4OWL - JenaLib

Title :   CRYSTAL STRUCTURE OF THE VIBRIO VULNIFICUS HEMOLYSIN/CYTOLYSIN BETA-TREFOIL LECTIN WITH N-ACETYL-D-LACTOSAMINE BOUND

Authors :   K. Kaus, R. Olson

Date :   02 Feb 14 (Deposition) - 28 May 14 (Release) - 07 Oct 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D,E,F,G
Biol. Unit 1: A,B,C,D,E,F,G  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)
Biol. Unit 4: C  (1x)
Biol. Unit 5: D  (1x)
Biol. Unit 6: E  (1x)
Biol. Unit 7: F  (1x)
Biol. Unit 8: G  (1x)

Keywords :   Lectin, Pore-Forming Toxin, Beta-Trefoil, R-Type Lectin, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Kaus, J. W. Lary, J. L. Cole, R. Olson
Glycan Specificity Of The Vibrio Vulnificus Hemolysin Lecti Outlines Evolutionary History Of Membrane Targeting By A Toxin Family.
J. Mol. Biol. V. 426 2800 2014
PubMed-ID: 24862282 | Reference-DOI: 10.1016/J.JMB.2014.05.021

Compounds

Molecule 1 - CYTOLYSIN
	Chains	:	A, B, C, D, E, F, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNGFP-BC
	Expression System Strain	:	NEB SHUFFLE T7 EXPRESS
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 338-471
	Gene	:	VV2_0404,VVHA
	Organism Scientific	:	VIBRIO VULNIFICUS
	Organism Taxid	:	216895
	Strain	:	CMCP6

Structural Features

Chains, Units

		1	2	3	4	5	6	7
Asymmetric Unit	:	A	B	C	D	E	F	G
Biological Unit 1 (1x)	:	A	B	C	D	E	F	G
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B
Biological Unit 4 (1x)	:			C
Biological Unit 5 (1x)	:				D
Biological Unit 6 (1x)	:					E
Biological Unit 7 (1x)	:						F
Biological Unit 8 (1x)	:							G

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 16)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	GAL	6	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	5	Ligand/Ion	GLYCEROL
3	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (3, 16)

No.	Name	Count	Type	Full Name
1	GAL	6	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	5	Ligand/Ion	GLYCEROL
3	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GAL	-1	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	1	Ligand/Ion	GLYCEROL
3	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	-1	Ligand/Ion	GLYCEROL
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 4 (3, 3)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	1	Ligand/Ion	GLYCEROL
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 5 (3, 3)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	1	Ligand/Ion	GLYCEROL
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 6 (3, 3)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	1	Ligand/Ion	GLYCEROL
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 7 (3, 3)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	1	Ligand/Ion	GLYCEROL
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 8 (1, 1)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	-1	Ligand/Ion	GLYCEROL
3	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Sites (11, 11)

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:353 , VAL A:354 , TYR A:355 , LYS A:361 , TRP A:371 , HIS A:374 , ASN A:378	binding site for residue GOL A 501
02	AC2	SOFTWARE	TRP C:422 , GLY C:424 , PRO C:464 , HOH C:616	binding site for residue GOL C 503
03	AC3	SOFTWARE	TRP D:422 , GLY D:424 , PRO D:464 , HOH D:652	binding site for residue GOL D 503
04	AC4	SOFTWARE	TRP E:422 , GLY E:424 , PRO E:464 , HOH E:650	binding site for residue GOL E 503
05	AC5	SOFTWARE	TRP F:422 , GLY F:424 , HOH F:663	binding site for residue GOL F 503
06	AC6	SOFTWARE	ASP G:353 , VAL G:354 , TRP G:371 , HIS G:374 , ASN G:378	binding site for residue GAL G 501
07	AC7	SOFTWARE	ASP B:353 , VAL B:354 , TYR B:355 , ASN B:358 , GLY B:359 , TRP B:371 , HIS B:374 , ASN B:378	binding site for Poly-Saccharide residues GAL B 501 through NAG B 502
08	AC8	SOFTWARE	ASP C:353 , VAL C:354 , TYR C:355 , ASN C:358 , GLY C:359 , LYS C:361 , TRP C:371 , HIS C:374 , ASN C:378 , HOH C:605	binding site for Poly-Saccharide residues GAL C 501 through NAG C 502
09	AC9	SOFTWARE	ASP D:353 , VAL D:354 , TYR D:355 , ASN D:358 , GLY D:359 , LYS D:361 , TRP D:371 , HIS D:374 , ASN D:378 , HOH D:698 , HOH D:701 , HOH D:702 , HOH D:719 , HOH D:727 , HOH D:736 , HOH D:742	binding site for Poly-Saccharide residues GAL D 501 through NAG D 502
10	AD1	SOFTWARE	ASP E:353 , VAL E:354 , TYR E:355 , GLY E:359 , LYS E:361 , TRP E:371 , HIS E:374 , ASN E:378 , HOH E:612 , HOH E:731 , HOH E:741	binding site for Poly-Saccharide residues GAL E 501 through NAG E 502
11	AD2	SOFTWARE	VAL C:444 , ASP F:353 , VAL F:354 , TYR F:355 , ASN F:358 , GLY F:359 , LYS F:361 , TRP F:371 , HIS F:374 , ASN F:378 , HOH F:612 , HOH F:682 , HOH F:714	binding site for Poly-Saccharide residues GAL F 501 through NAG F 502

