1j39

Crystal Structure of T4 phage BGT in complex with its UDP-glucose substrate

Method: X-RAY DIFFRACTION Dmax: 74.9 Å Quality: GOOD

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

DNA beta-glucosyltransferase

Enterobacteria phage T4

UniProt P04547

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 1–351 Not recorded UPG URIDINE-5'-DIPHOSPHATE-GLUCOSE × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;292 K;ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 1.87 Å R-free 0.232

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.

19 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GSTB_BPT4
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–351; UniProt 1–351

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 1j39

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1j39
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1j39
Deposition date deposition_date2003-01-21
Structure title titleCrystal Structure of T4 phage BGT in complex with its UDP-glucose substrate
Keywords keywordsglycosyltransferase, GT-B, UDP-glucose, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.86
Radius of gyration Rg (electron density) rg_electron20.99
Forward intensity I(0) i026160900.00
Molecular weight molecular_weight40352.0 kDa
Excluded volume excluded_volume51052 ų
Envelope volume envelope_volume58528 ų
Hydration-shell volume shell_volume23120 ų
Envelope diameter envelope_diameter78.0
Shell Rg shell_rg27.80
Envelope Rg envelope_rg21.32
Shape Rg shape_rg20.99
Total Rg total_rg21.89
Total atoms total_atoms2841
Residues n_residues344
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 dmax74.9
Rg (real space) rg_real21.83
Rg uncertainty (real space) rg_real_error0.50
I(0) (real space) i0_real2.6160e+07
I(0) uncertainty (real space) i0_real_error3.4250e+05
Rg (reciprocal space) rg_reciprocal21.84
I(0) (reciprocal space) i0_reciprocal26160000.0000
Solution quality estimate total_estimate0.8636
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.7
Skewness Skewness skewness0.354
Kurtosis Kurtosis kurtosis-0.277
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8903000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.757; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.979

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1j39a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.87 — UDP-Glycosyltransferase/glycogen phosphorylase
Superfamily Superfamily superfamilyc.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
Family Family familyc.87.1.1 — beta-Glucosyltransferase (DNA-modifying)

CATH v4.4 (2 domains)

Domain ID domain_id1j39A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2000 — Glycogen Phosphorylase B;
Domain ID domain_id1j39A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2000 — Glycogen Phosphorylase B;

8. Citations (1)

9. Files and Curves (10)