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3i8d

The Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography

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

Ribonuclease H

Bacillus halodurans

UniProt Q9KEI9

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(*CP*GP*CP*GP*AP*AP*TP*(DFT)P*CP*GP*CP*G)-3' × 2 GLYCEROL × 2 water × 4 Consistent with all polymers
2 Protein–DNA Homooligomer Protein 2 DNA 2 5'-D(*CP*GP*CP*GP*AP*AP*TP*(DFT)P*CP*GP*CP*G)-3' × 2 GLYCEROL × 6 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1zbf 8sv3 8sv3 9yjl 9yjm

5 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1zbi 2g8f 2g8h 2g8i 2g8k 2g8u 2g8v 2g8w 2r7y 3d0p 3d0p 3ey1

104 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RNH1_BACHD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–132； UniProt 62–193 Author chain C； PDBConstruct 1–132； UniProt 62–193

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_id3i8d
Deposition date deposition_date2009-07-09
Structure title titleThe Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography
Keywords keywords;RNase-H, RNase-H DNA-complex, 2, 4-Difluorotoluene, thymine isostere, hydrophobic base, Endonuclease, Hydrolase, Magnesium, Manganese, Metal-binding, Nuclease, HYDROLASE-DNA COMPLEX ;; HYDROLASE/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.

3i8d__assembly_1__model_1

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

Download this curve (.dat)

3i8d__assembly_1__model_1 | I(q)

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

3i8d__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）24.11 Å
Rg (electron density)24.41 Å
Total Rg24.98 Å
Atom count2652
Residues286
Excluded volume45803 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3i8d__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3i8d__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 (4)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3i8da_
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.55.3.1 — Ribonuclease H
Domain ID domain_idd3i8dc_
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.55.3.1 — Ribonuclease H

CATH v4.4 (2 domains)

Domain ID domain_id3i8dA00
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_id3i8dC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
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7. Citations (1)