5DK6 | pdb_00005dk6

CRYSTAL STRUCTURE OF A 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE (MTA/SAH) NUCLEOSIDASE (MTAN) FROM COLWELLIA PSYCHRERYTHRAEA 34H (CPS_4743, TARGET PSI-029300) IN COMPLEX WITH ADENINE AT 2.27 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb5DK6/pdb

• Classification: HYDROLASE
• Organism(s): Colwellia psychrerythraea 34H
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-03 Released: 2015-11-04 
• Deposition Author(s): Himmel, D.M., Bhosle, R., Toro, R., Ahmed, M., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Seidel, R.D., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.237 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.208 (Depositor) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

CRYSTAL STRUCTURE OF A 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE (MTA/SAH)NUCLEOSIDASE (MTAN) FROM COLWELLIA PSYCHRERYTHRAEA 34H (CPS_4743, TARGET PSI-029300) IN COMPLEX WITH ADENINE AT 2.27 A RESOLUTION

Himmel, D.M., Bhosle, R., Toro, R., Ahmed, M., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Seidel, R.D., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.7 kDa 
• Atom Count: 1,917 
• Modeled Residue Count: 242 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase	A	265	Colwellia psychrerythraea 34H	Mutation(s): 0  Gene Names: mtnN, CPS_4743 EC: 3.2.2.9
UniProt
Find proteins for Q47UY5 (Colwellia psychrerythraea (strain 34H / ATCC BAA-681)) Explore Q47UY5  Go to UniProtKB:  Q47UY5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	C [auth A]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
GLY	B [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-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: 2.27 Å
• R-Value Free:  0.237 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.208 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.427	α = 90
b = 145.427	β = 90
c = 70.341	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-04 
Deposition Author(s): Himmel, D.M., Bhosle, R., Toro, R., Ahmed, M., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Seidel, R.D., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2015-11-04
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary