223l

GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-CREATING SUBSTITUTIONS

Method: X-RAY DIFFRACTION Dmax: 58.1 Å Quality: GOOD

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

T4 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:L133G CL CHLORIDE ION × 1 BME BETA-MERCAPTOETHANOL × 3 BNZ BENZENE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;277 K;CRYSTALS GROWN IN HANGING DROPS AT 4 DEGREES C. PROTEIN 10-20 MG/ML IN A BUFFER CONTAINING 0.1M NA2PO4 PH 6.6, 0.55 M NACL WAS DILUTED 1/2 WITH A WELL SOLUTION CONTAINING 1.8-2.2M NA/KPO4 PH 6.3-7.1 WITH OXIDIZED/REDUCED BME. CRYSTALS WERE EXPOSED TO BENZENE VAPOR IN A CAPILLARY FOR SEVERAL DAYS AT ROOM TEMPERATURE., pH 7.0, vapor diffusion - hanging drop, temperature 277K Resolution 1.90 Å

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 223l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 223l
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2. Structure Basics 2. Structure Basics

Entry ID entry_id223l
Deposition date deposition_date1997-06-25
Structure title titleGENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-CREATING SUBSTITUTIONS
Keywords keywordsHYDROLASE, O-GLYCOSYL, T4 LYSOZYME, CAVITY MUTANTS, LIGAND BINDING, PROTEIN ENGINEERING, PROTEIN DESIGN; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.53
Radius of gyration Rg (electron density) rg_electron16.53
Forward intensity I(0) i06701460.00
Molecular weight molecular_weight18691.0 kDa
Excluded volume excluded_volume23367 ų
Envelope volume envelope_volume26755 ų
Hydration-shell volume shell_volume14145 ų
Envelope diameter envelope_diameter59.0
Shell Rg shell_rg21.84
Envelope Rg envelope_rg16.60
Shape Rg shape_rg16.48
Total Rg total_rg17.57
Total atoms total_atoms1307
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 dmax58.1
Rg (real space) rg_real17.51
Rg uncertainty (real space) rg_real_error0.42
I(0) (real space) i0_real6.7010e+06
I(0) uncertainty (real space) i0_real_error8.1950e+04
Rg (reciprocal space) rg_reciprocal17.52
I(0) (reciprocal space) i0_reciprocal6701000.0000
Solution quality estimate total_estimate0.7983
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.7
Skewness Skewness skewness0.344
Kurtosis Kurtosis kurtosis-0.244
Angular range angular_range— – 0.4550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1444000.0000
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: 0.980; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd223la_
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_id223lA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (4)

9. Files and Curves (10)