4L0M | pdb_00004l0m

Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Borrelia burgdorferi B31 bound to Adenine (Target NYSGRC-029268 )

• PDB DOI: https://doi.org/10.2210/pdb4L0M/pdb

• Classification: HYDROLASE
• Organism(s): Borreliella burgdorferi B31
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-31 Released: 2013-08-14 
• Deposition Author(s): Sampathkumar, P., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.267 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Borrelia burgdorferi B31 bound to Adenine (Target NYSGRC-029268 )

Sampathkumar, P., Ahmed, M., Attonito, J., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Eromenok, G., Fiser, A., Glenn, A.S., Hammonds, J., Himmel, D.M., Hillerich, B., Khafizov, K., Lafleur, J., Love, J.D., Stead, M., Seidel, R., Toro, R., Morisco, L.L., Sojitra, S.S., Wasserman, S.R., Haapalainen, A., Suarez, J., 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: 29.55 kDa 
• Atom Count: 2,047 
• Modeled Residue Count: 237 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase	A	259	Borreliella burgdorferi B31	Mutation(s): 0  Gene Names: BB_0375, BB_0375 pfs gene product, pfs EC: 3.2.2.16 (PDB Primary Data), 3.2.2.9 (PDB Primary Data)
UniProt
Find proteins for O50162 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31)) Explore O50162  Go to UniProtKB:  O50162

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	B [auth A]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.267 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.083	α = 90
b = 48.083	β = 90
c = 241.838	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
XDS	data reduction
Aimless	data scaling
SHELX	phasing
SHELXD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-14 
Deposition Author(s): Sampathkumar, P., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2013-11-27
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary