3txj

HEWL co-crystallization with NAG with silicone oil as the cryoprotectant

Method: X-RAY DIFFRACTION Dmax: 51.8 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 19–147 Fragment:UNP residues 19-147 CL CHLORIDE ION × 8 NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH;pH 4.7;295 K;49 mg HEWL + 117 mg N-acetylglucosamine in 1 mL 0.04 M sodium acetate + 1 mL 10% sodium chloride, with silicone oil as cryoprotectant, pH 4.7, BATCH, temperature 295K Resolution 2.48 Å R-free 0.289

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 1–129; UniProt 19–147

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 3txj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3txj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3txj
Deposition date deposition_date2011-09-23
Structure title titleHEWL co-crystallization with NAG with silicone oil as the cryoprotectant
Keywords keywordshen egg white lysozyme (HEWL), bacterial cell wall lysis, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier15.27
Radius of gyration Rg (electron density) rg_electron13.92
Forward intensity I(0) i05152540.00
Molecular weight molecular_weight14849.0 kDa
Excluded volume excluded_volume17932 ų
Envelope volume envelope_volume19755 ų
Hydration-shell volume shell_volume12150 ų
Envelope diameter envelope_diameter51.8
Shell Rg shell_rg19.60
Envelope Rg envelope_rg14.23
Shape Rg shape_rg13.85
Total Rg total_rg15.12
Total atoms total_atoms1025
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 dmax51.8
Rg (real space) rg_real15.20
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real5.1530e+06
I(0) uncertainty (real space) i0_real_error5.9270e+04
Rg (reciprocal space) rg_reciprocal15.20
I(0) (reciprocal space) i0_reciprocal5153000.0000
Solution quality estimate total_estimate0.8684
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.7
Skewness Skewness skewness0.249
Kurtosis Kurtosis kurtosis-0.208
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha986600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.989

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3txja_
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

CATH v4.4 (1 domains)

Domain ID domain_id3txjA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)