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1dgs

CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS

Method: X-RAY DIFFRACTION Dmax: 168.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA LIGASE

OrganismNot specified

UniProt Q9ZHI0

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 1–667 Not recorded ZN ZINC ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；pH 5.6, VAPOR DIFFUSION, HANGING DROP Resolution 2.90 Å R-free 0.298
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–667 Not recorded ZN ZINC ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；pH 5.6, VAPOR DIFFUSION, HANGING DROP Resolution 2.90 Å R-free 0.298

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 1DGS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1V9P Crystal Structure Of Nad+-Dependent DNA Ligase Deposited 2004-01-27 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–584（584 aa）
Not recorded ZN ZINC ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；5% methoxyPEG 5000, 100mM sodium citrate(pH 5.6), 5mM calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.90 Å R-free 0.293
1V9P Crystal Structure Of Nad+-Dependent DNA Ligase Deposited 2004-01-27 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–584（584 aa）
Not recorded ZN ZINC ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；5% methoxyPEG 5000, 100mM sodium citrate(pH 5.6), 5mM calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.90 Å R-free 0.293

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

View Construct and Data Evidence
UniProt name DNLJ_THEFI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–667； UniProt 1–667 Author chain B； PDBConstruct 1–667； UniProt 1–667

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 1dgs

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1dgs
Deposition date deposition_date1999-11-25
Structure title titleCRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS
Keywords keywordsAMP COMPLEX, NAD+-DEPENDENT, LIGASE; LIGASE
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_guinier52.40 Å
Radius of gyration Rg (electron density) rg_electron53.04 Å
Forward intensity I(0) i0264646000.00
Molecular weight molecular_weight133880.0 kDa
Excluded volume excluded_volume167620 ų
Envelope volume envelope_volume268040 ų
Hydration-shell volume shell_volume45224 ų
Envelope diameter envelope_diameter180.5 Å
Shell Rg shell_rg49.96 Å
Envelope Rg envelope_rg52.29 Å
Shape Rg shape_rg52.94 Å
Total Rg total_rg53.28 Å
Total atoms total_atoms9432
Residues n_residues1162
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 dmax168.9 Å
Rg (real space) rg_real52.98 Å
Rg uncertainty (real space) rg_real_error1.84 Å
I(0) (real space) i0_real2.6460e+08
I(0) uncertainty (real space) i0_real_error4.8010e+06
Rg (reciprocal space) rg_reciprocal51.89 Å
I(0) (reciprocal space) i0_reciprocal264200000.0000
Solution quality estimate total_estimate0.7496
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.7 Å
Skewness Skewness skewness0.526
Kurtosis Kurtosis kurtosis-0.573
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8328000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.641; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.789; Smooth: 0.030
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1dgsa1
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.2 — RuvA domain 2-like
Family Family familya.60.2.2 — NAD+-dependent DNA ligase, domain 3
Domain ID domain_idd1dgsa2
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.6 — DNA ligase/mRNA capping enzyme postcatalytic domain
Domain ID domain_idd1dgsa3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.142 — ATP-grasp
Superfamily Superfamily superfamilyd.142.2 — DNA ligase/mRNA capping enzyme, catalytic domain
Family Family familyd.142.2.2 — Adenylation domain of NAD+-dependent DNA ligase
Domain ID domain_idd1dgsb1
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.2 — RuvA domain 2-like
Family Family familya.60.2.2 — NAD+-dependent DNA ligase, domain 3
Domain ID domain_idd1dgsb2
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.6 — DNA ligase/mRNA capping enzyme postcatalytic domain
Domain ID domain_idd1dgsb3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.142 — ATP-grasp
Superfamily Superfamily superfamilyd.142.2 — DNA ligase/mRNA capping enzyme, catalytic domain
Family Family familyd.142.2.2 — Adenylation domain of NAD+-dependent DNA ligase

CATH v4.4 (12 domains)

Domain ID domain_id1dgsA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily610 — Helix hairpin bin
Domain ID domain_id1dgsA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily70 —
Domain ID domain_id1dgsA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily30 — DNA ligase/mRNA capping enzyme
Domain ID domain_id1dgsA04
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id1dgsA05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id1dgsA06
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id1dgsB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily610 — Helix hairpin bin
Domain ID domain_id1dgsB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily70 —
Domain ID domain_id1dgsB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily30 — DNA ligase/mRNA capping enzyme
Domain ID domain_id1dgsB04
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id1dgsB05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id1dgsB06
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
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8. Citations (1)

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9. Files and Curves (10)