2lcb

Solution Structure of a Minor and Transiently Formed State of a T4 Lysozyme Mutant

Method: SOLUTION NMR Dmax: 53.9 Å Quality: GOOD

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, L99A No other associated polymer SOLUTION NMR NMR measurement conditions:pH 5.5;298 K;Ionic strength (raw mmCIF value) 85;Pressure ambient NMR sample composition:1.5 mM [U-15N; U-2H] T4 L99A, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:1.5 mM [U-13C; U-15N; U-2H] T4 L99A, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:1.5 mM [U-13Ca; U-15N] T4 L99A, 100% D2O | 100% D2O NMR sample composition:1.5 mM [U-13C; U-15N; U-50% 2H] T4 L99A, 100% D2O | 100% D2O NMR sample composition:1.5 mM [ U-15N] 13CH3 Met T4 L99A, 100% D2O | 100% D2O Resolution not provided

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 2lcb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2lcb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2lcb
Deposition date deposition_date2011-04-26
Structure title titleSolution Structure of a Minor and Transiently Formed State of a T4 Lysozyme Mutant
Keywords keywordsExcited State, HYDROLASE; HYDROLASE
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier16.71
Radius of gyration Rg (electron density) rg_electron16.47
Forward intensity I(0) i0487400000.00
Molecular weight molecular_weight185670.0 kDa
Excluded volume excluded_volume232640 ų
Envelope volume envelope_volume29322 ų
Hydration-shell volume shell_volume15134 ų
Envelope diameter envelope_diameter58.8
Shell Rg shell_rg22.33
Envelope Rg envelope_rg16.81
Shape Rg shape_rg16.43
Total Rg total_rg16.73
Total atoms total_atoms26360
Residues n_residues1640
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 dmax53.9
Rg (real space) rg_real16.71
Rg uncertainty (real space) rg_real_error0.26
I(0) (real space) i0_real4.8740e+08
I(0) uncertainty (real space) i0_real_error5.2620e+06
Rg (reciprocal space) rg_reciprocal16.71
I(0) (reciprocal space) i0_reciprocal487400000.0000
Solution quality estimate total_estimate0.8817
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.0
Skewness Skewness skewness0.342
Kurtosis Kurtosis kurtosis-0.259
Angular range angular_range— – 0.4750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha814200.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2lcba_
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_id2lcbA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)