7D04 | pdb_00007d04

Lysozyme structure SS3 from SS mode

PDB DOI: https://doi.org/10.2210/pdb7D04/pdb

Classification: HYDROLASE
Organism(s): Gallus gallus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-09-09 Released: 2021-03-31
Deposition Author(s): Kang, H.S., Lee, S.J.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.248 (Depositor), 0.228 (DCC)
R-Value Work:
0.213 (Depositor), 0.207 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7D04

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

Literature

High-brightness self-seeded X-ray free-electron laser covering the 3.5 keV to 14.6 keV range

Nam, I., Min, C.K., Oh, B., Kim, G., Na, D., Suh, Y.J., Yang, H., Cho, M.H., Kim, C., Kim, M.J., Shim, C.H., Ko, J.H., Heo, H., Park, J., Kim, J., Park, S., Park, G., Kim, S., Chun, S.H., Hyun, H., Lee, J.H., Kim, K.S., Eom, I., Rah, S., Shu, D., Kim, K.J., Terentyev, S., Blank, V., Shvydko, Y., Lee, S.J., Kang, H.S.

(2021) Nat Photonics

DOI: https://doi.org/10.1038/s41566-021-00777-z

Macromolecule Content

Total Structure Weight: 16.26 kDa
Atom Count: 1,073
Modeled Residue Count: 129
Deposited Residue Count: 147
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	147	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.248 (Depositor), 0.228 (DCC)
R-Value Work: 0.213 (Depositor), 0.207 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.895	α = 90
b = 78.895	β = 90
c = 37.811	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-03-31

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2017R1A2B4007274
National Research Foundation (NRF, Korea)	Korea, Republic Of	2020R1F1A1075828
National Research Foundation (NRF, Korea)	Korea, Republic Of	2018R1A6B4023605

Revision History (Full details and data files)

Version 1.0: 2021-03-31
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
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.