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3kgd

Crystal structure of E. coli RNA 3' cyclase

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

;RNA 3'-terminal phosphate cyclase ;

Escherichia coli

UniProt P46849

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 ADENOSINE MONOPHOSPHATE × 1 GLYCEROL × 2 SODIUM ION × 1 SULFATE ION × 3 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 ADENOSINE MONOPHOSPHATE × 1 GLYCEROL × 2 SODIUM ION × 1 SULFATE ION × 2 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 ADENOSINE MONOPHOSPHATE × 1 GLYCEROL × 3 SODIUM ION × 2 SULFATE ION × 2 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 ADENOSINE MONOPHOSPHATE × 1 GLYCEROL × 3 SODIUM ION × 1 SULFATE ION × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3kgd 3kgd 3kgd 3kgd 3tut 3tux 3tv1 3tv1 3tw3

9 assemblies

Homodimer
1qmh 1qmi 1qmi

3 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name RTCA_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 21–358； UniProt 1–338 Author chain B； PDBConstruct 21–358； UniProt 1–338 Author chain C； PDBConstruct 21–358； UniProt 1–338 Author chain D； PDBConstruct 21–358； UniProt 1–338

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_id3kgd
Deposition date deposition_date2009-10-28
Structure title titleCrystal structure of E. coli RNA 3' cyclase
Keywords keywords;Cyclase, RNA processing, 3' modifying enzymes, adenylate, phosphoramidate, LIGASE ;; LIGASE
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.

3kgd__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3kgd__assembly_3__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3kgd__assembly_3__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）20.84 Å
Rg (electron density)19.72 Å
Total Rg20.64 Å
Atom count2569
Residues338
Excluded volume45741 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3kgd__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3kgd__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3kgd__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3kgd__assembly_4__model_1 monomeric （1） 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 (6)

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id3kgdA01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily20 — RNA 3'-terminal phosphate cyclase domain
Domain ID domain_id3kgdA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily20 — RNA 3'-terminal phosphate cyclase, insert domain
Domain ID domain_id3kgdB01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily20 — RNA 3'-terminal phosphate cyclase domain
Domain ID domain_id3kgdB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily20 — RNA 3'-terminal phosphate cyclase, insert domain
Domain ID domain_id3kgdC01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily20 — RNA 3'-terminal phosphate cyclase domain
Domain ID domain_id3kgdC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily20 — RNA 3'-terminal phosphate cyclase, insert domain
Domain ID domain_id3kgdD01
Class class3 — Alpha Beta
Architecture architecture65 — Alpha-beta prism
Topology topology10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily20 — RNA 3'-terminal phosphate cyclase domain
Domain ID domain_id3kgdD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily20 — RNA 3'-terminal phosphate cyclase, insert domain
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7. Citations (1)