70.77 kDa
Atom Count: 5,432
Modeled Residue Count: 642
Deposited Residue Count: 642
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylformylglycinamidine cyclo-ligase	A, B	321	Pyrococcus abyssi GE5	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UY56
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.213 (Depositor), 0.214 (DCC)
R-Value Work: 0.169 (Depositor), 0.171 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.23	α = 90
b = 113.116	β = 105.96
c = 70.824	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.