5ZMP | pdb_00005zmp

The structure of a lysine deacylase

• PDB DOI: https://doi.org/10.2210/pdb5ZMP/pdb

• Classification: HYDROLASE
• Organism(s): Picosynechococcus sp. PCC 73109
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-04-05 Released: 2019-02-06 
• Deposition Author(s): Ge, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.215 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.187 (DCC) 

Starting Model: experimental

Literature

The structure of a lysine deacylase

Ge, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.16 kDa 
• Atom Count: 2,614 
• Modeled Residue Count: 305 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lysine deacylase	A	307	Picosynechococcus sp. PCC 73109	Mutation(s): 0  Gene Names: SYNPCC7002_A2791

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.215 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.187 (DCC) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.79	α = 90
b = 56.79	β = 90
c = 112.52	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Ge, F.

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description