3fz2

Crystal structure of the tail terminator protein from phage lambda (gpU-D74A)

Method: X-RAY DIFFRACTION Dmax: 106.8 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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–131 Chain B; UniProt 1–131 Chain E; UniProt 1–131 Chain F; UniProt 1–131 Chain I; UniProt 1–131 Chain K; UniProt 1–131 Mutation:D74A Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;0.2M Di-ammonium tartrate, 2.2M Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å R-free 0.283
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 1–131 Chain D; UniProt 1–131 Chain G; UniProt 1–131 Chain H; UniProt 1–131 Chain J; UniProt 1–131 Chain L; UniProt 1–131 Mutation:D74A Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;0.2M Di-ammonium tartrate, 2.2M Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å R-free 0.283
3 Protein homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain A; UniProt 1–131 Chain B; UniProt 1–131 Chain C; UniProt 1–131 Chain D; UniProt 1–131 Chain E; UniProt 1–131 Chain F; UniProt 1–131 Chain G; UniProt 1–131 Chain H; UniProt 1–131 Chain I; UniProt 1–131 Chain J; UniProt 1–131 Chain K; UniProt 1–131 Chain L; UniProt 1–131 Mutation:D74A Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 13 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;0.2M Di-ammonium tartrate, 2.2M Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å R-free 0.283

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 8 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 Author chain K; PDBConstruct 4–134; UniProt 1–131 Author chain L; 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 3fz2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3fz2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3fz2
Deposition date deposition_date2009-01-23
Structure title titleCrystal structure of the tail terminator protein from phage lambda (gpU-D74A)
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_guinier37.70
Radius of gyration Rg (electron density) rg_electron36.98
Forward intensity I(0) i0489997000.00
Molecular weight molecular_weight173210.0 kDa
Excluded volume excluded_volume212450 ų
Envelope volume envelope_volume309360 ų
Hydration-shell volume shell_volume68394 ų
Envelope diameter envelope_diameter107.1
Shell Rg shell_rg45.40
Envelope Rg envelope_rg34.63
Shape Rg shape_rg37.03
Total Rg total_rg37.35
Total atoms total_atoms12012
Residues n_residues1520
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 dmax106.8
Rg (real space) rg_real37.27
Rg uncertainty (real space) rg_real_error0.34
I(0) (real space) i0_real4.9000e+08
I(0) uncertainty (real space) i0_real_error6.6500e+06
Rg (reciprocal space) rg_reciprocal37.54
I(0) (reciprocal space) i0_reciprocal490100000.0000
Solution quality estimate total_estimate0.8823
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary56.0
Skewness Skewness skewness-0.185
Kurtosis Kurtosis kurtosis-0.542
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha147500000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.899

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 34 domains

SCOP 2.08 (22 domains)

Domain ID domain_idd3fz2a1
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_idd3fz2a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fz2b1
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_idd3fz2b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fz2c_
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_idd3fz2d1
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_idd3fz2d2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fz2e1
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_idd3fz2e2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fz2f1
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_idd3fz2f2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fz2g1
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_idd3fz2g2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fz2h1
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_idd3fz2h2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fz2i_
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_idd3fz2j1
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_idd3fz2j2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fz2k1
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_idd3fz2k2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fz2l1
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_idd3fz2l2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (12 domains)

Domain ID domain_id3fz2A00
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_id3fz2B00
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_id3fz2C00
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_id3fz2D00
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_id3fz2E00
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_id3fz2F00
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_id3fz2G00
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_id3fz2H00
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_id3fz2I00
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_id3fz2J00
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_id3fz2K00
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_id3fz2L00
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)