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

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A059XVC6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

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 (Full details and data files)

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

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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.