5CD2

The crystal structure of endo-1,4-D-glucanase from Vibrio fischeri ES114

Structural Biology Knowledgebase: 5CD2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.176
  • R-Value Work: 0.135

Literature

Macromolecules
Sequence Display for 5CD2

Classification: HYDROLASE

Total Structure Weight: 42398.69

Macromolecule Entities
Molecule Chains Length Organism Details
Endo-1,4-D-glucanase A 372 Aliivibrio fischeri EC#: 3.2.1.4 IUBMB
Mutation: R120T, T258A, D288G, V294L, A339V, V340A, S351P
Gene Name(s): bcsZ VF_A0882
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
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: 1.55 Å
  • R-Value Free: 0.176
  • R-Value Work: 0.135
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 55.56 α = 90.00
b = 67.49 β = 90.00
c = 101.19 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-07-02
  • Released Date: 2015-07-22
  • Deposition author(s): Tan, K., Li, H., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

No revisions since initial release