4B49 | pdb_00004b49

1.15 A Structure of Lysozyme Crystallized without 2-methyl-2,4- pentanediol

• PDB DOI: https://doi.org/10.2210/pdb4B49/pdb

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


• Deposited: 2012-07-28 Released: 2012-08-22 
• Deposition Author(s): Jakoncic, J., Berger, J., Stauber, M., Axelbaum, A., Asherie, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.151 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.138 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

Starting Model: other

Literature

Crystallization of Lysozyme with (R)-, (S)- and (Rs)-2-Methyl-2,4-Pentanediol

Stauber, M., Jakoncic, J., Berger, J., Karp, J.M., Axelbaum, A., Sastow, D., Buldyrev, S.V., Hrnjez, B.J., Asherie, N.

(2015) Acta Crystallogr D Biol Crystallogr 71: 427

• PubMed: 25760593 
• DOI: https://doi.org/10.1107/S1399004714025061
• Primary Citation Related Structures: 
  4B49, 4B4E, 4B4I, 4B4J


• PubMed Abstract: 
  

  Chiral control of crystallization has ample precedent in the small-molecule world, but relatively little is known about the role of chirality in protein crystallization. In this study, lysozyme was crystallized in the presence of the chiral additive 2-methyl-2,4-pentanediol (MPD) separately using the R and S enantiomers as well as with a racemic RS mixture. Crystals grown with (R)-MPD had the most order and produced the highest resolution protein structures. This result is consistent with the observation that in the crystals grown with (R)-MPD and (RS)-MPD the crystal contacts are made by (R)-MPD, demonstrating that there is preferential interaction between lysozyme and this enantiomer. These findings suggest that chiral interactions are important in protein crystallization.

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Organizational Affiliation: 
• Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA.
National Synchrotron Light Source, Brookhaven National Laboratory, Building 725D, Upton, NY 11973-5000, USA.
Collegiate School, 260 West 78th Street, New York, NY 10024-6559, USA.

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: 14.56 kDa 
• Atom Count: 1,384 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CL	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.151 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.138 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.841	α = 90
b = 76.841	β = 90
c = 38.691	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-22 
Deposition Author(s): Jakoncic, J., Berger, J., Stauber, M., Axelbaum, A., Asherie, N.

Revision History  

• Version 1.0: 2012-08-22
  Type: Initial release
  
• Version 1.1: 2015-03-11
  Changes: Database references
• Version 1.2: 2015-03-25
  Changes: Database references
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-05-15
  Changes: Data collection, Experimental preparation
• Version 1.5: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.6: 2024-10-09
  Changes: Structure summary