4eks

T4 Lysozyme L99A/M102H with Isoxazole Bound

Method: X-RAY DIFFRACTION Dmax: 80.4 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:T21C/S38D/L99A/M102H/E108V/S117V/T142C/N144D BME BETA-MERCAPTOETHANOL × 2 0R1 1,2-benzisoxazole × 1 SO4 SULFATE ION × 3 ACT ACETATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;277 K;30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.64 Å R-free 0.198
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–164 Mutation:T21C/S38D/L99A/M102H/E108V/S117V/T142C/N144D BME BETA-MERCAPTOETHANOL × 2 0R1 1,2-benzisoxazole × 1 SO4 SULFATE ION × 2 ACT ACETATE ION × 1 HED 2-HYDROXYETHYL DISULFIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;277 K;30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.64 Å R-free 0.198
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–164 Chain B; UniProt 1–164 Mutation:T21C/S38D/L99A/M102H/E108V/S117V/T142C/N144D BME BETA-MERCAPTOETHANOL × 4 0R1 1,2-benzisoxazole × 2 SO4 SULFATE ION × 5 ACT ACETATE ION × 3 HED 2-HYDROXYETHYL DISULFIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;277 K;30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.64 Å R-free 0.198

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 844 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 24–187; UniProt 1–164 Author chain B; PDBConstruct 24–187; 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 4eks

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4eks
Deposition date deposition_date2012-04-09
Structure title titleT4 Lysozyme L99A/M102H with Isoxazole Bound
Keywords keywordsHydrolase, Alkylation of Cys97; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.71
Radius of gyration Rg (electron density) rg_electron23.10
Forward intensity I(0) i054532800.00
Molecular weight molecular_weight37644.0 kDa
Excluded volume excluded_volume35929 ų
Envelope volume envelope_volume61029 ų
Hydration-shell volume shell_volume22861 ų
Envelope diameter envelope_diameter82.7
Shell Rg shell_rg29.26
Envelope Rg envelope_rg23.16
Shape Rg shape_rg23.09
Total Rg total_rg23.67
Total atoms total_atoms2830
Residues n_residues349
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 dmax80.4
Rg (real space) rg_real23.72
Rg uncertainty (real space) rg_real_error0.54
I(0) (real space) i0_real5.4530e+07
I(0) uncertainty (real space) i0_real_error7.2180e+05
Rg (reciprocal space) rg_reciprocal23.72
I(0) (reciprocal space) i0_reciprocal54530000.0000
Solution quality estimate total_estimate0.8814
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.6
Skewness Skewness skewness0.362
Kurtosis Kurtosis kurtosis-0.305
Angular range angular_range— – 0.3350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6826000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.958

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4eksa1
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_idd4eksa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4eksb1
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_idd4eksb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id4eksA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40
Domain ID domain_id4eksB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)