4DR8

Crystal structure of a peptide deformylase from Synechococcus elongatus

Structural Biology Knowledgebase: 4DR8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.162

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DR8

Classification: HYDROLASE

Total Structure Weight: 86002.08

Macromolecule Entities
Molecule Chains Length Organism Details
Peptide deformylase A, B, C, D 192 Synechococcus elongatus EC#: 3.5.1.88 IUBMB
Gene Name(s): def syc0213_d

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A, B, C, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

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

A, B, C, D FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.162
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 43.40 α = 80.01
b = 65.36 β = 76.38
c = 69.03 γ = 81.71

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-17
  • Released Date: 2013-03-06
  • Deposition author(s): Lorimer, D., Abendroth, J., Craig, T., Burgin, A., Segall, A., Rohwer, F.

Revision History

  • 2013-07-10
    Type: Citation | Details: Citation update
  • 2013-06-05
    Type: Citation | Details: Citation update
  • 2013-03-06
    Type: Citation | Details: Citation update