4JWT | pdb_00004jwt

Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Sulfurimonas denitrificans DSM 1251 (Target NYSGRC-029304 )

• PDB DOI: https://doi.org/10.2210/pdb4JWT/pdb

• Classification: HYDROLASE
• Organism(s): Sulfurimonas denitrificans DSM 1251
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-27 Released: 2013-05-08 
• 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: 2.05 Å
• R-Value Free: 
  0.193 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Sulfurimonas denitrificans DSM 1251

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., Suarez, J., 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: 29.02 kDa 
• Atom Count: 2,046 
• Modeled Residue Count: 245 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylthioadenosine nucleosidase	A	259	Sulfurimonas denitrificans DSM 1251	Mutation(s): 0  Gene Names: Suden_1392 EC: 3.2.2.16 (PDB Primary Data), 3.2.2.9 (UniProt)
UniProt
Find proteins for Q30QR2 (Sulfurimonas denitrificans (strain ATCC 33889 / DSM 1251)) Explore Q30QR2  Go to UniProtKB:  Q30QR2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	F [auth A]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.193 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.598	α = 90
b = 77.598	β = 90
c = 228.425	γ = 120

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

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2013-11-27
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary