9LD4 | pdb_00009ld4

The Apo-form structure of TkoKptA

• PDB DOI: https://doi.org/10.2210/pdb9LD4/pdb

• Classification: TRANSFERASE
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-05 Released: 2025-11-12 
• Deposition Author(s): Cao, X.L., Yang, J., Zhang, W.Z., Gan, J.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.61 Å
• R-Value Free: 
  0.258 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: in silico

Literature

The Apo-form structure of TkoKptA

Cao, C.L., Yang, J., Zhang, W.Z., Gan, J.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 83.91 kDa 
• Atom Count: 5,545 
• Modeled Residue Count: 709 
• Deposited Residue Count: 720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable RNA 2'-phosphotransferase	A, B, C, D	180	Thermococcus kodakarensis KOD1	Mutation(s): 0  Gene Names: kptA, TK0302 EC: 2.7.1
UniProt
Find proteins for Q5JFX3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JFX3  Go to UniProtKB:  Q5JFX3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.61 Å
• R-Value Free:  0.258 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.78	α = 90
b = 234.65	β = 90
c = 74.58	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Cao, X.L., Yang, J., Zhang, W.Z., Gan, J.H.

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

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release