1SVD | pdb_00001svd

The structure of Halothiobacillus neapolitanus RuBisCo

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)
B [auth M]	d1svdm1	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	Ribulose 1,5-bisphosphate carboxylase-oxygenase	(Halothiobacillus neapolitanus ) [TaxId: 927 ],	SCOPe (2.08)
A	d1svda1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	Ribulose 1,5-bisphosphate carboxylase-oxygenase	(Halothiobacillus neapolitanus ) [TaxId: 927 ],	SCOPe (2.08)
A	d1svda2	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	Ribulose 1,5-bisphosphate carboxylase-oxygenase	Ribulose 1,5-bisphosphate carboxylase-oxygenase	(Halothiobacillus neapolitanus ) [TaxId: 927 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth M]	SCOP2 Family	RuBisCO, small subunit	8020022	4001455	SCOP2 (2022-06-29)
B [auth M]	SCOP2 Superfamily	RuBisCO, small subunit	8032402	3001622	SCOP2 (2022-06-29)
A	SCOP2 Family	RuBisCo, large subunit, C-terminal domain	8020018	4003287	SCOP2 (2022-06-29)
A	SCOP2 Family	Ribulose 1, 5-bisphosphate carboxylase-oxygenase	8020019	4001311	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RuBisCo, C-terminal domain	8032398	3000552	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8032399	3001258	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)
B [auth M]	RuBisCO_small	e1svdM1	A: a+b two layers	X: Reverse ferredoxin	H: RuBisCO, small subunit	T: RuBisCO, small subunit	F: RuBisCO_small	ECOD (v294.1)
A	RNase_P_Rpp14	e1svdA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)
A	DUF711	e1svdA2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth M]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
A	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
A	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth M]	PF00101	Ribulose bisphosphate carboxylase, small chain (RuBisCO_small)	Ribulose bisphosphate carboxylase, small chain		Domain
A	PF02788	Ribulose bisphosphate carboxylase large chain, N-terminal domain (RuBisCO_large_N)	Ribulose bisphosphate carboxylase large chain, N-terminal domain	The N-terminal domain of RuBisCO large chain adopts a ferredoxin-like fold.	Domain
A	PF00016	Ribulose bisphosphate carboxylase large chain, catalytic domain (RuBisCO_large)	Ribulose bisphosphate carboxylase large chain, catalytic domain	The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth M]	Ribulose bisphosphate carboxylase small chain	ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process cellular process carbon fixation	intracellular organelle bacterial microcompartment cellular anatomical structure intracellular anatomical structure organelle carboxysome membraneless organelle intracellular membraneless organelle
A	ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding monooxygenase activity oxidoreductase activity catalytic activity ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity carbon-carbon lyase activity	carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process cellular process carbon fixation	intracellular organelle bacterial microcompartment cellular anatomical structure intracellular anatomical structure organelle carboxysome membraneless organelle intracellular membraneless organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth M]	IPR036385	Ribulose bisphosphate carboxylase, small subunit superfamily	Homologous Superfamily
B [auth M]	IPR024681	Ribulose bisphosphate carboxylase, small subunit	Family
B [auth M]	IPR000894	Ribulose bisphosphate carboxylase small subunit, domain	Domain
A	IPR020888	Ribulose bisphosphate carboxylase large subunit, type I	Family
A	IPR036376	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily	Homologous Superfamily
A	IPR020878	Ribulose bisphosphate carboxylase, large chain, active site	Active Site
A	IPR000685	Ribulose bisphosphate carboxylase, large subunit, C-terminal	Domain
A	IPR033966	RuBisCO	Family
A	IPR036422	RuBisCO large subunit, N-terminal domain superfamily	Homologous Superfamily
A	IPR017443	Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal	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.