2CC3 - JenaLib

Title :   STRUCTURE OF AGROBACTERIUM TUMEFACIENS VIRB8 PROTEIN

Authors :   S. Bailey, D. Ward, R. Middleton, G. Grossmann, P. C. Zambryski

Date :   11 Jan 06 (Deposition) - 30 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B

Keywords :   Secretion System, Virb8, Agrobacterium, Type Iv Secretion System, Consurf (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Bailey, D. Ward, R. Middleton, J. G. Grossmann, P. C. Zambryski
Agrobacterium Tumefaciens Virb8 Structure Reveals Potential Protein-Protein Interactions Sites.
Proc. Natl. Acad. Sci. Usa V. 103 2582 2006
PubMed-ID: 16481621 | Reference-DOI: 10.1073/PNAS.0511216103

Compounds

Molecule 1 - PROTEIN VIRB8
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDW134
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28
	Fragment	:	PERIPLASMIC DOMAIN, RESIDUES 92-237
	Organism Scientific	:	AGROBACTERIUM TUMEFACIENS
	Organism Taxid	:	358
	Other Details	:	RESIDUES 88-91 ARE FROM TAG AND RESIDUES 92-231 CORRESPOND TO VIRB8
	Strain	:	PTIC58

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:119 , LEU A:123 , THR A:212 , HOH A:2010 , TRP B:103 , ARG B:107 , HOH B:2006	BINDING SITE FOR RESIDUE MPD A1232
2	AC2	SOFTWARE	SER B:101 , GLU B:104 , PHE B:127 , THR B:212 , ASN B:213 , LEU B:217	BINDING SITE FOR RESIDUE MPD B1232

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:144
 aligned with VIRB8_AGRFC | P17798 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:154
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227    
          VIRB8_AGRFC    78 GTVDSEVSVSRLPATQEEAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPMVRQNYQQFFNYPNPTSPQVILGKHGRLEVEHIASNDVTPGVQQIRYKRTLIVDGKMPMASTWTATVRYEKVTSLPGRLRLTNPGGLVVTSYQTSEDTVSN 231
               SCOP domains --------------d2cc3a1 A:92-231 Type IV secretion system protein VirB8                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----------..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhh...eeeeeeeeeeeeee..eeeeeeeeeeee.....eeeeeeeeeeeee....hhhhhh.....eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cc3 A  88 GP----------HMTQEEAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPMVRQNYQQFFNYPNPTSPQVILGKHGRLEVEHIASNDVTPGVQQIRYKRTLIVDGKMPMASTWTATVRYEKVTSLPGRLRLTNPGGLVVTSYQTSEDTVSN 231
                             |       -  |     97       107       117       127       137       147       157       167       177       187       197       207       217       227    
                             |         90                                                                                                                                             
                            89

Chain B from PDB  Type:PROTEIN  Length:144
 aligned with VIRB8_AGRFC | P17798 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:154
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227    
          VIRB8_AGRFC    78 GTVDSEVSVSRLPATQEEAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPMVRQNYQQFFNYPNPTSPQVILGKHGRLEVEHIASNDVTPGVQQIRYKRTLIVDGKMPMASTWTATVRYEKVTSLPGRLRLTNPGGLVVTSYQTSEDTVSN 231
               SCOP domains d2          cc3b_ B: automated matches                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----------..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhh...eeeeeeeeeeeeee..eeeeeeeeeeee.....eeeeeeeeeeeee....hhhhhh.....eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cc3 B  88 GP----------HMTQEEAVVNASLWEYVRLRESYDADTAQYAYDLVSNFSAPMVRQNYQQFFNYPNPTSPQVILGKHGRLEVEHIASNDVTPGVQQIRYKRTLIVDGKMPMASTWTATVRYEKVTSLPGRLRLTNPGGLVVTSYQTSEDTVSN 231
                             |       -  |     97       107       117       127       137       147       157       167       177       187       197       207       217       227    
                            89         90

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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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	Cis Peptide Bonds
		Tyr A:142 - Pro A:143	[ RasMol ]
		Tyr B:142 - Pro B:143	[ RasMol ]

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