5A0T - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CATALYSIS AND 5' END SENSING BY RIBONUCLEASE RNASE J OF THE METALLO-BETA-LACTAMASE FAMILY

Authors :   X. Y. Pei, P. Bralley, G. H. Jones, B. F. Luisi

Date :   22 Apr 15 (Deposition) - 19 Aug 15 (Release) - 07 Oct 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.28

Chains :   Asym. Unit : A,B,E,F
Biol. Unit 1: A,E  (1x)
Biol. Unit 2: B,F  (1x)

Keywords :   Hydrolase-Rna Complex, Ribonuclease, Rnase J, Endonuclease, Exonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Y. Pei, P. Bralley, G. H. Jones, B. F. Luisi
Linkage Of Catalysis And 5' End Recognition In Ribonuclease Rnase J
Nucleic Acids Res. V. 43 8066 2015
PubMed-ID: 26253740 | Reference-DOI: 10.1093/NAR/GKV732

Molecule 1 - RIBONUCLEASE J
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET19B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA2 PLYSS
	Expression System Vector Type	:	PLASMID
	Fragment	:	BETA-LACTMASE DOMAIN AND BETA-CASP DOMAIN, RESIDUES 1-561
	Organism Scientific	:	STREPTOMYCES COELICOLOR A3(2)
	Organism Taxid	:	100226

*Molecule 2 - 5'-R(CPGPCPCPUP)-3'**
	Chains	:	E, F
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	469008
	Strain	:	BL21(DE3)
	Variant	:	ROSETTA2 PLYSS

		1	2	3	4
Asymmetric Unit	:	A	B	E	F
Biological Unit 1 (1x)	:	A		E
Biological Unit 2 (1x)	:		B		F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
2	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN B:223 , ARG B:226 , GLN B:227 , ASN B:231	BINDING SITE FOR RESIDUE PEG B1453
2	AC2	SOFTWARE	ASN A:223 , ARG A:226 , GLN A:227 , ASN A:231	BINDING SITE FOR RESIDUE PEG A1456
3	AC3	SOFTWARE	ASP A:88 , HIS A:89 , ASP A:173 , HIS A:399 , ZN A:1458 , HOH A:2069 , G E:1	BINDING SITE FOR RESIDUE ZN A1457
4	AC4	SOFTWARE	HIS A:84 , HIS A:86 , HIS A:151 , ASP A:173 , ZN A:1457 , HOH A:2069 , G E:1	BINDING SITE FOR RESIDUE ZN A1458
5	AC5	SOFTWARE	ASP B:88 , HIS B:89 , ASP B:173 , HIS B:399 , ZN B:1455 , HOH B:2056 , G F:1	BINDING SITE FOR RESIDUE ZN B1454
6	AC6	SOFTWARE	HIS B:84 , HIS B:86 , HIS B:151 , ASP B:173 , ZN B:1454 , HOH B:2056 , G F:1	BINDING SITE FOR RESIDUE ZN B1455

(no "SS Bond" information available for 5A0T)

Asymmetric Unit

No.	Residues
1	Glu B:56	-	Gln B:57

(no "SAP(SNP)/Variant" information available for 5A0T)

(no "PROSITE Motif" information available for 5A0T)

(no "Exon" information available for 5A0T)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:454
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeee........eeeeee..eeeee...............eee..hhhhhhhhh.eeeeee...hhhhhhhhhhhhh......eeehhhhhhhhhhhhhhh.....eee.....eeee..eeeeeeee......eeeeeeee..eeeee................hhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh...........hhhhhhhhhhh.eeeee........hhhhhhhh...........eeee.......hhhhhhhhhhhhhhh..eee.............hhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh..hhhh.......eeeeee..eeeeeee.....eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a0t A   2 SHPHPELGRPPALPKGGLRVTPLGGLGEIGRNMTVFEYGGRLLIVDCGVLFPEEEQPGIDLILPDFTSIRDRLDDIEGIVLTHGHEDHIGGVPFLLREKPDIPLIGSKLTLALIEAKLQEHRIRPYTLEVAEGHRERVGPFDCEFVAVNHSIPDALAVAIRTPAGMVVHTGDFKMDQLPLDGRLTDLHAFARLSEEGIDLLLADSTNAEVPGFVPPERDISNVLRQVFANARKRIIVASFASHVHRIQQILDAAHEYGRRVAFVGRSMVRNMGIARDLGYLKVPPGLVVDVKTLDDLPDSEVVLVCTGSQGEPMAALSRMANRDHQIRIVNGDTVILASSLIPGNENAVYRVINGLTRWGANVVHKGNAKVHVSGHASAGELLYFYNICRPKNLMPVHGEWRHLRANAELGALTGVPHDRIVIAEDGVVVDLVEGKAKITGKVQAGYVYVDGLS 455
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451

Chain B from PDB  Type:PROTEIN  Length:451
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeee........eeeeee..eeeee...............eee..hhhhhhhhh.eeeee....hhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhh......eee.....eeee..eeeeeee........eeeeeee..eeeee................hhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.............hhhhhhhhh.eeeee........hhhhhhhh...........eeee.......hhhhhhhhhhhhhhh..eee.............hhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh..hhhh.......eeeeee..eeeeeee.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a0t B   2 SHPHPELGRPPALPKGGLRVTPLGGLGEIGRNMTVFEYGGRLLIVDCGVLFPEEEQPGIDLILPDFTSIRDRLDDIEGIVLTHGHEDHIGGVPFLLREKPDIPLIGSKLTLALIEAKLQEHRIRPYTLEVAEGHRERVGPFDCEFVAVNHSIPDALAVAIRTPAGMVVHTGDFKMDQLPLDGRLTDLHAFARLSEEGIDLLLADSTNAEVPGFVPPERDISNVLRQVFANARKRIIVASFASHVHRIQQILDAAHEYGRRVAFVGRSMVRNMGIARDLGYLKVPPGLVVDVKTLDDLPDSEVVLVCTGSQGEPMAALSRMANRDHQIRIVNGDTVILASSLIPGNENAVYRVINGLTRWGANVVHKGNAKVHVSGHASAGELLYFYNICRPKNLMPVHGEWRHLRANAELGALTGVPHDRIVIAEDGVVVDLVEGKAKITGKVQAGYVYVD 452
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451

Chain E from PDB  Type:DNA/RNA  Length:6
                                      
                 5a0t E   0 CGCCUC   5

Chain F from PDB  Type:DNA/RNA  Length:6
                                      
                 5a0t F   0 CGCCUC   5

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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5A0T)

(no "CATH Domain" information available for 5A0T)

(no "Pfam Domain" information available for 5A0T)

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	Cis Peptide Bonds
		Glu B:56 - Gln B:57	[ RasMol ]

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5a0v	CATALYSIS AND 5' END SENSING BY RIBONUCLEASE RNASE J OF THE METALLO-BETA-LACTAMASE FAMILY

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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Gene Ontology (11, 11)

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