2QJ6 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF A 14 REPEAT C-TERMINAL FRAGMENT OF TOXIN TCDA IN CLOSTRIDIUM DIFFICILE

Authors :   D. Albesa-Jove, T. Bertrand, L. Carpenter, J. Lim, K. A. Brown, N. Fairweather

Date :   06 Jul 07 (Deposition) - 15 Jul 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Clostridial Repetitive Oligo Peptides, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Albesa-Jove, T. Bertrand, L. Carpenter, J. Lim, E. Martinez, J. Zhang, I. Dmitri, K. A. Brown, N. Fairweather
Solution And Crystal Structures Of The Cell Binding Domain Of Toxins Tcda And Tcdb From Clostridium Difficile
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TOXIN A
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Vector Type	:	PLASMID
	Gene	:	TOXA, TCDA
	Organism Scientific	:	CLOSTRIDIUM DIFFICILE
	Strain	:	630

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2QJ6)

(no "Site" information available for 2QJ6)

(no "SS Bond" information available for 2QJ6)

Asymmetric Unit

No.	Residues
1	Ala A:50	-	Asn A:51
2	Leu A:184	-	His A:185
3	Ala B:50	-	Asn B:51
4	Leu B:184	-	His B:185

(no "SAP(SNP)/Variant" information available for 2QJ6)

Asymmetric Unit (1, 20)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CW	PS51170	Cell wall-binding repeat profile.	TOXA_CLODI	1810-1829 1851-1870 1872-1891 1923-1942 1943-1962 1964-1983 1985-2004 2006-2025 2057-2076 2077-2096 2098-2117 2119-2138 2140-2159 2191-2210 2211-2230 2232-2251 2252-2271 2305-2324 2325-2344 2346-2365 2367-2386 2388-2407 2439-2458 2459-2478 2480-2499 2501-2520 2572-2591 2552-2571 2593-2612 2663-2682 2643-2662 2685-2704	20	- - - - - - - - - - - - - - - - - - - - - - A:65-84 B:65-84 A:85-104 B:85-104 A:106-125 B:106-125 A:127-146 B:127-146 A:198-217 B:198-217 A:178-197 B:178-197 A:219-238 B:219-238 A:289-308 B:289-308 A:269-288 B:269-288 A:311-330 B:311-330

Biological Unit 1 (1, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CW	PS51170	Cell wall-binding repeat profile.	TOXA_CLODI	1810-1829 1851-1870 1872-1891 1923-1942 1943-1962 1964-1983 1985-2004 2006-2025 2057-2076 2077-2096 2098-2117 2119-2138 2140-2159 2191-2210 2211-2230 2232-2251 2252-2271 2305-2324 2325-2344 2346-2365 2367-2386 2388-2407 2439-2458 2459-2478 2480-2499 2501-2520 2572-2591 2552-2571 2593-2612 2663-2682 2643-2662 2685-2704	10	- - - - - - - - - - - - - - - - - - - - - - A:65-84 - A:85-104 - A:106-125 - A:127-146 - A:198-217 - A:178-197 - A:219-238 - A:289-308 - A:269-288 - A:311-330 -

Biological Unit 2 (1, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CW	PS51170	Cell wall-binding repeat profile.	TOXA_CLODI	1810-1829 1851-1870 1872-1891 1923-1942 1943-1962 1964-1983 1985-2004 2006-2025 2057-2076 2077-2096 2098-2117 2119-2138 2140-2159 2191-2210 2211-2230 2232-2251 2252-2271 2305-2324 2325-2344 2346-2365 2367-2386 2388-2407 2439-2458 2459-2478 2480-2499 2501-2520 2572-2591 2552-2571 2593-2612 2663-2682 2643-2662 2685-2704	10	- - - - - - - - - - - - - - - - - - - - - - - B:65-84 - B:85-104 - B:106-125 - B:127-146 - B:198-217 - B:178-197 - B:219-238 - B:289-308 - B:269-288 - B:311-330

(no "Exon" information available for 2QJ6)

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:317
 aligned with TOXA_CLODI | P16154 from UniProtKB/Swiss-Prot  Length:2710

    Alignment length:317
                                  2399      2409      2419      2429      2439      2449      2459      2469      2479      2489      2499      2509      2519      2529      2539      2549      2559      2569      2579      2589      2599      2609      2619      2629      2639      2649      2659      2669      2679      2689      2699       
          TOXA_CLODI   2390 GYTSINGKHFYFNTDGIMQIGVFKGPNGFEYFAPANTDANNIEGQAILYQNKFLTLNGKKYYFGSDSKAVTGLRTIDGKKYYFNTNTAVAVTGWQTINGKKYYFNTNTSIASTGYTIISGKHFYFNTDGIMQIGVFKGPDGFEYFAPANTDANNIEGQAIRYQNRFLYLHDNIYYFGNNSKAATGWVTIDGNRYYFEPNTAMGANGYKTIDNKNFYFRNGLPQIGVFKGSNGFEYFAPANTDANNIEGQAIRYQNRFLHLLGKIYYFGNNSKAVTGWQTINGKVYYFMPDTAMAAAGGLFEIDGVIYFFGVDGVKAP 2706
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eeee..eeeee.........eeee..eeee....................eeeee..eeeee.........--hhhhh---...........eeee..eeee..........eeeee..eeeee.........eeee..eeee....................eeeee..eeeee........eeeee..eeeee.........eeeee..eeeee........eeee..eeee....................eeeee..eeeee........eeeee..eeeee..........eeeee..eeeee........ Sec.struct. author (1)
     Sec.struct. author (2) ------------------------------------------------------------------------eeee--eeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CW  PDB: -        -------------------------------CW  PDB: A:65-84    CW  PDB: A:85-104   -CW  PDB: A:106-125  -CW  PDB: A:127-146  -------------------------------CW  PDB: A:178-197  CW  PDB: A:198-217  -CW  PDB: A:219-238  ------------------------------CW  PDB: A:269-288  CW  PDB: A:289-308  --CW  PDB: A:311-330  -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qj6 A   16 GYTSINGKHFYFNTDGIMQIGVFKGPNGFEYFAPANTDANNIEGQAILYQNKFLTLNGKKYYFGSDSKAVTGLRTIDGKKYYFNTNTAVAVTGWQTINGKKYYFNTNTSIASTGYTIISGKHFYFNTDGIMQIGVFKGPDGFEYFAPANTDANNIEGQAIRYQNRFLYLHDNIYYFGNNSKAATGWVTIDGNRYYFEPNTAMGANGYKTIDNKNFYFRNGLPQIGVFKGSNGFEYFAPANTDANNIEGQAIRYQNRFLHLLGKIYYFGNNSKAVTGWQTINGKVYYFMPDTAMAAAGGLFEIDGVIYFFGVDGVKAP  332
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325

