5GZI | pdb_00005gzi

Cyclodeaminase_PA

• PDB DOI: https://doi.org/10.2210/pdb5GZI/pdb

• Classification: LYASE
• Organism(s): Streptomyces pristinaespiralis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-28 Released: 2018-01-17 
• Deposition Author(s): Ying, H., Chen, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.228 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Cyclodeaminase_PA

Ying, H., Chen, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 77.8 kDa 
• Atom Count: 5,582 
• Modeled Residue Count: 700 
• Deposited Residue Count: 718 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine cyclodeaminase	A [auth B], B [auth A]	359	Streptomyces pristinaespiralis	Mutation(s): 0  Gene Names: pipA, SPRI_0308, SPRI_7045 EC: 4.3.1.12
UniProt
Find proteins for D9UBW0 (Streptomyces pristinaespiralis) Explore D9UBW0  Go to UniProtKB:  D9UBW0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth B], E [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
YCP	D [auth B], F [auth A]	(2S)-piperidine-2-carboxylic acid C6 H11 N O2 HXEACLLIILLPRG-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.228 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.926	α = 90
b = 74.06	β = 132.72
c = 95.718	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Ying, H., Chen, K.

---

Funding Organization	Location	Grant Number
	China	--

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references