5IBZ | pdb_00005ibz

Crystal structure of a novel cyclase (pfam04199).

• PDB DOI: https://doi.org/10.2210/pdb5IBZ/pdb

• Classification: LYASE
• Organism(s): uncultured organism
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-22 Released: 2017-08-09 
• Deposition Author(s): Nocek, B., Skarina, T., Brown, G., Joachimiak, A., Savchenko, A., Yakunin, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Literature

Crystal structure of a novel cyclase (pfam04199).

Nocek, B., Skarina, T., Brown, G., Joachimiak, A., Savchenko, A., Yakunin, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 141.4 kDa 
• Atom Count: 11,077 
• Modeled Residue Count: 1,215 
• Deposited Residue Count: 1,292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	323	uncultured organism	Mutation(s): 0
UniProt
Find proteins for A0A0G3FEK2 (uncultured organism) Explore A0A0G3FEK2  Go to UniProtKB:  A0A0G3FEK2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	H [auth C]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
UVW	E [auth A], F [auth B], G [auth C], I [auth D]	ACETYLPHOSPHATE C2 H5 O5 P LIPOUNRJVLNBCD-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.508	α = 90
b = 120.618	β = 90
c = 148.822	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Nocek, B., Skarina, T., Brown, G., Joachimiak, A., Savchenko, A., Yakunin, A.

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary