3TOL

Crystal structure of an engineered cytochrome cb562 that forms 1D, Zn-mediated coordination polymers

Structural Biology Knowledgebase: 3TOL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 3TOL

Classification: METAL BINDING PROTEIN

Total Structure Weight: 49336.55

Macromolecule Entities
Molecule Chains Length Organism Details
Soluble cytochrome b562 A, B, C, D 106 Escherichia coli Fragment: Soluble cytochrome b562
Mutation: K27E, D28K, T31E, R34L, L38A, Q41L, K59R, D66A, V69M, D73H, L76A, K77H, R98C, Y101C
Gene Name(s): cybC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.190
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.55 α = 90.00
b = 69.51 β = 90.00
c = 126.57 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-05
  • Released Date: 2012-07-04
  • Deposition author(s): Brodin, J.B., Tezcan, F.A.

Revision History

No revisions since initial release