3gul

T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--ethylbenzene binding

Method: X-RAY DIFFRACTION Dmax: 71.8 Å Quality: REASONABLE

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

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 Mutation:T21C/S38D/L99A/M102E/E108V/S117V/T142C/N144D Non-standard monomer:Yes (specific site not provided by mmCIF) PYJ PHENYLETHANE × 1 ACT ACETATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;30% PEG 8000, 0.14M magnesium/calcium sulfate, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.07 Å R-free 0.293
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–164 Mutation:T21C/S38D/L99A/M102E/E108V/S117V/T142C/N144D Non-standard monomer:Yes (specific site not provided by mmCIF) PYJ PHENYLETHANE × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;30% PEG 8000, 0.14M magnesium/calcium sulfate, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.07 Å R-free 0.293

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 845 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYS_BPT4
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–164; UniProt 1–164 Author chain B; 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 3gul

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3gul
Deposition date deposition_date2009-03-30
Structure title titleT4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--ethylbenzene binding
Keywords keywordsT4 lysozyme, apolar cavity, buried charge, ligand binding, Antimicrobial, Bacteriolytic enzyme, Glycosidase, Hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.27
Radius of gyration Rg (electron density) rg_electron21.21
Forward intensity I(0) i024161400.00
Molecular weight molecular_weight37297.0 kDa
Excluded volume excluded_volume46701 ų
Envelope volume envelope_volume55354 ų
Hydration-shell volume shell_volume22102 ų
Envelope diameter envelope_diameter73.0
Shell Rg shell_rg27.74
Envelope Rg envelope_rg21.37
Shape Rg shape_rg21.20
Total Rg total_rg22.10
Total atoms total_atoms2612
Residues n_residues322
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 dmax71.8
Rg (real space) rg_real22.19
Rg uncertainty (real space) rg_real_error0.42
I(0) (real space) i0_real2.4160e+07
I(0) uncertainty (real space) i0_real_error3.2220e+05
Rg (reciprocal space) rg_reciprocal22.21
I(0) (reciprocal space) i0_reciprocal24160000.0000
Solution quality estimate total_estimate0.7473
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.0
Skewness Skewness skewness0.199
Kurtosis Kurtosis kurtosis-0.530
Angular range angular_range— – 0.3550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5139000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 0.328; Positv: 1.000; Valcen: 1.000; Smooth: 0.995

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3gula_
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
Domain ID domain_idd3gulb_
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 (2 domains)

Domain ID domain_id3gulA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40
Domain ID domain_id3gulB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)