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1lv5

Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA POLYMERASE I

Geobacillus stearothermophilus

UniProt P52026

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*GP*GP*AP*TP*CP*AP*GP*CP*GP*A)-3' × 1 5'-D(*AP*CP*GP*TP*CP*GP*CP*TP*GP*AP*TP*CP*CP*G)-3' × 1 MANGANESE (II) ION × 1 MAGNESIUM ION × 1 SULFATE ION × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 water × 3 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*GP*GP*AP*TP*CP*AP*GP*CP*GP*A)-3' × 1 5'-D(*AP*CP*GP*TP*CP*GP*CP*TP*GP*AP*TP*CP*CP*G)-3' × 1 MANGANESE (II) ION × 1 SULFATE ION × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1xwl

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1l3s 1l3t 1l3u 1l3v 1l5u 1lv5 1lv5 1njx 1njy 1njz 1nk0 1nk4

30 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DPO1_BACST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 8–580； UniProt 304–876 Author chain B； PDBConstruct 8–580； UniProt 304–876

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id1lv5
Deposition date deposition_date2002-05-24
Structure title titleCrystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP
Keywords keywordsDNA POLYMERASE I, DNA REPLICATION, KLENOW FRAGMENT, PROTEIN-DNA-DNTP COMPLEX, CLOSED CONFORMATION, TRANSFERASE-DNA COMPLEX; TRANSFERASE/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1lv5__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1lv5__assembly_2__model_1 | I(q)

10-2 10-1 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1lv5__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）26.73 Å
Rg (electron density)26.10 Å
Total Rg26.81 Å
Atom count5168
Residues604
Excluded volume90675 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1lv5__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1lv5__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1lv5a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.5 — DnaQ-like 3'-5' exonuclease
Domain ID domain_idd1lv5a2
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.8 — DNA/RNA polymerases
Superfamily Superfamily superfamilye.8.1 — DNA/RNA polymerases
Family Family familye.8.1.1 — DNA polymerase I
Domain ID domain_idd1lv5b1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.5 — DnaQ-like 3'-5' exonuclease
Domain ID domain_idd1lv5b2
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.8 — DNA/RNA polymerases
Superfamily Superfamily superfamilye.8.1 — DNA/RNA polymerases
Family Family familye.8.1.1 — DNA polymerase I

CATH v4.4 (8 domains)

Domain ID domain_id1lv5A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id1lv5A02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1060 — Taq DNA Polymerase; Chain T, domain 4
Homologous superfamily homologous superfamily10 — Taq DNA Polymerase; Chain T, domain 4
Domain ID domain_id1lv5A03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily370 —
Domain ID domain_id1lv5A04
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_id1lv5B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id1lv5B02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1060 — Taq DNA Polymerase; Chain T, domain 4
Homologous superfamily homologous superfamily10 — Taq DNA Polymerase; Chain T, domain 4
Domain ID domain_id1lv5B03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily370 —
Domain ID domain_id1lv5B04
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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7. Citations (3)