3WVY | pdb_00003wvy

Structure of D48A hen egg white lysozyme in complex with (GlcNAc)4

PDB DOI: https://doi.org/10.2210/pdb3WVY/pdb

Classification: HYDROLASE
Organism(s): Gallus gallus
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2014-06-11 Released: 2015-06-10
Deposition Author(s): Kawaguchi, Y., Yoneda, K., Araki, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free:
0.243 (Depositor), 0.203 (DCC)
R-Value Work:
0.198 (Depositor), 0.189 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history.

Literature

The role of Asp48 in the hydrogen bonding network involving Asp52 of hen egg white lysozyme

Kawaguchi, Y., Yoneda, K., Araki, T.

To be published.

Macromolecule Content

Total Structure Weight: 15.12 kDa
Atom Count: 1,207
Modeled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 1 Gene Names: LYZ EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G01361SX GlyCosmos: G01361SX GlyGen: G01361SX

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.243 (Depositor), 0.203 (DCC)
R-Value Work: 0.198 (Depositor), 0.189 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.219	α = 90
b = 77.219	β = 90
c = 38.273	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-06-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-06-10
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-09
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.