2GV0

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.232
R-Value Work: 0.207

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystallization and the 1.9 angstroms of the egg-white lysozyme from a taiwanese soft-shelled turtle (trionyx sinensis wiegmann)

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7LZQ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.232
R-Value Work: 0.207
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-05-08

Deposition Author(s):

Siritapetawee, J.

Thammasirirak, S.

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.