← Back to search
4hcc

The zinc ion bound form of crystal structure of E.coli ExoI-ssDNA complex

Method: X-RAY DIFFRACTION
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Exodeoxyribonuclease I

Escherichia coli

UniProt P04995

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Monomer Protein 1 DNA 1 ;DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') ; × 1 SULFATE ION × 3 ZINC ION × 1 ISOPROPYL ALCOHOL × 1 PHOSPHATE ION × 1 water × 2 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 1 ;DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') ; × 1 SULFATE ION × 4 ZINC ION × 1 ISOPROPYL ALCOHOL × 2 PHOSPHATE ION × 1 water × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1fxx 2qxf 3c95 3hl8 3hp9

5 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3c94 4hcb 4hcb 4hcc 4hcc 4jrp 4jrp 4jrp 4jrq 4jrq 4jrq 4js4

16 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name EX1_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–475； UniProt 1–475 Author chain B； PDBConstruct 1–475； UniProt 1–475

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id4hcc
Deposition date deposition_date2012-09-29
Structure title titleThe zinc ion bound form of crystal structure of E.coli ExoI-ssDNA complex
Keywords keywordsDnaQ family, Exonuclease C-terminal family, HYDROLASE-DNA complex; HYDROLASE/DNA
Experimental Method methodX-RAY DIFFRACTION
▼

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.

4hcc__assembly_2__model_1

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

Download this curve (.dat)

4hcc__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.

4hcc__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）24.83 Å
Rg (electron density)24.08 Å
Total Rg24.94 Å
Atom count4001
Residues473
Excluded volume70005 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4hcc__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4hcc__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

▼

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id4hccA01
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_id4hccA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1520 — PX Domain
Homologous superfamily homologous superfamily20 — Exonuclease ExoI, domain 2
Domain ID domain_id4hccA03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily70 — Exonuclease ExoI, domain 3
Domain ID domain_id4hccA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily1240 —
Domain ID domain_id4hccB01
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_id4hccB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1520 — PX Domain
Homologous superfamily homologous superfamily20 — Exonuclease ExoI, domain 2
Domain ID domain_id4hccB03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily70 — Exonuclease ExoI, domain 3
Domain ID domain_id4hccB04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily1240 —
▶

7. Citations (1)