3sb7

Cu-mediated Trimer of T4 Lysozyme D61H/K65H/R76H/R80H by Synthetic Symmetrization

Method: X-RAY DIFFRACTION Dmax: 67.2 Å Quality: EXCELLENT

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1–162 Mutation:C54T, D61H, K65H, R76H, R80H, C97A CU COPPER (II) ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;290 K;0.2M Potassium Thiocyanate, 25% PEG 3350, vapor diffusion, hanging drop, temperature 290K Resolution 2.70 Å R-free 0.226
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–162 Chain B; UniProt 1–162 Mutation:C54T, D61H, K65H, R76H, R80H, C97A GOL GLYCEROL × 1 CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;290 K;0.2M Potassium Thiocyanate, 25% PEG 3350, vapor diffusion, hanging drop, temperature 290K Resolution 2.70 Å R-free 0.226

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 845 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 4–165; UniProt 1–162 Author chain B; PDBConstruct 4–165; UniProt 1–162

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 3sb7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3sb7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3sb7
Deposition date deposition_date2011-06-03
Structure title titleCu-mediated Trimer of T4 Lysozyme D61H/K65H/R76H/R80H by Synthetic Symmetrization
Keywords keywordsmetal-mediated synthetic symmetrization, synthetic symmetrization, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.66
Radius of gyration Rg (electron density) rg_electron20.63
Forward intensity I(0) i023256300.00
Molecular weight molecular_weight36332.0 kDa
Excluded volume excluded_volume45352 ų
Envelope volume envelope_volume53103 ų
Hydration-shell volume shell_volume21806 ų
Envelope diameter envelope_diameter67.0
Shell Rg shell_rg26.61
Envelope Rg envelope_rg20.53
Shape Rg shape_rg20.61
Total Rg total_rg21.48
Total atoms total_atoms2557
Residues n_residues325
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 dmax67.2
Rg (real space) rg_real21.55
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real2.3260e+07
I(0) uncertainty (real space) i0_real_error3.2300e+05
Rg (reciprocal space) rg_reciprocal21.57
I(0) (reciprocal space) i0_reciprocal23260000.0000
Solution quality estimate total_estimate0.9083
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.1
Skewness Skewness skewness0.171
Kurtosis Kurtosis kurtosis-0.504
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5392000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.993

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3sb7a1
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_idd3sb7a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3sb7b_
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 (2 domains)

Domain ID domain_id3sb7A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40
Domain ID domain_id3sb7B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)