7l3b

T4 Lysozyme L99A - iodobenzene - RT

Method: X-RAY DIFFRACTION Dmax: 60.4 Å Quality: GOOD

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

Endolysin

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:R12G/I137R/L99A TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 BME BETA-MERCAPTOETHANOL × 2 CL CHLORIDE ION × 1 PIH iodobenzene × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;Crystals were grown from a 10 mg/mL frozen protein solution by the hanging drop method at 291-293K, with a 1:1 drop ratio of protein to solution and over a well solution of 0.1 M Tris-hydrochloride (pH 8), 20%-26% (w/v) PEG 4000, 70-170 mM lithium citrate, 8%-18% 2-propanol, 50 mM 2-mercaptoethanol, and 50 mM 2-hydroxyethyl disulfide Resolution 1.27 Å R-free 0.167

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 ENLYS_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 7l3b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7l3b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7l3b
Deposition date deposition_date2020-12-17
Structure title titleT4 Lysozyme L99A - iodobenzene - RT
Keywords keywordsRT, iodobenzene, L99A, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.37
Radius of gyration Rg (electron density) rg_electron16.43
Forward intensity I(0) i06965260.00
Molecular weight molecular_weight18875.0 kDa
Excluded volume excluded_volume23486 ų
Envelope volume envelope_volume26853 ų
Hydration-shell volume shell_volume14197 ų
Envelope diameter envelope_diameter58.1
Shell Rg shell_rg21.73
Envelope Rg envelope_rg16.59
Shape Rg shape_rg16.42
Total Rg total_rg17.36
Total atoms total_atoms1313
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 dmax60.4
Rg (real space) rg_real17.36
Rg uncertainty (real space) rg_real_error0.46
I(0) (real space) i0_real6.9650e+06
I(0) uncertainty (real space) i0_real_error9.3250e+04
Rg (reciprocal space) rg_reciprocal17.36
I(0) (reciprocal space) i0_reciprocal6965000.0000
Solution quality estimate total_estimate0.8585
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.7
Skewness Skewness skewness0.352
Kurtosis Kurtosis kurtosis-0.242
Angular range angular_range— – 0.4600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1758000.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.733; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.998

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7l3bA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)