1PS5 | pdb_00001ps5

STRUCTURE OF THE MONOCLINIC C2 FORM OF HEN EGG-WHITE LYSOZYME AT 2.0 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1PS5/pdb

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


• Deposited: 2003-06-20 Released: 2003-09-09 
• Deposition Author(s): Majeed, S., Ofek, G., Belachew, A., Huang, C., Zhou, T., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.250 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Enhancing Protein Crystallization through Precipitant Synergy

Majeed, S., Ofek, G., Belachew, A., Huang, C., Zhou, T., Kwong, P.D.

(2003) Structure 11: 1061-1070

• PubMed: 12962625 
• DOI: https://doi.org/10.1016/s0969-2126(03)00185-0
• Primary Citation of Related Structures:  
  1PS5


• PubMed Abstract: 
  

  Suitable conditions for protein crystallization are commonly identified by screening combinations of independent factors that affect crystal formation. Because precipitating agents are prime determinants of crystallization, we investigated whether a systematic exploration of combinations of mechanistically distinct precipitants would enhance crystallization. A crystallization screen containing 64 precipitant mixtures was devised. Tests with ten HIV envelope-related proteins demonstrated that use of precipitant mixtures significantly enhanced both the probability of crystallization as well as the quality of optimized crystals. Tests with hen egg white lysozyme generated a novel C2 crystal from a salt/organic solvent mixture; structure solution at 2 A resolution revealed a lattice held together by both hydrophobic and electrostatic dyad interactions. The results indicate that mechanistically distinct precipitants can synergize, with precipitant combinations adding unique dimensions to protein crystallization.

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Organizational Affiliation: 

Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.52 kDa 
• Atom Count: 1,158 
• Modelled 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.250 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.944	α = 90
b = 53.143	β = 97.32
c = 50.211	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-09 
Deposition Author(s): Majeed, S., Ofek, G., Belachew, A., Huang, C., Zhou, T., Kwong, P.D.

Revision History  

• Version 1.0: 2003-09-09
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary