1lye

DISSECTION OF HELIX CAPPING IN T4 LYSOZYME BY STRUCTURAL AND THERMODYNAMIC ANALYSIS OF SIX AMINO ACID SUBSTITUTIONS AT THR 59

Method: X-RAY DIFFRACTION Dmax: 61.3 Å Quality: GOOD

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

T4 LYSOZYME

Enterobacteria phage T4

UniProt P00720

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 1–164 Not recorded CL CHLORIDE ION × 2 BME BETA-MERCAPTOETHANOL × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.80 Å

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.

721 other PDB entries and 846 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYCV_BPT4
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–164; UniProt 1–164

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 1lye

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1lye
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1lye
Deposition date deposition_date1992-08-10
Structure title titleDISSECTION OF HELIX CAPPING IN T4 LYSOZYME BY STRUCTURAL AND THERMODYNAMIC ANALYSIS OF SIX AMINO ACID SUBSTITUTIONS AT THR 59
Keywords keywordsHYDROLASE(O-GLYCOSYL); HYDROLASE(O-GLYCOSYL)
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.45
Radius of gyration Rg (electron density) rg_electron16.49
Forward intensity I(0) i06589250.00
Molecular weight molecular_weight18590.0 kDa
Excluded volume excluded_volume23290 ų
Envelope volume envelope_volume26611 ų
Hydration-shell volume shell_volume14096 ų
Envelope diameter envelope_diameter59.4
Shell Rg shell_rg21.76
Envelope Rg envelope_rg16.59
Shape Rg shape_rg16.47
Total Rg total_rg17.47
Total atoms total_atoms1302
Residues n_residues162
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 dmax61.3
Rg (real space) rg_real17.44
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real6.5890e+06
I(0) uncertainty (real space) i0_real_error7.8070e+04
Rg (reciprocal space) rg_reciprocal17.44
I(0) (reciprocal space) i0_reciprocal6589000.0000
Solution quality estimate total_estimate0.7718
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.4
Skewness Skewness skewness0.362
Kurtosis Kurtosis kurtosis-0.195
Angular range angular_range— – 0.4550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1546000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.698; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.935; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1lyea_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.2 — Lysozyme-like
Superfamily Superfamily superfamilyd.2.1 — Lysozyme-like
Family Family familyd.2.1.3 — Phage lysozyme

CATH v4.4 (1 domains)

Domain ID domain_id1lyeA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)