1ZCC

Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens str.C58

Structural Biology Knowledgebase: 1ZCC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.244

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1ZCC

Classification: HYDROLASE

Total Structure Weight: 165091.86

Macromolecule Entities
Molecule Chains Length Organism Details
glycerophosphodiester phosphodiesterase A, B, C..., D, E, FA, B, C, D, E, F 248 Agrobacterium fabrum Gene Name(s): ugpQ Atu4212

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A, B, C, D, E, F SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B, C, D, E, F ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.244
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 78.56 α = 90.00
b = 140.22 β = 90.53
c = 88.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-04-11
  • Released Date: 2005-05-03
  • Deposition author(s): Krishnamurthy, N.R., Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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