1YPN

REDUCED FORM HYDROXYMETHYLBILANE SYNTHASE (K59Q MUTANT) CRYSTAL STRUCTURE AFTER 2 HOURS IN A FLOW CELL DETERMINED BY TIME-RESOLVED LAUE DIFFRACTION

Structural Biology Knowledgebase: 1YPN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YPN

Classification: TRANSFERASE

Total Structure Weight: 34311.43

Macromolecule Entities
Molecule Chains Length Organism Details
HYDROXYMETHYLBILANE SYNTHASE A 313 Escherichia coli EC#: 2.5.1.61 IUBMB
Fragment: THREE DOMAINS
Mutation: K59Q
Details: CONTAINS A DIPYRROMETHANE COFACTOR LINKED TO CYSTEINE 242
Gene Name(s): hemC popE b3805 JW5932

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

A 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)- 5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)- 1H-pyrrol-3-yl]propanoic acid
DIPYRROMETHANE COFACTOR (Synonym)
C20 H24 N2 O8
LCAXMKQKEYTFDM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.199
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 88.47 α = 90.00
b = 76.15 β = 90.00
c = 50.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-06-26
  • Released Date: 1999-03-02
  • Deposition author(s): Helliwell, J.R., Nieh, Y.P., Raftery, J., Cassetta, A., Habash, J., Carr, P.D., Ursby, T., Wulff, M., Thompson, A.W., Niemann, A.C., Haedener, A.

Revision History

  • 2013-09-18
    Type: Non-polymer description | Details: Ligand DPM updated
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4