3AZ6 | pdb_00003az6

Crystal structure of Co/T-HEWL

• PDB DOI: https://doi.org/10.2210/pdb3AZ6/pdb

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


• Deposited: 2011-05-20 Released: 2012-05-09 
• Deposition Author(s): Abe, S., Tsujimoto, M., Yoneda, K., Ohba, M., Hikage, T., Takano, M., Kitagawa, S., Ueno, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.222 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Porous protein crystals as reaction vessels for controlling magnetic properties of nanoparticles

Abe, S., Tsujimoto, M., Yoneda, K., Ohba, M., Hikage, T., Takano, M., Kitagawa, S., Ueno, T.

(2012) Small 8: 1314-1319

• PubMed: 22383363 
• DOI: https://doi.org/10.1002/smll.201101866
• Primary Citation Related Structures: 
  3AZ4, 3AZ5, 3AZ6, 3AZ7


• PubMed Abstract: 
  

  Magnetic bimetallic CoPt nanoparticles are synthesized in the solvent channels of hen egg white lysozyme crystals by the reduction of Co(2+) and Pt(2+) ions pre-organized on the interior surface of the solvent channels. By using different lysozyme crystal systems, the magnetic properties of CoPt nanoparticles can be controlled.

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Organizational Affiliation: 
• Institute for Integrated Cell-Material Sciences, (WPI-iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto, Japan.

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: 14.65 kDa 
• Atom Count: 1,138 
• 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
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.222 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.702	α = 90
b = 78.702	β = 90
c = 36.73	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Abe, S., Tsujimoto, M., Yoneda, K., Ohba, M., Hikage, T., Takano, M., Kitagawa, S., Ueno, T.

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary