9IUW | pdb_00009iuw

Structure of AlaX-M trans-editing enzyme from Pyrococcus furiosus

• PDB DOI: https://doi.org/10.2210/pdb9IUW/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-22 Released: 2025-07-30 
• Deposition Author(s): Pawar, K.I., Gogoi, J., Sankaranarayanan, R.
• Funding Organization(s): Council of Scientific & Industrial Research (CSIR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.217 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structure of AlaX-M trans-editing enzyme from Pyrococcus furiosus

Pawar, K.I., Gogoi, J., Sankaranarayanan, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 25.23 kDa 
• Atom Count: 1,759 
• Modeled Residue Count: 212 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Partial alanyl-tRNA synthetase matches COOH terminus	A	214	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF0086
UniProt
Find proteins for Q8U4J9 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U4J9  Go to UniProtKB:  Q8U4J9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.217 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.23	α = 90
b = 37.08	β = 103.56
c = 59.07	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Pawar, K.I., Gogoi, J., Sankaranarayanan, R.

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Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research (CSIR)	India	MLP-0162

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release