3l2x

Crystal Structure of Spin Labeled T4 Lysozyme Mutant 115-119RX

Method: X-RAY DIFFRACTION Dmax: 60.9 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:C54T, C97A, T115C, R119C RXR [2,2,5,5-tetramethyl-3,4-bis(sulfanylmethyl)-2,5-dihydro-1H-pyrrol-1-yl]oxidanyl radical × 1 AZI AZIDE ION × 1 CL CHLORIDE ION × 2 HED 2-HYDROXYETHYL DISULFIDE × 1 BME BETA-MERCAPTOETHANOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;277 K;2.0M dibasic potassium phosphate and monobasic sodium phosphate, 0.25M sodium chloride, 0.04% sodium azide, saturated with bis(2-hydroxyethyl) disulfide, pH 6.4, vapor diffusion, hanging drop, temperature 277K Resolution 1.80 Å R-free 0.232

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 3l2x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3l2x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3l2x
Deposition date deposition_date2009-12-15
Structure title titleCrystal Structure of Spin Labeled T4 Lysozyme Mutant 115-119RX
Keywords keywordsHydrolase, NITROXIDE SPIN LABEL, EPR, MODIFIED CYSTEINE, Antimicrobial, Bacteriolytic enzyme, Glycosidase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.66
Radius of gyration Rg (electron density) rg_electron16.61
Forward intensity I(0) i07061380.00
Molecular weight molecular_weight19135.0 kDa
Excluded volume excluded_volume23877 ų
Envelope volume envelope_volume27245 ų
Hydration-shell volume shell_volume14280 ų
Envelope diameter envelope_diameter59.8
Shell Rg shell_rg22.01
Envelope Rg envelope_rg16.74
Shape Rg shape_rg16.55
Total Rg total_rg17.70
Total atoms total_atoms1334
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 dmax60.9
Rg (real space) rg_real17.65
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real7.0610e+06
I(0) uncertainty (real space) i0_real_error8.2290e+04
Rg (reciprocal space) rg_reciprocal17.65
I(0) (reciprocal space) i0_reciprocal7061000.0000
Solution quality estimate total_estimate0.6535
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary60.1
Skewness Skewness skewness0.342
Kurtosis Kurtosis kurtosis-0.253
Angular range angular_range— – 0.4500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1551000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.756; Stabil: 1.000; Sysdev: 0.424; Positv: 1.000; Valcen: 0.952; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3l2xa_
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_id3l2xA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)