Macromolecule Content

Total Structure Weight: 14.65 kDa
Atom Count: 1,203
Modelled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

8CVW

20ns Temperature-Jump (Dark2) XFEL structure of Lysozyme

PDB DOI: https://doi.org/10.2210/pdb8CVW/pdb

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

Deposited: 2022-05-18 Released: 2022-06-22
Deposition Author(s): Wolff, A.M., Thompson, M.C., Fraser, J.S., Nango, E.
Funding Organization(s): National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.167
R-Value Work: 0.146
R-Value Observed: 0.147

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography

Wolff, A.M., Nango, E., Young, I.D., Brewster, A.S., Kubo, M., Nomura, T., Sugahara, M., Owada, S., Barad, B.A., Ito, K., Bhowmick, A., Carbajo, S., Hino, T., Holton, J.M., Im, D., O'Riordan, L.J., Tanaka, T., Tanaka, R., Sierra, R.G., Yumoto, F., Tono, K., Iwata, S., Sauter, N.K., Fraser, J.S., Thompson, M.C.

(2022) Biorxiv

DOI: https://doi.org/10.1101/2022.06.10.495662

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00698
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.167
R-Value Work: 0.146
R-Value Observed: 0.147
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.441	α = 90
b = 79.441	β = 90
c = 38.191	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
cctbx.xfel	data reduction
cxi.merge	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-06-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1231306
Department of Energy (DOE, United States)	United States	DE-AC02-76SF00515

Revision History (Full details and data files)

Version 1.0: 2022-06-22
Type: Initial release

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.