4JOS

Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Francisella philomiragia ATCC 25017 (Target NYSGRC-029335)

• PDB DOI: https://doi.org/10.2210/pdb4JOS/pdb

• Classification: HYDROLASE
• Organism(s): Francisella philomiragia subsp. philomiragia ATCC 25017
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-18 Released: 2013-04-03 
• Deposition Author(s): Sampathkumar, P., Schramm, V.L., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.175 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 

Literature

Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Francisella philomiragia ATCC 25017 (Target NYSGRC-029335)

Sampathkumar, P., Gizzi, A., Ahmed, M., Banu, N., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Fiser, A., Glenn, A.S., Hammonds, J., Hillerich, B., Khafizov, K., Lafleur, J., Morisco, L.L., Sojitra, S.S., Wasserman, S.R., Haapalainen, A., Love, J.D., Stead, M., Seidel, R., Toro, R., Schramm, V.L., Almo, S.C.

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: 56.62 kDa 
• Atom Count: 4,252 
• Modelled Residue Count: 458 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteine nucleosidase	A, B	250	Francisella philomiragia subsp. philomiragia ATCC 25017	Mutation(s): 0  Gene Names: Fphi_0356 EC: 3.2.2.9
UniProt
Find proteins for B0TZL4 (Francisella philomiragia subsp. philomiragia (strain ATCC 25017 / CCUG 19701 / FSC 153 / O#319-036)) Explore B0TZL4  Go to UniProtKB:  B0TZL4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	C [auth A], G [auth B]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
EDO	D [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.175 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.747	α = 90
b = 74.937	β = 90
c = 114.542	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
SCALEPACK	data scaling
SHELX	phasing
SHELXD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Sampathkumar, P., Schramm, V.L., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary