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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE YERSINIA SECRETION CHAPERONE SYCE

Authors :   A. G. Evdokimov, J. E. Tropea, K. M. Routzahn, D. S. Waugh

Date :   17 Oct 01 (Deposition) - 31 Oct 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Secretion, Chaperone, Yersinia Pestis, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. G. Evdokimov, J. E. Tropea, K. M. Routzahn, D. S. Waugh
Three-Dimensional Structure Of The Type Iii Secretion Chaperone Syce From Yersinia Pestis.
Acta Crystallogr. , Sect. D V. 58 398 2002
PubMed-ID: 11856824 | Reference-DOI: 10.1107/S090744490200015X
(for further references see the PDB file header)

Molecule 1 - TYPE III SECRETION CHAPERONE SYCE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PKM596
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	SYCE
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632
	Synonym	:	YOPE CHAPERONE SYCE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	IMD	2	Ligand/Ion	IMIDAZOLE
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:1082 , VAL A:1083	BINDING SITE FOR RESIDUE IMD A 2501
2	AC2	SOFTWARE	GLU B:2082 , VAL B:2083 , GLY B:2085	BINDING SITE FOR RESIDUE IMD B 2502

(no "SS Bond" information available for 1K6Z)

Asymmetric/Biological Unit

No.	Residues
1	His A:1041	-	Pro A:1042
2	His B:2041	-	Pro B:2042

(no "SAP(SNP)/Variant" information available for 1K6Z)

(no "PROSITE Motif" information available for 1K6Z)

(no "Exon" information available for 1K6Z)

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
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Chain A from PDB  Type:PROTEIN  Length:122
 aligned with YERA_YERPE | P31491 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:130
                                                                                                                                                         130  
                                    12        22        32        42        52        62        72        82        92       102       112       122       | -
          YERA_YERPE      3 SFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQTSSLISPPRSFS--    -
               SCOP domains d1k6za_ A: YopE chaperone SycE                                                                                                     SCOP domains
               CATH domains 1k6zA00 A:1003-1132  [code=3.30.1460.10, no name defined]                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.........eeeeee..eeeeeee....eeeeee........hhhhhhhh..........eeeee....eeeeeeeee.hhh..hhhhhhhhhhhhhhhhh.--------..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                1k6z A 1003 SFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILmFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEmLVQGAERLQ--------RSFSHH 1132
                                  1012      1022      1032      1042     |1052      1062      1072      1082      1092      1102      1112     |   -    | 1132
                                                                      1048-MSE                                                     1109-MSE 1118     1127

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

    Alignment length:130
                                                                                                                                                         130  
                                    12        22        32        42        52        62        72        82        92       102       112       122       | -
          YERA_YERPE      3 SFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQTSSLISPPRSFS--    -
               SCOP domains d1k6zb_ B: YopE chaperone SycE                                                                                                     SCOP domains
               CATH domains 1k6zB00 B:2003-2132  [code=3.30.1460.10, no name defined]                                                                          CATH domains
           Pfam domains (1) ---CesT-1k6zB01 B:2006-2117                                                                                        --------------- Pfam domains (1)
           Pfam domains (2) ---CesT-1k6zB02 B:2006-2117                                                                                        --------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhh.........eeeeee..eeeeeee....eeeeee........hhhhhhhhhh........eeeee....eeeeeeeee.hhh..hhhhhhhhhhhhhhhhh---------..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                1k6z B 2003 SFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILmFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEmLVQGAERL---------RSFSHH 2132
                                  2012      2022      2032      2042     |2052      2062      2072      2082      2092      2102      2112    |    -    | 2132
                                                                      2048-MSE                                                     2109-MSE2117      2127

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	d1k6za_	A:
1b	d1k6zb_	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 pestis. Organism_taxid: 632. (1)

1a	1k6zA00	A:1003-1132
1b	1k6zB00	B:2003-2132

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TypeIII_Chap (8)

Family: CesT (7)

Yersinia pestis (2)

1a	CesT-1k6zB01	B:2006-2117
1b	CesT-1k6zB02	B:2006-2117

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.

Asymmetric/Biological Unit
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		His B:2041 - Pro B:2042	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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