3F0D | pdb_00003f0d

High resolution crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphatase synthase from Burkholderia pseudomallei

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
F	d3f0df_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	automated matches	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
E	d3f0de_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	automated matches	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
D	d3f0dd_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	automated matches	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
C	d3f0dc_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	automated matches	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
B	d3f0db_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	automated matches	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
A	d3f0da_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	automated matches	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	IpsF-like	8081212	3000926	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	IpsF-like	8081212	3000926	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	IpsF-like	8081212	3000926	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	IpsF-like	8081212	3000926	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	IpsF-like	8081212	3000926	SCOP2B (2022-06-29)
A	SCOP2 Family	IpsF-like	8081211	4003475	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	IpsF-like	8081212	3000926	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)
F	HSP70	e3f0dF1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: HSP70	ECOD (develop294)
E	HSP70	e3f0dE1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: HSP70	ECOD (develop294)
D	HSP70	e3f0dD1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: HSP70	ECOD (develop294)
C	HSP70	e3f0dC1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: HSP70	ECOD (develop294)
B	HSP70	e3f0dB1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: HSP70	ECOD (develop294)
A	PID	e3f0dA1	A: alpha bundles	X: Profilin-like	H: sensor domains	T: sensor domains	F: PID	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
E	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
D	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
C	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
A	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	cation binding ion binding binding metal ion binding small molecule binding phosphorus-oxygen lyase activity 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity lyase activity catalytic activity	isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway isopentenyl diphosphate biosynthetic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid biosynthetic process aldehyde metabolic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway isopentenyl diphosphate biosynthetic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid biosynthetic process aldehyde metabolic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process lipid metabolic process isoprenoid metabolic process isopentenyl diphosphate metabolic process terpenoid biosynthetic process terpenoid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036571	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR003526	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	Domain
A, B, C, D, E A, B, C, D, E, F	IPR020555	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, conserved site	Conserved Site

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.