4J7H

Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-benzene and dTDP-rhamnose

Structural Biology Knowledgebase: 4J7H SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.191
  • R-Value Work: 0.165

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4J7H

Classification: BIOSYNTHETIC PROTEIN

Total Structure Weight: 108428.45

Macromolecule Entities
Molecule Chains Length Organism Details
EvaA 2,3-dehydratase A, B 471 Amycolatopsis orientalis Mutation: R381A
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
C16 H26 N2 O15 P2
ZOSQFDVXNQFKBY-CGAXJHMRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TLO
Query on TLO

A, B 5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine
thymidine diphosphate phenol (Synonym)
C16 H20 N2 O11 P2
BANJVYKYIQPYKP-BFHYXJOUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.191
  • R-Value Work: 0.165
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 104.68 α = 90.00
b = 108.64 β = 90.00
c = 110.13 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-02-13
  • Released Date: 2013-05-22
  • Deposition author(s): Holden, H.M., Kubiak, R.L., Thoden, J.B.

Revision History

  • 2013-12-25
    Type: Citation | Details: Citation update
  • 2013-11-20
    Type: Citation | Details: Citation update