ISDA: 9YK3

Deposition Date 2025-10-06

Release Date 2026-03-18

Last Version Date 2026-04-01

Entry Detail

PDB ID:

9YK3

Keywords:

HYDROLASE/RNA/DNA

Title:

Room-temperature X-ray structure of D132N Bacillus halodurans RNase H1 in complex with complementary RNA/DNA duplex

Biological Source:

Source Organism(s):

Halalkalibacterium halodurans (Taxon ID: 86665)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.90 Å

R-Value Free:

0.23

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

C 1 2 1

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribonuclease H
Gene (Uniprot):rnhA
Mutagens:D132N
Chain IDs:A
Chain Length:139
Number of Molecules:1
Biological Source:Halalkalibacterium halodurans

UniProt ID:Q9KEI9 EC:3.1.13.2

Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*CP*GP*AP*CP*AP*U)-
Chain IDs:B
Chain Length:6
Number of Molecules:1
Biological Source:Halalkalibacterium halodurans

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*TP*GP*TP*CP*G)-
Chain IDs:C
Chain Length:6
Number of Molecules:1
Biological Source:Halalkalibacterium halodurans

Ligand Molecules

Primary Citation

Structural insights into RNase H catalytic mechanism from room-temperature X-ray and neutron crystallography of apo- and RNA/DNA hybrid-bound enzyme.

Gerlits, O, Collins, A, Kovalevsky, A, Adams, P.D, Mustyakimov, M, Afonine, P.V, Langan, P, Gerlits, O, Collins, A, Kovalevsky, A.Show

Curr Res Struct Biol 11 100188 100188 (2026)

PMID: 41853683 DOI: 10.1016/j.crstbi.2026.100188

Primary Citation of related structures

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