9Y1L | pdb_00009y1l

Crystal Structure of Putative Restriction Endonuclease Domain-Containing Protein from Leptospirillum ferriphilum YSK

• PDB DOI: https://doi.org/10.2210/pdb9Y1L/pdb

• Classification: HYDROLASE
• Organism(s): Leptospirillum ferriphilum YSK
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-08-29 Released: 2025-09-10 
• Deposition Author(s): Kim, Y., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.177 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.158 (DCC) 

Starting Model: in silico

Literature

Crystal Structure of Putative Restriction Endonuclease Domain-Containing Protein from Leptospirillum ferriphilum YSK

Kim, Y., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A.

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: 42.33 kDa 
• Atom Count: 2,656 
• Modeled Residue Count: 304 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative restriction endonuclease domain-containing protein	A, B	188	Leptospirillum ferriphilum YSK	Mutation(s): 0  Gene Names: BOX24_03850, LptCag_1749
UniProt
Find proteins for A0A059XVC6 (Leptospirillum ferriphilum YSK) Explore A0A059XVC6  Go to UniProtKB:  A0A059XVC6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	C [auth A], D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.177 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.158 (DCC) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.989	α = 90
b = 76.989	β = 90
c = 45.84	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Kim, Y., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release