4KXI | pdb_00004kxi

Crystallographic study of the complex of Ni(II) Schiff base complex and HEW Lysozyme

• PDB DOI: https://doi.org/10.2210/pdb4KXI/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2013-05-27 Released: 2014-05-28 
• Deposition Author(s): Koley Seth, B., Ray, A., Basu, S., Biswas, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.256 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Crystallographic study of the complex of Ni(II) Schiff base complex and HEW Lysozyme

Koley Seth, B., Ray, A., Biswas, S., Basu, S.

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)

Macromolecule Content 

• Total Structure Weight: 15.23 kDa 
• Atom Count: 1,108 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SNF	C [auth A]	(N1E, N2E)-N1, N2-bis(pyridine-2-ylmethylene)propane-1,2-diamine, nickel(II) salt C15 H16 N4 Ni YWFIBUKMYHZULK-UBTITEMDSA-N
LCP	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	PERCHLORATE ION Cl O4 VLTRZXGMWDSKGL-UHFFFAOYSA-M
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.256 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.589	α = 90
b = 77.589	β = 90
c = 36.39	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345dtb	data collection
AUTOMAR	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-28 
Deposition Author(s): Koley Seth, B., Ray, A., Basu, S., Biswas, S.

Revision History  

• Version 1.0: 2014-05-28
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary