7e02

Room temperature structure of lysozyme delivered in beef tallow by serial millisecond crystallography

Method: X-RAY DIFFRACTION Dmax: 50.6 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Lysozyme C

OrganismNot specified

UniProt P00698

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–147 Not recorded NA SODIUM ION × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:SMALL TUBES;pH 4.5;293.5 K;sodium acetate, PEG 8000, NaCl Resolution 1.55 Å R-free 0.188

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

1320 other PDB entries and 1450 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYSC_CHICK
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–147; UniProt 1–147

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7e02

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7e02
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7e02
Deposition date deposition_date2021-01-26
Structure title titleRoom temperature structure of lysozyme delivered in beef tallow by serial millisecond crystallography
Keywords keywordsserial crystallography, beef tallow, room temperature, lysozyme, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.32
Radius of gyration Rg (electron density) rg_electron14.03
Forward intensity I(0) i04756430.00
Molecular weight molecular_weight14415.0 kDa
Excluded volume excluded_volume17531 ų
Envelope volume envelope_volume19623 ų
Hydration-shell volume shell_volume12054 ų
Envelope diameter envelope_diameter50.7
Shell Rg shell_rg19.57
Envelope Rg envelope_rg14.27
Shape Rg shape_rg14.01
Total Rg total_rg15.14
Total atoms total_atoms1961
Residues n_residues129
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax50.6
Rg (real space) rg_real15.24
Rg uncertainty (real space) rg_real_error0.28
I(0) (real space) i0_real4.7560e+06
I(0) uncertainty (real space) i0_real_error5.2170e+04
Rg (reciprocal space) rg_reciprocal15.25
I(0) (reciprocal space) i0_reciprocal4756000.0000
Solution quality estimate total_estimate0.8791
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.9
Skewness Skewness skewness0.217
Kurtosis Kurtosis kurtosis-0.243
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha777700.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.992

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd7e02a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.2 — Lysozyme-like
Superfamily Superfamily superfamilyd.2.1 — Lysozyme-like
Family Family familyd.2.1.2 — C-type lysozyme

8. Citations (1)

9. Files and Curves (10)