2PAU

Crystal structure of the 5'-deoxynucleotidase YfbR mutant E72A complexed with Co(2+) and dAMP

Structural Biology Knowledgebase: 2PAU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.193

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2PAU

Classification: HYDROLASE

Total Structure Weight: 46635.24

Macromolecule Entities
Molecule Chains Length Organism Details
5'-deoxynucleotidase YfbR A, B 201 Escherichia coli EC#: 3.1.3.89 IUBMB
Mutation: E72A
Gene Name(s): yfbR b2291 JW2288

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

A, B COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
D5M
Query on D5M

A, B 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
Ligand Explorer
 
JSmol
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.193
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 135.60 α = 90.00
b = 135.60 β = 90.00
c = 54.94 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-03-27
  • Released Date: 2008-03-04
  • Deposition author(s): Zimmerman, M.D., Proudfoot, M., Yakunin, A., Minor, W.

Revision History

  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values