SS Bonds (14, 14)

Asymmetric Unit

No.	Residues
1	A:351	-	A:373
2	A:398	-	A:412
3	B:351	-	B:373
4	B:398	-	B:412
5	C:351	-	C:373
6	C:398	-	C:412
7	D:351	-	D:373
8	D:398	-	D:412
9	E:351	-	E:373
10	E:398	-	E:412
11	F:351	-	F:373
12	F:398	-	F:412
13	G:351	-	G:373
14	G:398	-	G:412

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee......eeeeee..........eeeee....hhh.eeee.....eee......eeee.....eeee....hhhh.eeee..eeee.........eeeee.....eeeee.hhh....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4owl A 337 MAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDKEERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGNNTRYLLNIVGGRNVQVTPENEANQARWKPTLQQ 468
                                   346       356       366       376       386       396       406       416       426       436       446       456       466

Chain B from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......eeeeee..........eeeee....hhhh.eee.....eee......eeee.....eeee....hhhh.eeee..eeee.........eeeeeee..eeeeee.hhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4owl B 337 MAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDKEERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGNNTRYLLNIVGGRNVQVTPENEANQARWKPTLQ 467
                                   346       356       366       376       386       396       406       416       426       436       446       456       466

Chain C from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......eeeeee.........eeeeee....hhhh.eee.....eee......eeee.....eeee....hhhh.eeee..eeee.........eeeeeee..eeeeee.hhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4owl C 337 MAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDKEERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGNNTRYLLNIVGGRNVQVTPENEANQARWKPTLQ 467
                                   346       356       366       376       386       396       406       416       426       436       446       456       466

Chain D from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......eeeeee.........eeeeee....hhhh.eee.....eee......eeee.....eeee....hhhh.eeee..eeee.........eeeeeee..eeeeee.hhh....eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4owl D 335 SAMAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDKEERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGNNTRYLLNIVGGRNVQVTPENEANQARWKPTLQQVKL 471
                                   344       354       364       374       384       394       404       414       424       434       444       454       464

Chain E from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee......eeeeee.........eeeeee....hhhh.eee.....eee......eeee.....eeee....hhhh.eeee..eeee.........eeeeeee..eeeeee.hhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4owl E 336 AMAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDKEERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGNNTRYLLNIVGGRNVQVTPENEANQARWKPTLQ 467
                                   345       355       365       375       385       395       405       415       425       435       445       455       465

Chain F from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......eeeeee..........eeeee....hhhh.eee.....eee......eeee.....eeee....hhhh.eeee..eeee.........eeeeeee..eeeeee.hhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4owl F 337 MAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDKEERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGNNTRYLLNIVGGRNVQVTPENEANQARWKPTLQ 467
                                   346       356       366       376       386       396       406       416       426       436       446       456       466

Chain G from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......eeeeee.........eeeeee....hhh.eeee.....eee......eeee.....eeee....hhhh.eeee..eeee.........eeeeeee..eeeeee.hhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4owl G 337 MAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDKEERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGNNTRYLLNIVGGRNVQVTPENEANQARWKPTLQ 467
                                   346       356       366       376       386       396       406       416       426       436       446       456       466

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

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Gene Ontology (5, 5)

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