1LM4

Structure of Peptide Deformylase from Staphylococcus aureus at 1.45 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.170

Literature

Macromolecules
Sequence Display for 1LM4

Classification: HYDROLASE

Total Structure Weight: 44137.80

Macromolecule Entities
Molecule Chains Length Organism Details
peptide deformylase PDF1 A, B 194 Staphylococcus aureus EC#: 3.5.1.88 IUBMB
Mutation: C111X
Gene Name(s): def def1 pdf1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

A, B FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
OCS
Query on OCS
A, B L-PEPTIDE LINKING C3 H7 N O5 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.170
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 38.22 α = 90.00
b = 76.70 β = 90.00
c = 112.12 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-04-30
  • Released Date: 2003-06-24
  • Deposition author(s): Kreusch, A., Spraggon, G., Lee, C.C., Klock, H., McMullan, D., Ng, K., Shin, T., Vincent, J., Warner, I., Ericson, C., Lesley, S.A.

Revision History

  • Version 1_0: 2003-06-24

    Type: Initial release

  • Version 1_1: 2008-04-28

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Non-polymer description, Version format compliance

  • Version 1_3: 2014-11-12

    Type: Derived calculations, Structure summary