3dmx

Benzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant

Method: X-RAY DIFFRACTION Dmax: 58.2 Å Quality: GOOD

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

Lysozyme

Bacteriophage 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:C54T, C97A, L99A PO4 PHOSPHATE ION × 2 CL CHLORIDE ION × 1 HED 2-HYDROXYETHYL DISULFIDE × 2 BNZ BENZENE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.9;277 K;2.0-2.2 M K/Na phosphate, pH 6.9, 5mM BME and 5mM oxidized BME. Complexes were prepared by soaking or vapor diffusion methods, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.80 Å R-free 0.208

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 LYS_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 3dmx

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3dmx
Deposition date deposition_date2008-07-01
Structure title titleBenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant
Keywords keywordsT4 lysozyme, halogen bond, hydrophobic cavity, halogenated benzene, 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_guinier17.51
Radius of gyration Rg (electron density) rg_electron16.43
Forward intensity I(0) i07269040.00
Molecular weight molecular_weight19179.0 kDa
Excluded volume excluded_volume23850 ų
Envelope volume envelope_volume27325 ų
Hydration-shell volume shell_volume14412 ų
Envelope diameter envelope_diameter59.5
Shell Rg shell_rg21.83
Envelope Rg envelope_rg16.61
Shape Rg shape_rg16.40
Total Rg total_rg17.45
Total atoms total_atoms1339
Residues n_residues164
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 dmax58.2
Rg (real space) rg_real17.49
Rg uncertainty (real space) rg_real_error0.37
I(0) (real space) i0_real7.2690e+06
I(0) uncertainty (real space) i0_real_error8.3690e+04
Rg (reciprocal space) rg_reciprocal17.49
I(0) (reciprocal space) i0_reciprocal7269000.0000
Solution quality estimate total_estimate0.7980
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.9
Skewness Skewness skewness0.352
Kurtosis Kurtosis kurtosis-0.205
Angular range angular_range— – 0.4550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1917000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3dmxa_
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_id3dmxA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)