4M1E

Crystal structure of purine nucleoside phosphorylase I from Planctomyces limnophilus DSM 3776, NYSGRC Target 029364.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of purine nucleoside phosphorylase I from Planctomyces limnophilus DSM 3776, NYSGRC Target 029364.

Malashkevich, V.N.Bonanno, J.B.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.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine nucleoside phosphorylaseA, B, C, E [auth D], D [auth E], F297Planctopirus limnophila DSM 3776Mutation(s): 0 
Gene Names: Plim_2216
EC: 2.4.2.1
Find proteins for D5SMY7 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / 290))
Explore D5SMY7 
Go to UniProtKB:  D5SMY7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADE
Query on ADE

Download Ideal Coordinates CCD File 
H [auth A], K [auth B], N [auth C], Q [auth E], U [auth D], W [auth F]ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
 Ligand Interaction
6PC
Query on 6PC

Download Ideal Coordinates CCD File 
I [auth A], L [auth B], O [auth C], R [auth E], S [auth D], X [auth F]PYRIDINE-2-CARBOXYLIC ACID
C6 H5 N O2
SIOXPEMLGUPBBT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A], J [auth B], M [auth C], P [auth E], T [auth D], V [auth F]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D [auth E], E [auth D], FL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.95α = 103.42
b = 81.06β = 105.36
c = 91.616γ = 112.73
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History