3fzb

Crystal structure of the tail terminator protein from phage lambda (gpU-WT)

Method: X-RAY DIFFRACTION Dmax: 108.5 Å Quality: GOOD

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

Minor tail protein U

Enterobacteria phage lambda

UniProt P03732

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–131 Chain B; UniProt 1–131 Chain F; UniProt 1–131 Chain H; UniProt 1–131 Chain I; UniProt 1–131 Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;0.2M Tri-sodium citrate, 2.2M Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.80 Å R-free 0.309
2 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 1–131 Chain D; UniProt 1–131 Chain E; UniProt 1–131 Chain G; UniProt 1–131 Chain J; UniProt 1–131 Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;0.2M Tri-sodium citrate, 2.2M Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.80 Å R-free 0.309

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.

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VMTU_LAMBD
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–134; UniProt 1–131 Author chain B; PDBConstruct 4–134; UniProt 1–131 Author chain C; PDBConstruct 4–134; UniProt 1–131 Author chain D; PDBConstruct 4–134; UniProt 1–131 Author chain E; PDBConstruct 4–134; UniProt 1–131 Author chain F; PDBConstruct 4–134; UniProt 1–131 Author chain G; PDBConstruct 4–134; UniProt 1–131 Author chain H; PDBConstruct 4–134; UniProt 1–131 Author chain I; PDBConstruct 4–134; UniProt 1–131 Author chain J; PDBConstruct 4–134; UniProt 1–131

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 3fzb

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3fzb
Deposition date deposition_date2009-01-24
Structure title titleCrystal structure of the tail terminator protein from phage lambda (gpU-WT)
Keywords keywordsMixed Alpha-Beta fold, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier34.99
Radius of gyration Rg (electron density) rg_electron34.33
Forward intensity I(0) i0291271000.00
Molecular weight molecular_weight136350.0 kDa
Excluded volume excluded_volume169440 ų
Envelope volume envelope_volume224850 ų
Hydration-shell volume shell_volume53467 ų
Envelope diameter envelope_diameter111.7
Shell Rg shell_rg41.92
Envelope Rg envelope_rg33.52
Shape Rg shape_rg34.27
Total Rg total_rg35.09
Total atoms total_atoms9639
Residues n_residues1289
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 dmax108.5
Rg (real space) rg_real34.79
Rg uncertainty (real space) rg_real_error0.67
I(0) (real space) i0_real2.9130e+08
I(0) uncertainty (real space) i0_real_error4.3980e+06
Rg (reciprocal space) rg_reciprocal34.92
I(0) (reciprocal space) i0_reciprocal291300000.0000
Solution quality estimate total_estimate0.8877
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.8
Skewness Skewness skewness0.125
Kurtosis Kurtosis kurtosis-0.403
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha61980000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.925

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (17 domains)

Domain ID domain_idd3fzba1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.323 — Phage tail protein-like
Superfamily Superfamily superfamilyd.323.1 — Phage tail protein-like
Family Family familyd.323.1.1 — Lambda phage gpU-like
Domain ID domain_idd3fzba2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fzbb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.323 — Phage tail protein-like
Superfamily Superfamily superfamilyd.323.1 — Phage tail protein-like
Family Family familyd.323.1.1 — Lambda phage gpU-like
Domain ID domain_idd3fzbb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fzbc1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.323 — Phage tail protein-like
Superfamily Superfamily superfamilyd.323.1 — Phage tail protein-like
Family Family familyd.323.1.1 — Lambda phage gpU-like
Domain ID domain_idd3fzbc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fzbd1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.323 — Phage tail protein-like
Superfamily Superfamily superfamilyd.323.1 — Phage tail protein-like
Family Family familyd.323.1.1 — Lambda phage gpU-like
Domain ID domain_idd3fzbd2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fzbe_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.323 — Phage tail protein-like
Superfamily Superfamily superfamilyd.323.1 — Phage tail protein-like
Family Family familyd.323.1.1 — Lambda phage gpU-like
Domain ID domain_idd3fzbf1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.323 — Phage tail protein-like
Superfamily Superfamily superfamilyd.323.1 — Phage tail protein-like
Family Family familyd.323.1.1 — Lambda phage gpU-like
Domain ID domain_idd3fzbf2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fzbg1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.323 — Phage tail protein-like
Superfamily Superfamily superfamilyd.323.1 — Phage tail protein-like
Family Family familyd.323.1.1 — Lambda phage gpU-like
Domain ID domain_idd3fzbg2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fzbh_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.323 — Phage tail protein-like
Superfamily Superfamily superfamilyd.323.1 — Phage tail protein-like
Family Family familyd.323.1.1 — Lambda phage gpU-like
Domain ID domain_idd3fzbi_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.323 — Phage tail protein-like
Superfamily Superfamily superfamilyd.323.1 — Phage tail protein-like
Family Family familyd.323.1.1 — Lambda phage gpU-like
Domain ID domain_idd3fzbj1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.323 — Phage tail protein-like
Superfamily Superfamily superfamilyd.323.1 — Phage tail protein-like
Family Family familyd.323.1.1 — Lambda phage gpU-like
Domain ID domain_idd3fzbj2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (10 domains)

Domain ID domain_id3fzbA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1700 — Phage minor tail protein U
Domain ID domain_id3fzbB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1700 — Phage minor tail protein U
Domain ID domain_id3fzbC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1700 — Phage minor tail protein U
Domain ID domain_id3fzbD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1700 — Phage minor tail protein U
Domain ID domain_id3fzbE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1700 — Phage minor tail protein U
Domain ID domain_id3fzbF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1700 — Phage minor tail protein U
Domain ID domain_id3fzbG00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1700 — Phage minor tail protein U
Domain ID domain_id3fzbH00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1700 — Phage minor tail protein U
Domain ID domain_id3fzbI00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1700 — Phage minor tail protein U
Domain ID domain_id3fzbJ00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1700 — Phage minor tail protein U

8. Citations (1)

9. Files and Curves (10)