4KN5

Crystal structure of a putative methylthioadenosine nucleosidase from Weissella paramesenteroides ATCC 33313 (Target NYSGRC-029342 )

• PDB DOI: https://doi.org/10.2210/pdb4KN5/pdb

• Classification: HYDROLASE
• Organism(s): Weissella paramesenteroides ATCC 33313
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-05-08 Released: 2013-05-29 
• 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: 
  0.211 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Crystal structure of a putative methylthioadenosine nucleosidase from Weissella paramesenteroides ATCC 33313 (Target NYSGRC-029342)

Sampathkumar, P., Ahmed, M., Attonito, J., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Eromenok, G., Fiser, A., Glenn, A.S., Hammonds, J., Hillerich, B., Himmel, D.M., 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: 55.21 kDa 
• Atom Count: 3,853 
• Modelled Residue Count: 461 
• Deposited Residue Count: 506 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylthioadenosine nucleosidase	A, B	253	Weissella paramesenteroides ATCC 33313	Mutation(s): 0  Gene Names: HMPREF0877_0999 EC: 3.2.2.16 (PDB Primary Data), 3.2.2.9 (UniProt)
UniProt
Find proteins for C5RAK4 (Weissella paramesenteroides ATCC 33313) Explore C5RAK4  Go to UniProtKB:  C5RAK4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	C [auth A], D [auth B], E [auth B], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.70 Å
• R-Value Free:  0.211 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.252	α = 90
b = 89.252	β = 90
c = 127.545	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: 2013-05-29 
Deposition Author(s): Sampathkumar, P., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2013-11-27
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary