1JYA - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SYCE

Authors :   P. Ghosh, S. Birtalan

Date :   11 Sep 01 (Deposition) - 31 Oct 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.74

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

Keywords :   Specific Chaperone, Type Iii Secretion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Birtalan, P. Ghosh
Structure Of The Yersinia Type Iii Secretory System Chaperone Syce.
Nat. Struct. Biol. V. 8 974 2001
PubMed-ID: 11685245 | Reference-DOI: 10.1038/NSB1101-974
(for further references see the PDB file header)

Molecule 1 - YOPE REGULATOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	SYCE
	Organism Scientific	:	YERSINIA PSEUDOTUBERCULOSIS
	Organism Taxid	:	633
	Synonym	:	YOPE CHAPERONE SYCE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1JYA)

(no "SS Bond" information available for 1JYA)

Asymmetric/Biological Unit

No.	Residues
1	His A:41	-	Pro A:42
2	His B:41	-	Pro B:42

(no "SAP(SNP)/Variant" information available for 1JYA)

(no "PROSITE Motif" information available for 1JYA)

(no "Exon" information available for 1JYA)

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:117
 aligned with Q663P0_YERPS | Q663P0 from UniProtKB/TrEMBL  Length:130

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
         Q663P0_YERPS     2 YSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQ 118
               SCOP domains d1jyaa_ A: YopE chaperone SycE                                                                                        SCOP domains
               CATH domains 1jyaA00 A:2-118  [code=3.30.1460.10, no name defined]                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.........eeeeee..eeeeeee....eeeeee........hhhhhhhhhh........eeeee....eeeeeeeee.hhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1jya A   2 YSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILmFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEmLVQGAERLQ 118
                                    11        21        31        41      | 51        61        71        81        91       101       111       
                                                                         48-MSE                                                      109-MSE

Chain A from PDB  Type:PROTEIN  Length:117
 aligned with YERA_YERPE | P31491 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           YERA_YERPE     2 YSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQ 118
               SCOP domains d1jyaa_ A: YopE chaperone SycE                                                                                        SCOP domains
               CATH domains 1jyaA00 A:2-118  [code=3.30.1460.10, no name defined]                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.........eeeeee..eeeeeee....eeeeee........hhhhhhhhhh........eeeee....eeeeeeeee.hhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1jya A   2 YSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILmFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEmLVQGAERLQ 118
                                    11        21        31        41      | 51        61        71        81        91       101       111       
                                                                         48-MSE                                                      109-MSE

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with Q663P0_YERPS | Q663P0 from UniProtKB/TrEMBL  Length:130

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
         Q663P0_YERPS     2 YSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQTSSL 122
               SCOP domains d1jyab_ B: YopE chaperone SycE                                                                                            SCOP domains
               CATH domains 1jyaB00 B:2-122  [code=3.30.1460.10, no name defined]                                                                     CATH domains
           Pfam domains (1) ----CesT-1jyaB01 B:6-118                                                                                             ---- Pfam domains (1)
           Pfam domains (2) ----CesT-1jyaB02 B:6-118                                                                                             ---- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhh..........eeeeee..eeeeeee....eeeeee........hhhhhhhhhh........eeeee....eeeeeeeee.hhh..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jya B   2 YSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILmFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEmLVQGAERLQTSSL 122
                                    11        21        31        41      | 51        61        71        81        91       101       111       121 
                                                                         48-MSE                                                      109-MSE

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with YERA_YERPE | P31491 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
           YERA_YERPE     2 YSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQTSSL 122
               SCOP domains d1jyab_ B: YopE chaperone SycE                                                                                            SCOP domains
               CATH domains 1jyaB00 B:2-122  [code=3.30.1460.10, no name defined]                                                                     CATH domains
           Pfam domains (1) ----CesT-1jyaB01 B:6-118                                                                                             ---- Pfam domains (1)
           Pfam domains (2) ----CesT-1jyaB02 B:6-118                                                                                             ---- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhh..........eeeeee..eeeeeee....eeeeee........hhhhhhhhhh........eeeee....eeeeeeeee.hhh..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jya B   2 YSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILmFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEmLVQGAERLQTSSL 122
                                    11        21        31        41      | 51        61        71        81        91       101       111       121 
                                                                         48-MSE                                                      109-MSE

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Secretion chaperone-like (60)

Superfamily: Type III secretory system chaperone-like (19)

Family: Type III secretory system chaperone (14)

Protein domain: YopE chaperone SycE (4)

Yersinia pestis [TaxId: 632] (3)

1a	d1jyaa_	A:
1b	d1jyab_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Yope Regulator; Chain: A, (26)

Homologous Superfamily: [code=3.30.1460.10, no name defined] (12)

Yersinia pseudotuberculosis. Organism_taxid: 633. (2)

1a	1jyaB00	B:2-122
1b	1jyaA00	A:2-118

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TypeIII_Chap (8)

Family: CesT (7)

Yersinia pseudotuberculosis (1)

1a	CesT-1jyaB01	B:6-118
1b	CesT-1jyaB02	B:6-118

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (YERA_YERPE | P31491)

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:0050708	regulation of protein secretion	Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B (Q663P0_YERPS | Q663P0)

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:0050708	regulation of protein secretion	Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Sites
(no "Sites" information available for 1jya)

	Cis Peptide Bonds
		His A:41 - Pro A:42	[ RasMol ]
		His B:41 - Pro B:42	[ RasMol ]

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	1jya
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(no "Related Entries Specified in the PDB File" available for 1JYA)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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