4RVE | PDE003 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS

Authors :   F. K. Winkler, D. W. Banner, C. Oefner, D. Tsernoglou, R. S. Brown, S. P. Heathman, R. K. Bryan, P. D. Martin, K. Petratos, K. S. Wilso

Date :   18 Feb 93 (Deposition) - 15 Apr 93 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Protein-Dna Complex, Double Helix, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. K. Winkler, D. W. Banner, C. Oefner, D. Tsernoglou, R. S. Brown, S. P. Heathman, R. K. Bryan, P. D. Martin, K. Petratos, K. S. Wilson
The Crystal Structure Of Ecorv Endonuclease And Of Its Complexes With Cognate And Non-Cognate Dna Fragments.
Embo J. V. 12 1781 1993
PubMed-ID: 8491171
(for further references see the PDB file header)

*Molecule 1 - DNA (5'-D(GPGPGPAPTPAPTPCPCPC)-3')*
	Chains	:	D, E, F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - PROTEIN (ECO RV (E.C.3.1.21.4))
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B		D	E
Biological Unit 2 (2x)	:			C			F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4RVE)

(no "Site" information available for 4RVE)

(no "SS Bond" information available for 4RVE)

Asymmetric Unit

No.	Residues
1	Tyr A:72	-	Pro A:73
2	Tyr B:72	-	Pro B:73
3	Tyr C:72	-	Pro C:73

(no "SAP(SNP)/Variant" information available for 4RVE)

(no "PROSITE Motif" information available for 4RVE)

(no "Exon" information available for 4RVE)

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:240
                                                                                                                                                                                                                                                                                
               SCOP domains d4rvea_ A: Restriction endonuclease EcoRV                                                                                                                                                                                                        SCOP domains
               CATH domains 4rveA00 A:2-241  [code=3.40.600.10, no name defined]                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh.........eeee....eee...hhhhhhhhhhhhhhhhhhhhhhh...eee..........eeeee..eeeeeeeeeeeeeee.........eeee..hhhhhh......hhh.eeeeeeeeeeeee...........hhhhhhh....eeeeeeeeeehhhheeeeeee....eeee...hhhhhhhh.....hhhhhhhhhhhh..hhhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rve A   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIY 241
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain B from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains d4rveb_ B: Restriction endonuclease EcoRV                                                                                                                                                                                                        SCOP domains
               CATH domains 4rveB00 B:2-241  [code=3.40.600.10, no name defined]                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh.......eeeee.....eee...hhhhhhhhhhhhhhhhhhhhhhh...ee.............ee..........eeeeeeee.........eeee..hhhhhh......hhhh....eeeeeeeee.............hhhhh....eeeeeeeeeehhhhh..........eee....hhhhhhh......hhhhhhhhhhh...hhhhhhh...hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rve B   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIY 241
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain C from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains d4rvec_ C: Restriction endonuclease EcoRV                                                                                                                                                                                                        SCOP domains
               CATH domains 4rveC00 C:2-241  [code=3.40.600.10, no name defined]                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh.........eee.....eee...hhhhhhhhhhhhhhhhhhhhhhhh..eee..........eeee.......eeeeeeeeeee.........eeee..hhhhhh......hhh.eeeeeeeeeeeee......................eeeeeeeeeehhhheeeee......eeee...hhhhhhhh.....hhhhhhhhhhh...hhhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rve C   2 SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIY 241
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain D from PDB  Type:DNA  Length:10
                                          
                 4rve D   1 GGGATATCCC  10
                                    10

Chain E from PDB  Type:DNA  Length:10
                                          
                 4rve E   1 GGGATATCCC  10
                                    10

Chain F from PDB  Type:DNA  Length:10
                                          
                 4rve F   1 GGGATATCCC  10
                                    10

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Restriction endonuclease-like (209)

Superfamily: Restriction endonuclease-like (170)

Family: Restriction endonuclease EcoRV (30)

Protein domain: Restriction endonuclease EcoRV (30)

Escherichia coli [TaxId: 562] (30)

1a	d4rvea_	A:
1b	d4rveb_	B:
1c	d4rvec_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: ECO RV Endonuclease; Chain A (56)

Homologous Superfamily: [code=3.40.600.10, no name defined] (55)

[unclassified] (40)

1a	4rveA00	A:2-241
1b	4rveB00	B:2-241
1c	4rveC00	C:2-241

(no "Pfam Domain" information available for 4RVE)

Asymmetric Unit(hide GO term definitions)

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	Cis Peptide Bonds
		Tyr A:72 - Pro A:73	[ RasMol ]
		Tyr B:72 - Pro B:73	[ RasMol ]
		Tyr C:72 - Pro C:73	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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