1OJN

SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE: COMPLEX OF THE TYR408PHE MUTANT WITH 6-SULPHATED CHONDROITIN DISACCHARIDE

Structural Biology Knowledgebase: 1OJN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 1OJN

Classification: LYASE

Total Structure Weight: 84390.29

Macromolecule Entities
Molecule Chains Length Organism Details
HYALURONATE LYASE A 731 Streptococcus pneumoniae EC#: 4.2.2.1 IUBMB
Fragment: HYALURONATE LYASE, RESIDUES 285-1009
Mutation: A173T, E196D, T223I, Y408F, C496R, P541T, G704S, F736S, R790G
Gene Name(s): SP_0314
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NG6
Query on NG6

A N-ACETYL-D-GALACTOSAMINE 6-SULFATE
C8 H15 N O9 S
WJFVEEAIYIOATH-JAJWTYFOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GCD
Query on GCD

A 4,5-DEHYDRO-D-GLUCURONIC ACID
C6 H8 O6
IAKKJSVSFCTLRY-YKKSOZKNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.194
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 83.91 α = 90.00
b = 104.20 β = 90.00
c = 101.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-07-11
  • Released Date: 2003-10-30
  • Deposition author(s): Rigden, D.J., Jedrzejas, M.J.

Revision History

  • 2013-01-23
    Type: Refinement description | Details: REMARK 3
  • 2013-01-23
    Type: Other | Details: TER,REMARK 525,REMARK 290
  • 2013-01-23
    Type: Atom nomenclature | Details: HETATM
  • 2013-01-23
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2013-01-23
    Type: Linkage | Details: CONECT,LINK
  • 2013-01-23
    Type: Polymer description | Details: COMPND
  • 2013-01-23
    Type: Sequence database correspondence | Details: DBREF,SEQADV
  • 2013-01-23
    Type: Binding sites and description | Details: REMARK 800,SITE
  • 2013-01-23
    Type: Non-polymer description | Details: FORMUL,HETNAM,HET
  • 2013-01-23
    Type: Geometry validation | Details: REMARK 500
  • 2013-01-23
    Type: Version format compliance | Details: REMARK 4