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6dt1

Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate

Method: X-RAY DIFFRACTION Dmax: 127.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA ligase

Enterobacteria phage T4

UniProt P00970

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–DNA Monomer Protein × 1 DNA 3 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain A； UniProt 1–487 Not recorded ;DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(DOC))-3') ; × 1 ;DNA (5'-D((AMP)*GP*TP*CP*GP*GP*AP*CP*TP*GP*AP*)-3') ; × 1 ;DNA (5'-D(*TP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') ; × 1 GOL GLYCEROL × 12 1PE PENTAETHYLENE GLYCOL × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 5 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；PEG3350 Resolution 2.75 Å R-free 0.219

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.

Other PDB Difference from Current Entry 6DT1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5WFY Crystal structure of DNA-binding domain of the bacteriophage T4 ligase Deposited 2017-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–129（129 aa） Fragment：DNA binding domain (UNP residues 1-129)
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350
Resolution 1.40 Å R-free 0.181
6DRT Crystal structure of the processivity clamp GP45 complexed with recognition peptide of ligase from bacteriophage T4 Deposited 2018-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 225–237（13 aa）
Chain E 225–237（13 aa）
Chain F 225–237（13 aa）
Not recorded EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；PEG3350
Resolution 2.12 Å R-free 0.240

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DNLI_BPT4
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 21–507； UniProt 1–487 Author chain E； PDBConstruct 21–507； UniProt 1–487

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 6dt1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6dt1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6dt1
Deposition date deposition_date2018-06-14
Structure title titleCrystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate
Keywords keywordsLIGASE-DNA COMPLEX, LIGASE; LIGASE/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.04 Å
Radius of gyration Rg (electron density) rg_electron38.02 Å
Forward intensity I(0) i0334063000.00
Molecular weight molecular_weight133320.0 kDa
Excluded volume excluded_volume160510 ų
Envelope volume envelope_volume216610 ų
Hydration-shell volume shell_volume48786 ų
Envelope diameter envelope_diameter139.4 Å
Shell Rg shell_rg42.55 Å
Envelope Rg envelope_rg37.57 Å
Shape Rg shape_rg37.98 Å
Total Rg total_rg38.36 Å
Total atoms total_atoms9247
Residues n_residues1005
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax127.5 Å
Rg (real space) rg_real38.24 Å
Rg uncertainty (real space) rg_real_error1.18 Å
I(0) (real space) i0_real3.3410e+08
I(0) uncertainty (real space) i0_real_error6.3770e+06
Rg (reciprocal space) rg_reciprocal38.12 Å
I(0) (reciprocal space) i0_reciprocal334000000.0000
Solution quality estimate total_estimate0.8620
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.4 Å
Skewness Skewness skewness0.429
Kurtosis Kurtosis kurtosis-0.491
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha42480000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.842
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (11)

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8. Citations (1)

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9. Files and Curves (10)