1NJR

Crystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatase

Structural Biology Knowledgebase: 1NJR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.206

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1NJR

Classification: STRUCTURAL GENOMICS UNKNOWN FUNCTION

Total Structure Weight: 32727.65

Macromolecule Entities
Molecule Chains Length Organism Details
32.1 kDa protein in ADH3-RCA1 intergenic region A 284 Saccharomyces cerevisiae EC#: 3.1.3.84 IUBMB
Mutation: M1M, M17M, M58M, M61M, M174M, M179M, M209M, M217M, M232M, M260M
Gene Name(s): YMR087W YM9582.12

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
XYL
Query on XYL

A D-XYLITOL
C5 H12 O5
HEBKCHPVOIAQTA-SCDXWVJYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.206
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 107.69 α = 90.00
b = 38.15 β = 112.21
c = 64.74 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-01-02
  • Released Date: 2004-08-17
  • Deposition author(s): Kumaran, D., Eswaramoorthy, S., Studier, F.W., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4