4LYB | pdb_00004lyb

CdS within a lysoyzme single crystal

• PDB DOI: https://doi.org/10.2210/pdb4LYB/pdb

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


• Deposited: 2013-07-30 Released: 2015-02-25 
• Deposition Author(s): Wei, H., House, S., Wu, J., Zhang, J., Wang, Z., He, Y., Gao, Y.-G., Robinson, H., Li, W., Zuo, J.-M., Robertson, I.M., Lu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 
  0.238 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.214 (DCC) 

Literature

Enhanced and tunable fluorescent quantum dots within a single crystal of protein

Wei, H., House, S., Wu, J., Zhang, J., Wang, Z., He, Y., Gao, Y.-G., Robinson, H., Li, W., Zuo, J.-M., Robertson, I.M., Lu, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.89 kDa 
• Atom Count: 1,207 
• 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  Gene Names: LYZ EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free:  0.238 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.214 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.677	α = 90
b = 78.677	β = 90
c = 37.251	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-25 
Deposition Author(s): Wei, H., House, S., Wu, J., Zhang, J., Wang, Z., He, Y., Gao, Y.-G., Robinson, H., Li, W., Zuo, J.-M., Robertson, I.M., Lu, Y.

Revision History  

• Version 1.0: 2015-02-25
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary