9IBQ | pdb_00009ibq

Structure of BstEII with DNA substrate

• PDB DOI: https://doi.org/10.2210/pdb9IBQ/pdb
• NAKB: 9IBQ

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus, Escherichia coli
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-02-13 Released: 2026-03-04 
• Deposition Author(s): Rety, S., Xi, X.G.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.216 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: in silico

Literature

Structure of BstEII with DNA substrate

Rety, S., Xi, X.G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.13 kDa 
• Atom Count: 3,072 
• Modeled Residue Count: 307 
• Deposited Residue Count: 309 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BstEII	A	288	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: bstEIIR
UniProt
Find proteins for E5Q8U2 (Geobacillus stearothermophilus) Explore E5Q8U2  Go to UniProtKB:  E5Q8U2

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*TP*AP*CP*AP*TP*TP*GP*GP*TP*TP*AP*CP*CP*T)-3')	B [auth D]	15	Escherichia coli

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*TP*GP*TP*AP*G)-3')	C	6	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.216 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.719	α = 90
b = 74.738	β = 90
c = 66.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-04 
Deposition Author(s): Rety, S., Xi, X.G.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32301042, 32071291, 32071225

Revision History  

• Version 1.0: 2026-03-04
  Type: Initial release