4w58

T4 Lysozyme L99A with n-Pentylbenzene Bound

Method: X-RAY DIFFRACTION Dmax: 57.5 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:L99A 3H2 pentylbenzene × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;277 K;20% (w/v) PEGF-4000, 10% 2-propanol, 0.1 M HEPES, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide Resolution 1.80 Å R-free 0.184

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 4w58

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4w58
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4w58
Deposition date deposition_date2014-08-16
Structure title titleT4 Lysozyme L99A with n-Pentylbenzene Bound
Keywords keywordsHYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.41
Radius of gyration Rg (electron density) rg_electron16.37
Forward intensity I(0) i06638700.00
Molecular weight molecular_weight18767.0 kDa
Excluded volume excluded_volume23545 ų
Envelope volume envelope_volume26609 ų
Hydration-shell volume shell_volume14170 ų
Envelope diameter envelope_diameter57.6
Shell Rg shell_rg21.72
Envelope Rg envelope_rg16.49
Shape Rg shape_rg16.34
Total Rg total_rg17.38
Total atoms total_atoms1318
Residues n_residues165
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 dmax57.5
Rg (real space) rg_real17.39
Rg uncertainty (real space) rg_real_error0.34
I(0) (real space) i0_real6.6390e+06
I(0) uncertainty (real space) i0_real_error8.3690e+04
Rg (reciprocal space) rg_reciprocal17.40
I(0) (reciprocal space) i0_reciprocal6639000.0000
Solution quality estimate total_estimate0.7987
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.5
Skewness Skewness skewness0.344
Kurtosis Kurtosis kurtosis-0.224
Angular range angular_range— – 0.4550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1441000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4w58a1
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_idd4w58a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id4w58A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)