8WDI | pdb_00008wdi

Crystal structure of lysozyme by fixed-target pink-beam serial synchrotron crystallography

PDB DOI: https://doi.org/10.2210/pdb8WDI/pdb

Classification: HYDROLASE
Organism(s): Gallus gallus
Mutation(s): No

Deposited: 2023-09-15 Released: 2023-10-04
Deposition Author(s): Nam, K.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.299 (Depositor), 0.299 (DCC)
R-Value Work:
0.251 (Depositor), 0.251 (DCC)
R-Value Observed:
0.256 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Fixed-Target Pink-Beam Serial Synchrotron Crystallography at Pohang Light Source II.

(2023) Crystals (Basel) 13: 1544-1544

DOI: https://doi.org/10.3390/cryst13111544

Macromolecule Content

Total Structure Weight: 14.4 kDa
Atom Count: 1,094
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): 0 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.299 (Depositor), 0.299 (DCC)
R-Value Work: 0.251 (Depositor), 0.251 (DCC)
R-Value Observed: 0.256 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.83	α = 90
b = 78.83	β = 90
c = 38.2	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1I1A1A01050838
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017M3A9F6029736
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2020M3H1A1075314

Revision History (Full details and data files)

Version 1.0: 2023-10-04
Type: Initial release
Version 1.1: 2024-04-17
Changes: Database references
Version 1.2: 2024-10-30
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.