4ZV7 | pdb_00004zv7

Crystal structure of hexagonal form of lipase B from Candida antarctica

• PDB DOI: https://doi.org/10.2210/pdb4ZV7/pdb

• Classification: HYDROLASE
• Organism(s): Moesziomyces antarcticus
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2015-05-18 Released: 2016-01-13 
• Deposition Author(s): Strzelczyk, P., Blaszczyk, J., Bujacz, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.193 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Crystal and molecular structure of hexagonal form of lipase B from Candida antarctica.

Strzelczyk, P., Bujacz, G.D., Kiebasinski, P., Baszczyk, J.

(2016) Acta Biochim Pol 63: 103-109

• PubMed: 26716135 
• DOI: https://doi.org/10.18388/abp.2015_1065
• Primary Citation Related Structures: 
  4ZV7


• PubMed Abstract: 
  

  During crystallization screenings of commercially available hydrolytic enzymes, the new, hexagonal crystal form of CAL-B, has been discovered and hereby reported. The NAG molecules, which were closing the glycosylation site in the orthorhombic form, in hexagonal structure make the glycosylation site open. It is unknown whether the opening and closing of the glycosylation site by the 'lid' NAG molecules, could be related to the opening and closing of the active center of the enzyme upon substrate binding and product release.

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Organizational Affiliation: 
• Lodz University of Technology, Institute of Technical Biochemistry, Łódź, Poland.
Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Heteroorganic Chemistry, Łódź, Poland.

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: 33.46 kDa 
• Atom Count: 2,713 
• Modeled Residue Count: 317 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase B	A	317	Moesziomyces antarcticus	Mutation(s): 0  EC: 3.1.1.3
UniProt
Find proteins for P41365 (Pseudozyma antarctica) Explore P41365  Go to UniProtKB:  P41365
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.193 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.034	α = 90
b = 89.034	β = 90
c = 137.257	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Strzelczyk, P., Blaszczyk, J., Bujacz, G.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-03-30
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary