3dd6

Crystal structure of Rph, an exoribonuclease from Bacillus anthracis at 1.7 A resolution

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

Ribonuclease PH

Bacillus anthracis

UniProt Q81LA9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 6 SULFATE ION × 30 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RNPH_BACAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 11–255; UniProt 1–245

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_id3dd6
Deposition date deposition_date2008-06-05
Structure title titleCrystal structure of Rph, an exoribonuclease from Bacillus anthracis at 1.7 A resolution
Keywords keywords;Exoribonuclease, Bacillus anthracis, tRNA maturation, RNase Ph., Transferase, Structural Genomics, Structural Proteomics in Europe 2, SPINE-2 ;; TRANSFERASE
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.

3dd6__assembly_1__model_1

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

Download this curve (.dat)

3dd6__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3dd6__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)35.69 Å
Rg (electron density)34.97 Å
Total Rg35.49 Å
Atom count11442
Residues1464
Excluded volume202740 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3dd6__assembly_1__model_1 hexameric (6) 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 (3)

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3dd6a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamilyd.14.1 — Ribosomal protein S5 domain 2-like
Family Family familyd.14.1.4 — Ribonuclease PH domain 1-like
Domain ID domain_idd3dd6a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.101 — Ribonuclease PH domain 2-like
Superfamily Superfamily superfamilyd.101.1 — Ribonuclease PH domain 2-like
Family Family familyd.101.1.1 — Ribonuclease PH domain 2-like

CATH v4.4 (1 domains)

Domain ID domain_id3dd6A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily70 — GHMP Kinase, N-terminal domain
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7. Citations (1)