Chain B from PDB  Type:PROTEIN  Length:317
 aligned with TOXA_CLODI | P16154 from UniProtKB/Swiss-Prot  Length:2710

    Alignment length:317
                                  2399      2409      2419      2429      2439      2449      2459      2469      2479      2489      2499      2509      2519      2529      2539      2549      2559      2569      2579      2589      2599      2609      2619      2629      2639      2649      2659      2669      2679      2689      2699       
          TOXA_CLODI   2390 GYTSINGKHFYFNTDGIMQIGVFKGPNGFEYFAPANTDANNIEGQAILYQNKFLTLNGKKYYFGSDSKAVTGLRTIDGKKYYFNTNTAVAVTGWQTINGKKYYFNTNTSIASTGYTIISGKHFYFNTDGIMQIGVFKGPDGFEYFAPANTDANNIEGQAIRYQNRFLYLHDNIYYFGNNSKAATGWVTIDGNRYYFEPNTAMGANGYKTIDNKNFYFRNGLPQIGVFKGSNGFEYFAPANTDANNIEGQAIRYQNRFLHLLGKIYYFGNNSKAVTGWQTINGKVYYFMPDTAMAAAGGLFEIDGVIYFFGVDGVKAP 2706
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2qj--------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2qj--------------------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2qj--------------------------- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2qj--------------------------- Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2qj--------------------------- Pfam domains (5)
           Pfam domains (6) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2qj--------------------------- Pfam domains (6)
     Sec.struct. author (1) .eeee..eeeee.........eeee..eeee....................eeeee..eeeee.........--hhhhh---...........eeee..eeee..........eeeee..eeeee.........eeee..eeee....................eeeee..eeeee........eeeee..eeeee.........eeeee..eeeee........eeee..eeee....................eeeee..eeeee........eeeee..eeeee..........eeeee..eeeee........ Sec.struct. author (1)
     Sec.struct. author (2) ------------------------------------------------------------------------eeee--eeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CW  PDB: -        -------------------------------CW  PDB: B:65-84    CW  PDB: B:85-104   -CW  PDB: B:106-125  -CW  PDB: B:127-146  -------------------------------CW  PDB: B:178-197  CW  PDB: B:198-217  -CW  PDB: B:219-238  ------------------------------CW  PDB: B:269-288  CW  PDB: B:289-308  --CW  PDB: B:311-330  -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qj6 B   16 GYTSINGKHFYFNTDGIMQIGVFKGPNGFEYFAPANTDANNIEGQAILYQNKFLTLNGKKYYFGSDSKAVTGLRTIDGKKYYFNTNTAVAVTGWQTINGKKYYFNTNTSIASTGYTIISGKHFYFNTDGIMQIGVFKGPDGFEYFAPANTDANNIEGQAIRYQNRFLYLHDNIYYFGNNSKAATGWVTIDGNRYYFEPNTAMGANGYKTIDNKNFYFRNGLPQIGVFKGSNGFEYFAPANTDANNIEGQAIRYQNRFLHLLGKIYYFGNNSKAVTGWQTINGKVYYFMPDTAMAAAGGLFEIDGVIYFFGVDGVKAP  332
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325

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 '\|'

(no "SCOP Domain" information available for 2QJ6)

(no "CATH Domain" information available for 2QJ6)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: CW_binding_1] (12)

Family: CW_binding_1 (12)

Clostridium difficile (1)

1a	CW_binding_1-2qj6B01	B:290-305
1b	CW_binding_1-2qj6B02	B:290-305
1c	CW_binding_1-2qj6B03	B:290-305
1d	CW_binding_1-2qj6B04	B:290-305
1e	CW_binding_1-2qj6B05	B:290-305
1f	CW_binding_1-2qj6B06	B:290-305

Asymmetric Unit(hide GO term definitions)

Chain A,B (TOXA_CLODI | P16154)

molecular function
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2qj6)

	Sites
(no "Sites" information available for 2qj6)

	Cis Peptide Bonds
		Ala A:50 - Asn A:51	[ RasMol ]
		Ala B:50 - Asn B:51	[ RasMol ]
		Leu A:184 - His A:185	[ RasMol ]
		Leu B:184 - His B:185	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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	2qj6
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	TOXA_CLODI \| P16154	:	2f6e 2g7c 3ho6 4dmv 4dmw 4r04 5uqk 5uql

(no "Related Entries Specified in the PDB File" available for 2QJ6)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 20)

Exons (0, 0)

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