2D98

Structure of VIL (extra KI/I2 added)-xylanase

Structural Biology Knowledgebase: 2D98 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.209

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2D98

Classification: HYDROLASE

Total Structure Weight: 21861.60

Macromolecule Entities
Molecule Chains Length Organism Details
Endo-1,4-beta-xylanase 2 A 189 Trichoderma reesei EC#: 3.2.1.8 IUBMB
Mutation: Y9X, Y73X, Y96X, Y135X, Y171X, Y179X
Gene Name(s): xyn2

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

A IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Ligand Explorer
 
JSmol
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
IYR
Query on IYR
A L-PEPTIDE LINKING C9 H10 I N O3 TYR
TYI
Query on TYI
A L-PEPTIDE LINKING C9 H9 I2 N O3 TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.209
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 40.19 α = 90.00
b = 38.56 β = 110.18
c = 56.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-12-09
  • Released Date: 2006-07-11
  • Deposition author(s): Miyatake, H., Hasegawa, T., Yamano, A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4