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4ez9

Bacillus DNA Polymerase I Large Fragment Complex 2

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

DNA polymerase

Geobacillus kaustophilus

UniProt Q5KWC1

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 ;DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3') ; × 1 ;DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3') ; × 1 SULFATE ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 3 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 ;DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3') ; × 1 ;DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3') ; × 1 SULFATE ION × 1 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2hhq 2hhs 2hht 2hhu 2hhv 2hhw 2hhw 2hvh 2hvh 2hvi 2hvi 2hw3

52 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q5KWC1_GEOKA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–592； UniProt 287–878 Author chain D； PDBConstruct 1–592； UniProt 287–878

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_id4ez9
Deposition date deposition_date2012-05-02
Structure title titleBacillus DNA Polymerase I Large Fragment Complex 2
Keywords keywordsDNA Polymerase I, protein-DNA complex, closed form, 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.

4ez9__assembly_1__model_1

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

Download this curve (.dat)

4ez9__assembly_1__model_1 | I(q)

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

4ez9__assembly_1__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）27.03 Å
Rg (electron density)26.34 Å
Total Rg27.09 Å
Atom count9998
Residues597
Excluded volume89162 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4ez9__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4ez9__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 (7)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4ez9a1
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.55.3.0 — automated matches
Domain ID domain_idd4ez9a2
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_idd4ez9d1
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.55.3.0 — automated matches
Domain ID domain_idd4ez9d2
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_id4ez9A01
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_id4ez9A02
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_id4ez9A03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily370 —
Domain ID domain_id4ez9A04
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_id4ez9D01
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_id4ez9D02
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_id4ez9D03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily370 —
Domain ID domain_id4ez9D04
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 (2)