3IPO - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF YNJE

Authors :   P. Haenzelmann, J. Kuper, H. Schindelin

Date :   18 Aug 09 (Deposition) - 08 Dec 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Triple-Domain Rhodanese, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Hanzelmann, J. U. Dahl, J. Kuper, A. Urban, U. Muller-Theissen, S. Leimkuhler, H. Schindelin
Crystal Structure Of Ynje From Escherichia Coli, A Sulfurtransferase With Three Rhodanese Domains.
Protein Sci. V. 18 2480 2009
PubMed-ID: 19798741 | Reference-DOI: 10.1002/PRO.260

Molecule 1 - PUTATIVE THIOSULFATE SULFURTRANSFERASE YNJE
	Chains	:	A, B
	EC Number	:	2.8.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Gene	:	B1757, JW5287, YNJE
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Strain	:	ESCHERICHIA COLI

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 10)

No.	Name	Count	Type	Full Name
1	CSS	2	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	GOL	1	Ligand/Ion	GLYCEROL
3	NA	2	Ligand/Ion	SODIUM ION
4	PE4	1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
5	PG0	2	Ligand/Ion	2-(2-METHOXYETHOXY)ETHANOL
6	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (5, 8)

No.	Name	Count	Type	Full Name
1	CSS	2	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	GOL	1	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	PE4	1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
5	PG0	2	Ligand/Ion	2-(2-METHOXYETHOXY)ETHANOL
6	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (5, 8)

No.	Name	Count	Type	Full Name
1	CSS	2	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	GOL	1	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	PE4	1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
5	PG0	2	Ligand/Ion	2-(2-METHOXYETHOXY)ETHANOL
6	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP B:175 , TYR B:234 , GLY B:325 , TYR B:326 , SER B:327 , TYR B:328 , SER B:347 , THR B:348	BINDING SITE FOR RESIDUE PE4 B 6061
2	AC2	SOFTWARE	SER B:315 , TRP B:316 , HIS B:342 , GLY B:344 , ASP B:352 , PG0 B:6108	BINDING SITE FOR RESIDUE GOL B 3968
3	AC3	SOFTWARE	THR B:113 , GLN B:116 , TRP B:316 , PRO B:317 , HOH B:570 , GOL B:3968	BINDING SITE FOR RESIDUE PG0 B 6108
4	AC4	SOFTWARE	GLU B:297 , ARG B:300 , GLY B:301 , LEU B:303 , HIS B:304	BINDING SITE FOR RESIDUE PG0 B 436
5	AC5	SOFTWARE	GLU A:172 , ALA A:174 , ALA A:177 , LYS A:179 , LEU A:180 , TYR A:181 , TYR A:191	BINDING SITE FOR RESIDUE PO4 A 1
6	AC6	SOFTWARE	GLU B:172 , ALA B:174 , ALA B:177 , LYS B:179 , LEU B:180 , TYR B:181 , TYR B:191	BINDING SITE FOR RESIDUE PO4 B 2
7	AC7	SOFTWARE	TRP A:203 , ASN A:204 , THR A:387 , ASP A:410 , HOH A:594	BINDING SITE FOR RESIDUE NA A 436
8	AC8	SOFTWARE	TRP B:203 , ASN B:204 , ARG B:238 , THR B:387 , ASP B:410 , HOH B:598	BINDING SITE FOR RESIDUE NA B 1

(no "SS Bond" information available for 3IPO)

Asymmetric Unit

No.	Residues
1	Glu A:200	-	Pro A:201
2	Ile A:286	-	Pro A:287
3	Glu B:200	-	Pro B:201
4	Ile B:286	-	Pro B:287

(no "SAP(SNP)/Variant" information available for 3IPO)

Asymmetric Unit (3, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHODANESE_3	PS50206	Rhodanese domain profile.	YNJE_ECOLI	36-138 164-270 304-425	6	A:36-138 B:36-138 A:164-270 B:164-270 A:304-425 B:304-425
2	RHODANESE_1	PS00380	Rhodanese signature 1.	YNJE_ECOLI	181-192	2	A:181-192 B:181-192
3	RHODANESE_2	PS00683	Rhodanese C-terminal signature.	YNJE_ECOLI	406-416	2	A:406-416 B:406-416

Biological Unit 1 (3, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHODANESE_3	PS50206	Rhodanese domain profile.	YNJE_ECOLI	36-138 164-270 304-425	6	A:36-138 B:36-138 A:164-270 B:164-270 A:304-425 B:304-425
2	RHODANESE_1	PS00380	Rhodanese signature 1.	YNJE_ECOLI	181-192	2	A:181-192 B:181-192
3	RHODANESE_2	PS00683	Rhodanese C-terminal signature.	YNJE_ECOLI	406-416	2	A:406-416 B:406-416

Biological Unit 2 (3, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHODANESE_3	PS50206	Rhodanese domain profile.	YNJE_ECOLI	36-138 164-270 304-425	6	A:36-138 B:36-138 A:164-270 B:164-270 A:304-425 B:304-425
2	RHODANESE_1	PS00380	Rhodanese signature 1.	YNJE_ECOLI	181-192	2	A:181-192 B:181-192
3	RHODANESE_2	PS00683	Rhodanese C-terminal signature.	YNJE_ECOLI	406-416	2	A:406-416 B:406-416

(no "Exon" information available for 3IPO)

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:412
 aligned with YNJE_ECOLI | P78067 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:412
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433  
           YNJE_ECOLI    24 AELAKPLTLDQLQQQNGKAIDTRPSAFYNGWPQTLNGPSGHELAALNLSASWLDKMSTEQLNAWIKQHNLKTDAPVALYGNDKDVDAVKTRLQKAGLTHISILSDALSEPSRLQKLPHFEQLVYPQWLHDLQQGKEVTAKPAGDWKVIEAAWGAPKLYLISHIPGADYIDTNEVESEPLWNKVSDEQLKAMLAKHGIRHDTTVILYGRDVYAAARVAQIMLYAGVKDVRLLDGGWQTWSDAGLPVERGTPPKVKAEPDFGVKIPAQPQLMLDMEQARGLLHRQDASLVSIRSWPEFIGTTSGYSYIKPKGEIAGARWGHAGSDSTHMEDFHNPDGTMRSADDITAMWKAWNIKPEQQVSFYCGTGWRASETFMYARAMGWKNVSVYDGGWYEWSSDPKNPVATGERGPDSSK 435
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh..eeee..hhhhhh...........ee...ee.hhhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh....eee......hhh.ee...hhh.eehhhhhhhhhh...........eeeeeee....hhhhhh.....eeee....ee....ee.hhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhhh...eeee..hhhhhhhhh.......................hhh.eehhhhhhh......eeeee..hhhhhh.............ee...ee.........hhhhh.......hhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhh....eeee.hhhhhhh......ee....hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------RHODANESE_3  PDB: A:36-138 UniProt: 36-138                                                             -------------------------RHODANESE_3  PDB: A:164-270 UniProt: 164-270                                                               ---------------------------------RHODANESE_3  PDB: A:304-425 UniProt: 304-425                                                                              ---------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------RHODANESE_1 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RHODANESE_2------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ipo A  24 AELAKPLTLDQLQQQNGKAIDTRPSAFYNGWPQTLNGPSGHELAALNLSASWLDKMSTEQLNAWIKQHNLKTDAPVALYGNDKDVDAVKTRLQKAGLTHISILSDALSEPSRLQKLPHFEQLVYPQWLHDLQQGKEVTAKPAGDWKVIEAAWGAPKLYLISHIPGADYIDTNEVESEPLWNKVSDEQLKAMLAKHGIRHDTTVILYGRDVYAAARVAQIMLYAGVKDVRLLDGGWQTWSDAGLPVERGTPPKVKAEPDFGVKIPAQPQLMLDMEQARGLLHRQDASLVSIRSWPEFIGTTSGYSYIKPKGEIAGARWGHAGSDSTHMEDFHNPDGTMRSADDITAMWKAWNIKPEQQVSFYcGTGWRASETFMYARAMGWKNVSVYDGGWYEWSSDPKNPVATGERGPDSSK 435
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383 |     393       403       413       423       433  
                                                                                                                                                                                                                                                                                                                                                                                                   385-CSS

