1B4K

High resolution crystal structure of a MG2-dependent 5-aminolevulinic acid dehydratase

Structural Biology Knowledgebase: 1B4K SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 1B4K

Classification: LYASE

Total Structure Weight: 74605.11

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE) A, B 337 Pseudomonas aeruginosa EC#: 4.2.1.24 IUBMB
Details: SCHIFF BASE LINK BETWEEN ATOM NZ OF LYS260 AND ATOM C4 OF LEVULINIC ACID
Gene Name(s): hemB PA5243
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B LAEVULINIC ACID
LEVULINIC ACID (Synonym)
C5 H8 O3
JOOXCMJARBKPKM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.178
  • Space Group: P 4 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 128.24 α = 90.00
b = 128.24 β = 90.00
c = 86.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-12-22
  • Released Date: 1999-07-13
  • Deposition author(s): Frankenberg, N., Jahn, D., Heinz, D.W.

Revision History

  • 2012-01-18
    Type: Non-polymer description | Details: --
  • 2012-01-18
    Type: Linkage | Details: --
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 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