2R7D | pdb_00002r7d

Crystal structure of ribonuclease II family protein from Deinococcus radiodurans, triclinic crystal form. NorthEast Structural Genomics target DrR63

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d2r7dc1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Ribonuclease II family protein DR0020	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
C	d2r7dc2	All beta proteins	OB-fold	Nucleic acid-binding proteins	RNB domain-like	Ribonuclease II family protein DR0020	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
B	d2r7db1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Ribonuclease II family protein DR0020	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
B	d2r7db2	All beta proteins	OB-fold	Nucleic acid-binding proteins	RNB domain-like	Ribonuclease II family protein DR0020	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
A	d2r7da1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Ribonuclease II family protein DR0020	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
A	d2r7da2	All beta proteins	OB-fold	Nucleic acid-binding proteins	RNB domain-like	Ribonuclease II family protein DR0020	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
A	d2r7da3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Nucleic acid-binding proteins	8036612	3000135	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleic acid-binding proteins	8036613	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8036612	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8036613	3000135	SCOP2B (2022-06-29)
A	SCOP2 Family	Cold shock DNA-binding domain-like	8024233	4001909	SCOP2 (2022-06-29)
A	SCOP2 Family	RNB domain-like	8024234	4001753	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8036612	3000135	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8036613	3000135	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Stap_Strp_toxin	e2r7dC1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (v294.1)
C	Cpn10	e2r7dC2	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Cpn10	ECOD (v294.1)
B	Stap_Strp_toxin	e2r7dB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (v294.1)
B	Cpn10	e2r7dB2	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Cpn10	ECOD (v294.1)
A	RNase_II_C_S1	e2r7dA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: RNase_II_C_S1	ECOD (v294.1)
A	RNB	e2r7dA2	A: beta barrels	X: OB-fold	H: RNB domain-like	T: RNB domain-like	F: RNB	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF23161	Double HTH domain (HTH_RNase_II)	Double HTH domain	This entry represents a double HTH domain found in a set of largely bacterial ribonuclease II domain proteins [1].	Domain
A, B, C	PF00773	RNB domain (RNB)	RNB domain	This domain is the catalytic domain of ribonuclease II [1].	Domain
A, B, C	PF18614	RNase II-type exonuclease C-terminal S1 domain (RNase_II_C_S1)	RNase II-type exonuclease C-terminal S1 domain	This entry describes the C-terminal S1 domain found in type 2 RNase exonucleases. DrR63 proteins from Deinococcus radiodurans are an RNase II-type enzymes (DrII). Structure analysis of DrII indicates that it has an N-terminal HTH domain which interac ...	This entry describes the C-terminal S1 domain found in type 2 RNase exonucleases. DrR63 proteins from Deinococcus radiodurans are an RNase II-type enzymes (DrII). Structure analysis of DrII indicates that it has an N-terminal HTH domain which interacts with a flexible loop that connects two beta-strands from the conserved C-terminal S1 domain, forming a beta-wing fold common in wHTH domains [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Ribonuclease II family protein	RNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding nuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR056404	Ribonuclease II-like, double HTH domain	Domain
A, B, C	IPR001900	Ribonuclease II/R	Domain
A, B, C	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B, C	IPR050180	RNR Ribonuclease	Family
A, B, C	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C	IPR040596	RNase II-type exonuclease, C-terminal S1 domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.