Chain B from PDB  Type:PROTEIN  Length:416
 aligned with YNJE_ECOLI | P78067 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:416
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429      
           YNJE_ECOLI    20 SSWAAELAKPLTLDQLQQQNGKAIDTRPSAFYNGWPQTLNGPSGHELAALNLSASWLDKMSTEQLNAWIKQHNLKTDAPVALYGNDKDVDAVKTRLQKAGLTHISILSDALSEPSRLQKLPHFEQLVYPQWLHDLQQGKEVTAKPAGDWKVIEAAWGAPKLYLISHIPGADYIDTNEVESEPLWNKVSDEQLKAMLAKHGIRHDTTVILYGRDVYAAARVAQIMLYAGVKDVRLLDGGWQTWSDAGLPVERGTPPKVKAEPDFGVKIPAQPQLMLDMEQARGLLHRQDASLVSIRSWPEFIGTTSGYSYIKPKGEIAGARWGHAGSDSTHMEDFHNPDGTMRSADDITAMWKAWNIKPEQQVSFYCGTGWRASETFMYARAMGWKNVSVYDGGWYEWSSDPKNPVATGERGPDSSK 435
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhh..eeee..hhhhhhh...............ee.hhhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh....eee......hhhhh....hhh.eehhhhhhhhhh...........eeeeeee....hhhhhh....eeeee....ee....ee.hhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhhh...eeee..hhhhhhhh........................hhh.eehhhhhhh......eeeee..hhhhhh.............ee...ee.........hhhhh.......hhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh....eeee.hhhhhhhhh....ee....hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------RHODANESE_3  PDB: B:36-138 UniProt: 36-138                                                             -------------------------RHODANESE_3  PDB: B:164-270 UniProt: 164-270                                                               ---------------------------------RHODANESE_3  PDB: B:304-425 UniProt: 304-425                                                                              ---------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------RHODANESE_1 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RHODANESE_2------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ipo B  20 SSWAAELAKPLTLDQLQQQNGKAIDTRPSAFYNGWPQTLNGPSGHELAALNLSASWLDKMSTEQLNAWIKQHNLKTDAPVALYGNDKDVDAVKTRLQKAGLTHISILSDALSEPSRLQKLPHFEQLVYPQWLHDLQQGKEVTAKPAGDWKVIEAAWGAPKLYLISHIPGADYIDTNEVESEPLWNKVSDEQLKAMLAKHGIRHDTTVILYGRDVYAAARVAQIMLYAGVKDVRLLDGGWQTWSDAGLPVERGTPPKVKAEPDFGVKIPAQPQLMLDMEQARGLLHRQDASLVSIRSWPEFIGTTSGYSYIKPKGEIAGARWGHAGSDSTHMEDFHNPDGTMRSADDITAMWKAWNIKPEQQVSFYcGTGWRASETFMYARAMGWKNVSVYDGGWYEWSSDPKNPVATGERGPDSSK 435
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379     | 389       399       409       419       429      
                                                                                                                                                                                                                                                                                                                                                                                                       385-CSS

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 3IPO)

(no "CATH Domain" information available for 3IPO)

(no "Pfam Domain" information available for 3IPO)

Asymmetric Unit(hide GO term definitions)

Chain A,B (YNJE_ECOLI | P78067)

molecular function
	GO:0016783	sulfurtransferase activity	Catalysis of the transfer of sulfur atoms from one compound (donor) to another (acceptor).
	GO:0004792	thiosulfate sulfurtransferase activity	Catalysis of the reaction: hydrogen cyanide + thiosulfate = H(+) + sulfite + thiocyanate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		CSS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Glu A:200 - Pro A:201	[ RasMol ]
		Glu B:200 - Pro B:201	[ RasMol ]
		Ile A:286 - Pro A:287	[ RasMol ]
		Ile B:286 - Pro B:287	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	YNJE_ECOLI \| P78067	:	2wlr 2wlx 3ipp

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Description

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Ligands, Modified Residues, Ions (6, 10)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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