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3fmt

Crystal structure of SeqA bound to DNA

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

Protein seqA

Escherichia coli

UniProt P0AFY8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 2 DNA 2 5'-D(*GP*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*CP*GP*GP*GP*(6MA)P*TP*CP*CP*TP*TP*A)-3' × 1 5'-D(*TP*CP*TP*AP*AP*GP*GP*AP*TP*CP*CP*CP*GP*CP*CP*GP*AP*TP*CP*GP*AP*C)-3' × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 4 Consistent with all polymers
2 Protein–DNA Homooligomer Protein 2 DNA 2 5'-D(*GP*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*CP*GP*GP*GP*(6MA)P*TP*CP*CP*TP*TP*A)-3' × 1 5'-D(*TP*CP*TP*AP*AP*GP*GP*AP*TP*CP*CP*CP*GP*CP*CP*GP*AP*TP*CP*GP*AP*C)-3' × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 4 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
3fmt 3fmt

2 assemblies

View Construct and Data Evidence
UniProt name SEQA_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–40； UniProt 1–40 Author chain A； PDBConstruct 41–162； UniProt 60–181 Author chain B； PDBConstruct 1–40； UniProt 1–40 Author chain B； PDBConstruct 41–162； UniProt 60–181 Author chain E； PDBConstruct 1–40； UniProt 1–40 Author chain E； PDBConstruct 41–162； UniProt 60–181 Author chain F； PDBConstruct 1–40； UniProt 1–40 Author chain F； PDBConstruct 41–162； UniProt 60–181

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_id3fmt
Deposition date deposition_date2008-12-22
Structure title titleCrystal structure of SeqA bound to DNA
Keywords keywords;protein-DNA complex, hemimethylated GATC, DNA replication, sequestration, DNA replication inhibitor, DNA-binding, REPLICATION INHIBITOR-DNA COMPLEX ;; REPLICATION INHIBITOR/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.

3fmt__assembly_2__model_1

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

Download this curve (.dat)

3fmt__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.

3fmt__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）25.45 Å
Rg (electron density)24.50 Å
Total Rg25.30 Å
Atom count3458
Residues360
Excluded volume59077 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3fmt__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3fmt__assembly_2__model_1 tetrameric （4） 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 (5)

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id3fmtA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily10 — Met repressor-like
Domain ID domain_id3fmtA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1380 — Replication modulator SeqA, C-terminal DNA-binding domain
Homologous superfamily homologous superfamily10 — Replication modulator SeqA, C-terminal DNA-binding domain
Domain ID domain_id3fmtB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1380 — Replication modulator SeqA, C-terminal DNA-binding domain
Homologous superfamily homologous superfamily10 — Replication modulator SeqA, C-terminal DNA-binding domain
Domain ID domain_id3fmtE01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily10 — Met repressor-like
Domain ID domain_id3fmtE02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1380 — Replication modulator SeqA, C-terminal DNA-binding domain
Homologous superfamily homologous superfamily10 — Replication modulator SeqA, C-terminal DNA-binding domain
Domain ID domain_id3fmtF00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1380 — Replication modulator SeqA, C-terminal DNA-binding domain
Homologous superfamily homologous superfamily10 — Replication modulator SeqA, C-terminal DNA-binding domain
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7. Citations (2)