2BPU | pdb_00002bpu

The Kedge Holmium Derivative of Hen Egg-White Lysozyme at high resolution from Single Wavelength Anomalous Diffraction

• PDB DOI: https://doi.org/10.2210/pdb2BPU/pdb

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


• Deposited: 2005-04-25 Released: 2006-08-24 
• Deposition Author(s): Jakoncic, J., Di Michiel, M., Zhong, Z., Honkimaki, V., Jouanneau, Y., Stojanoff, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.207 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Anomalous Diffraction at Ultra-High Energy for Protein Crystallography.

Jakoncic, J., Di Michiel, M., Zhong, Z., Honkimaki, V., Jouanneau, Y., Stojanoff, V.

(2006) J Appl Crystallogr 39: 831

• DOI: https://doi.org/10.1107/S0021889806036387

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 14.96 kDa 
• Atom Count: 1,130 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HO	F [auth A], G [auth A], H [auth A]	HOLMIUM ATOM Ho KJZYNXUDTRRSPN-UHFFFAOYSA-N
CL	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.207 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.707	α = 90
b = 78.707	β = 90
c = 37.325	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-24 
Deposition Author(s): Jakoncic, J., Di Michiel, M., Zhong, Z., Honkimaki, V., Jouanneau, Y., Stojanoff, V.

Revision History  

• Version 1.0: 2006-08-24
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary