1Y0G - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI YCEI PROTEIN, STRUCTURAL GENOMICS

Authors :   Y. V. Patskovsky, B. Strokopytov, U. Ramagopal, S. C. Almo, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   15 Nov 04 (Deposition) - 21 Dec 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Lipid Binding Protein, Lipocalin, Cofactor, Coenzyme, Dehydrogenase, Hydrolase, Predicted, Structural Genomics, Protein Structure Initiative, Psi, Nysgxrc, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. V. Patskovsky, B. Strokopytov, U. Ramagopal, S. C. Almo
Crystal Structure Of The Escherichia Coli Ycei Periplasmic Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROTEIN YCEI
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	YCEI
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	8PP	4	Ligand/Ion	2-[(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL]PHENOL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	8PP	2	Ligand/Ion	2-[(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL]PHENOL

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	8PP	2	Ligand/Ion	2-[(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL]PHENOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:36 , ILE A:40 , GLN A:41 , HIS A:42 , LEU A:48 , PHE A:52 , THR A:60 , LYS A:70 , VAL A:71 , VAL A:73 , ILE A:75 , ARG A:87 , PHE A:96 , ALA A:105 , PHE A:155 , ILE A:161 , LEU A:163 , LEU A:172 , ILE A:183 , VAL A:185 , HIS B:33	BINDING SITE FOR RESIDUE 8PP A 320
2	AC2	SOFTWARE	HIS A:33 , VAL B:36 , PHE B:38 , ILE B:40 , GLN B:41 , HIS B:42 , LEU B:48 , PHE B:52 , THR B:60 , PHE B:61 , LYS B:70 , VAL B:71 , VAL B:73 , ILE B:75 , ARG B:87 , LEU B:91 , ALA B:105 , PHE B:107 , PHE B:155 , ILE B:161 , LEU B:163 , ILE B:183 , VAL B:185 , GLY C:149	BINDING SITE FOR RESIDUE 8PP B 321
3	AC3	SOFTWARE	VAL C:36 , PHE C:38 , ILE C:40 , HIS C:42 , LEU C:48 , PHE C:52 , THR C:60 , LYS C:70 , VAL C:71 , VAL C:73 , ILE C:75 , ARG C:87 , LEU C:91 , ALA C:105 , PHE C:107 , PHE C:155 , ILE C:161 , LEU C:163 , ILE C:183 , VAL C:185 , HIS D:33	BINDING SITE FOR RESIDUE 8PP C 322
4	AC4	SOFTWARE	HIS C:33 , VAL D:36 , PHE D:38 , ILE D:40 , HIS D:42 , PHE D:52 , THR D:60 , PHE D:61 , ASP D:69 , LYS D:70 , VAL D:71 , VAL D:73 , ILE D:75 , LEU D:91 , ALA D:105 , PHE D:107 , LEU D:136 , PHE D:155 , ILE D:161 , LEU D:163 , LEU D:172 , ILE D:183 , VAL D:185 , HOH D:347	BINDING SITE FOR RESIDUE 8PP D 323

(no "SS Bond" information available for 1Y0G)

(no "Cis Peptide Bond" information available for 1Y0G)

(no "SAP(SNP)/Variant" information available for 1Y0G)

(no "PROSITE Motif" information available for 1Y0G)

(no "Exon" information available for 1Y0G)

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:169
 aligned with YCEI_ECOLI | P0A8X2 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:169
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182         
           YCEI_ECOLI    23 ADYKIDKEGQHAFVNFRIQHLGYSWLYGTFKDFDGTFTFDEKNPAADKVNVTINTTSVDTNHAERDKHLRSADFLNTAKYPQATFTSTSVKKDGDELDITGDLTLNGVTKPVTLEAKLIGQGDDPWGGKRAGFEAEGKIKLKDFNIKTDLGPASQEVDLIISVEGVQQK 191
               SCOP domains d1y0ga_ A: Lipid binding protein YceI                                                                                                                                     SCOP domains
               CATH domains 1y0gA00 A:23-191 Protein ycei                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeeeeeeee...eeeeeee..eeeeee....hhhhheeeeeee...ee..hhhhhhhhhh..........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeeeee.....eeeeeeeeeeee.hhhh.....hhhh.eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y0g A  23 ADYKIDKEGQHAFVNFRIQHLGYSWLYGTFKDFDGTFTFDEKNPAADKVNVTINTTSVDTNHAERDKHLRSADFLNTAKYPQATFTSTSVKKDGDELDITGDLTLNGVTKPVTLEAKLIGQGDDPWGGKRAGFEAEGKIKLKDFNIKTDLGPASQEVDLIISVEGVQQK 191
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with YCEI_ECOLI | P0A8X2 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:169
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182         
           YCEI_ECOLI    23 ADYKIDKEGQHAFVNFRIQHLGYSWLYGTFKDFDGTFTFDEKNPAADKVNVTINTTSVDTNHAERDKHLRSADFLNTAKYPQATFTSTSVKKDGDELDITGDLTLNGVTKPVTLEAKLIGQGDDPWGGKRAGFEAEGKIKLKDFNIKTDLGPASQEVDLIISVEGVQQK 191
               SCOP domains d1y0gb_ B: Lipid binding protein YceI                                                                                                                                     SCOP domains
               CATH domains 1y0gB00 B:23-191 Protein ycei                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeeeeeeee...eeeeeee..eeeeee....hhhhheeeeeee...ee..hhhhhhhhhh..........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeeeee.....eeeeeeeeeeee.hhhh.....hhhh.eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y0g B  23 ADYKIDKEGQHAFVNFRIQHLGYSWLYGTFKDFDGTFTFDEKNPAADKVNVTINTTSVDTNHAERDKHLRSADFLNTAKYPQATFTSTSVKKDGDELDITGDLTLNGVTKPVTLEAKLIGQGDDPWGGKRAGFEAEGKIKLKDFNIKTDLGPASQEVDLIISVEGVQQK 191
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain C from PDB  Type:PROTEIN  Length:169
 aligned with YCEI_ECOLI | P0A8X2 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:169
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182         
           YCEI_ECOLI    23 ADYKIDKEGQHAFVNFRIQHLGYSWLYGTFKDFDGTFTFDEKNPAADKVNVTINTTSVDTNHAERDKHLRSADFLNTAKYPQATFTSTSVKKDGDELDITGDLTLNGVTKPVTLEAKLIGQGDDPWGGKRAGFEAEGKIKLKDFNIKTDLGPASQEVDLIISVEGVQQK 191
               SCOP domains d1y0gc_ C: Lipid binding protein YceI                                                                                                                                     SCOP domains
               CATH domains 1y0gC00 C:23-191 Protein ycei                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeeeeeeee...eeeeeee..eeeeee....hhhhheeeeeee...ee..hhhhhhhhhh..........eeeeeeeeeee....eeeeeeeee..eeeeeeeeeeeeeeee.....eeeeeeeeeeee.hhhh..........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y0g C  23 ADYKIDKEGQHAFVNFRIQHLGYSWLYGTFKDFDGTFTFDEKNPAADKVNVTINTTSVDTNHAERDKHLRSADFLNTAKYPQATFTSTSVKKDGDELDITGDLTLNGVTKPVTLEAKLIGQGDDPWGGKRAGFEAEGKIKLKDFNIKTDLGPASQEVDLIISVEGVQQK 191
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain D from PDB  Type:PROTEIN  Length:169
 aligned with YCEI_ECOLI | P0A8X2 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:169
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182         
           YCEI_ECOLI    23 ADYKIDKEGQHAFVNFRIQHLGYSWLYGTFKDFDGTFTFDEKNPAADKVNVTINTTSVDTNHAERDKHLRSADFLNTAKYPQATFTSTSVKKDGDELDITGDLTLNGVTKPVTLEAKLIGQGDDPWGGKRAGFEAEGKIKLKDFNIKTDLGPASQEVDLIISVEGVQQK 191
               SCOP domains d1y0gd_ D: Lipid binding protein YceI                                                                                                                                     SCOP domains
               CATH domains 1y0gD00 D:23-191 Protein ycei                                                                                                                                             CATH domains
           Pfam domains (1) -YceI-1y0gD01 D:24-188                                                                                                                                                --- Pfam domains (1)
           Pfam domains (2) -YceI-1y0gD02 D:24-188                                                                                                                                                --- Pfam domains (2)
           Pfam domains (3) -YceI-1y0gD03 D:24-188                                                                                                                                                --- Pfam domains (3)
           Pfam domains (4) -YceI-1y0gD04 D:24-188                                                                                                                                                --- Pfam domains (4)
         Sec.struct. author .eeee......eeeeeeeee...eeeeeee..eeeeee....hhhhh..eeeee...ee..hhhhhhhhhh..........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeeeee.....eeeeeeeeeeee.hhhh..........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y0g D  23 ADYKIDKEGQHAFVNFRIQHLGYSWLYGTFKDFDGTFTFDEKNPAADKVNVTINTTSVDTNHAERDKHLRSADFLNTAKYPQATFTSTSVKKDGDELDITGDLTLNGVTKPVTLEAKLIGQGDDPWGGKRAGFEAEGKIKLKDFNIKTDLGPASQEVDLIISVEGVQQK 191
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Streptavidin-like (225)

Superfamily: YceI-like (3)

Family: YceI-like (2)

Protein domain: Lipid binding protein YceI (1)

Escherichia coli [TaxId: 562] (1)

1a	d1y0ga_	A:
1b	d1y0gb_	B:
1c	d1y0gc_	C:
1d	d1y0gd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lipocalin (526)

Homologous Superfamily: Protein ycei (2)

Escherichia coli. Organism_taxid: 562. (1)

1a	1y0gA00	A:23-191
1b	1y0gB00	B:23-191
1c	1y0gC00	C:23-191
1d	1y0gD00	D:23-191

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: YceI] (5)

Family: YceI (5)

Escherichia coli (strain K12) (1)

1a	YceI-1y0gD01	D:24-188
1b	YceI-1y0gD02	D:24-188
1c	YceI-1y0gD03	D:24-188
1d	YceI-1y0gD04	D:24-188

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (YCEI_ECOLI | P0A8X2)

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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Description

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Ligands, Modified Residues, Ions (1, 4)

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