2GV0 | pdb_00002gv0

The structure of the orthorhombic form of soft-shelled turtle lysozyme at 1.9 angstroms resolution

• PDB DOI: https://doi.org/10.2210/pdb2GV0/pdb

• Classification: HYDROLASE
• Organism(s): Pelodiscus sinensis
• Mutation(s): No 


• Deposited: 2006-05-02 Released: 2007-05-08 
• Deposition Author(s): Siritapetawee, J., Thammasirirak, S., Yuvaniyama, J., Robinson, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.232 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.205 (DCC) 

Literature

The 1.9 A X-ray structure of egg-white lysozyme from Taiwanese soft-shelled turtle (Trionyx Sinensis Wiegmann) exhibits structural differences from the standard chicken-type lysozyme.

Siritapetawee, J., Thammasirirak, S., Robinson, R.C., Yuvaniyama, J.

(2009) J Biochem 145: 193-198

• PubMed: 19029145 
• DOI: https://doi.org/10.1093/jb/mvn156
• Primary Citation Related Structures: 
  2GV0


• PubMed Abstract: 
  

  Lysozyme from Taiwanese soft-shelled turtle (SSTLB) has been purified from turtle egg white and crystallized. The crystals diffract X-rays beyond 2 A resolution and belong to the orthorhombic P2(1)2(1)2(1) space group containing one molecule per asymmetric unit. The structure was elucidated using pheasant egg-white lysozyme as the molecular replacement search template. The overall structure of SSTLB is very similar to that of hen egg-white lysozyme (HEWL). Nevertheless, Pro104 in the substrate subsite A and other amino acids in the substrate subsites E and F differ from those of HEWL. These substitutions result in local conformational differences in the substrate binding sites of the two enzymes, effecting substrate binding and transglycosylation efficiency, translating into differing ranges of products.

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Organizational Affiliation: 
• College of Medicine and Public Health, Ubon Rajathanee University, Ubon Ratchathani, Thailand.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.85 kDa 
• Atom Count: 1,136 
• Modeled Residue Count: 131 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	131	Pelodiscus sinensis	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for Q7LZQ1 (Pelodiscus sinensis) Explore Q7LZQ1  Go to UniProtKB:  Q7LZQ1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.232 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.205 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.758	α = 90
b = 55.561	β = 90
c = 72.234	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-08 
Deposition Author(s): Siritapetawee, J., Thammasirirak, S., Yuvaniyama, J., Robinson, R.C.

Revision History  

• Version 1.0: 2007-05-08
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2025-01-29
  Changes: Database references