2H5Z | pdb_00002h5z

Crystallographic structure of digestive lysozyme 1 from Musca domestica bound to chitotetraose at 1.92 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2H5Z/pdb

• Classification: HYDROLASE
• Organism(s): Musca domestica
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2006-05-29 Released: 2007-06-05 
• Deposition Author(s): Valerio, A.A., Cancado, F.C., Marana, S.R., Barbosa, J.A.R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.242 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.175 (Depositor) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystallization, data collection and phasing of two digestive lysozymes from Musca domestica

Marana, S.R., Cancado, F.C., Valerio, A.A., Ferreira, C., Terra, W.R., Barbosa, J.A.R.G.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 750-752

• PubMed: 16880547 
• DOI: https://doi.org/10.1107/S1744309106024201
• Primary Citation Related Structures: 
  2FBD, 2H5Z


• PubMed Abstract: 
  

  Lysozymes are mostly known for their defensive role against bacteria, but in several animals lysozymes have a digestive function. Here, the initial crystallographic characterization of two digestive lysozymes from Musca domestica are presented. The proteins were crystallized using the sitting-drop vapour-diffusion method in the presence of ammonium sulfate or PEG/2-propanol as the precipitant. X-ray diffraction data were collected to a maximum resolution of 1.9 angstroms using synchrotron radiation. The lysozyme 1 and 2 crystals belong to the monoclinic space group P2(1) (unit-cell parameters a = 36.52, b = 79.44, c = 45.20 angstroms, beta = 102.97 degrees) and the orthorhombic space group P2(1)2(1)2 (unit-cell parameters a = 73.90, b = 96.40, c = 33.27 angstroms), respectively. The crystal structures were solved by molecular replacement and structure refinement is in progress.

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Organizational Affiliation: 
• Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.28 kDa 
• Atom Count: 2,155 
• Modeled Residue Count: 244 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme 1	A, B	122	Musca domestica	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for Q7YT16 (Musca domestica) Explore Q7YT16  Go to UniProtKB:  Q7YT16

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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017	C	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.242 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.175 (Depositor) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.953	α = 90
b = 78.809	β = 102.16
c = 44.792	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-05 
Deposition Author(s): Valerio, A.A., Cancado, F.C., Marana, S.R., Barbosa, J.A.R.G.

Revision History  

• Version 1.0: 2007-06-05
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary