4M3N | pdb_00004m3n

Crystal structure of purine nucleoside phosphorylase from Meiothermus ruber DSM 1279, NYSGRC Target 029804.

• PDB DOI: https://doi.org/10.2210/pdb4M3N/pdb

• Classification: TRANSFERASE
• Organism(s): Meiothermus ruber DSM 1279
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-06 Released: 2013-08-28 
• Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., 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., Khafizov, K., Seidel, R., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Crystal structure of purine nucleoside phosphorylase from Meiothermus ruber DSM 1279, NYSGRC Target 029804.

Malashkevich, V.N., Bhosle, R., Toro, R., 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., Khafizov, K., Seidel, R., Bonanno, J.B., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 85.45 kDa 
• Atom Count: 5,932 
• Modeled Residue Count: 693 
• Deposited Residue Count: 762 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase DeoD-type	A, B, C	254	Meiothermus ruber DSM 1279	Mutation(s): 0  Gene Names: deoD, Mrub_2947, K649_07785 EC: 2.4.2.1 (PDB Primary Data), 2.4.2.3 (UniProt)
UniProt
Find proteins for D3PPS9 (Meiothermus ruber (strain ATCC 35948 / DSM 1279 / VKM B-1258 / 21)) Explore D3PPS9  Go to UniProtKB:  D3PPS9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], F [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.629	α = 90
b = 188.93	β = 90
c = 153.002	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., 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., Khafizov, K., Seidel, R., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary