1O67 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AN HYPOTHETICAL PROTEIN

Authors :   Structural Genomix

Date :   23 Oct 03 (Deposition) - 11 Nov 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.54

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622 | Reference-DOI: 10.1002/PROT.20541
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL PROTEIN YIIM
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	YIIM, B3910
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 18)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1O67)

(no "SS Bond" information available for 1O67)

Asymmetric Unit

No.	Residues
1	Ala A:91	-	Pro A:92
2	Ala B:91	-	Pro B:92
3	Ala C:91	-	Pro C:92

(no "SAP(SNP)/Variant" information available for 1O67)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MOSC	PS51340	MOSC domain profile.	YIIM_ECOLI	26-163	3	A:36-173 B:36-173 C:36-173

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MOSC	PS51340	MOSC domain profile.	YIIM_ECOLI	26-163	1	A:36-173 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MOSC	PS51340	MOSC domain profile.	YIIM_ECOLI	26-163	1	- B:36-173 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MOSC	PS51340	MOSC domain profile.	YIIM_ECOLI	26-163	1	- - C:36-173

(no "Exon" information available for 1O67)

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:214
 aligned with YIIM_ECOLI | P32157 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:233
                                   1                                                                                                                                                                                                                            224  
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223|  
           YIIM_ECOLI     - -------MRYPVDVYTGKIQAYPEGKPSAIAKIQVDGELMLTELGLEGDEQAEKKVHGGPDRALCHYPREHYLYWAREFPEQAELFVAPAFGENLSTDGLTESNVYMGDIFRWGEALIQVSQPRSPCYKLNYHFDISDIAQLMQNTGKVGWLYSVIAPGKVSADAPLELVSRVSDVTVQEAAAIAWHMPFDDDQYHRLLSAAGLSKSWTRTMQKRRLSGKIEDFSRRLWGK--   -
               SCOP domains d1o67a_ A: Hypothe            tical protein YiiM                                                                                                                                                                                          SCOP domains
               CATH domains 1o67A00 A:4-236 PK             beta-barrel domain-       like                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.ee..eeee..------------..eee..eeeee..ee....-------hhhhhheeeeehhhhhhhhhhhhhhhhhh........eee............eeee..eeeeeeee...hhhhhhhhh..hhhhhhhhhh...eeeeeee.eeee....eeeee.....hhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------MOSC  PDB: A:36-173 UniProt: 26-163                                                                                                       --------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o67 A   4 FLVEREQmRYPVDVYTGK------------AKIQVDGELmLTELGLEGDE-------GGPDRALCHYPREHYLYWAREFPEQAELFVAPAFGENLSTDGLTESNVYmGDIFRWGEALIQVSQPRSPCYKLNYHFDISDIAQLmQNTGKVGWLYSVIAPGKVSADAPLELVSRVSDVTVQEAAAIAWHmPFDDDQYHRLLSAAGLSKSWTRTmQKRRLSGKIEDFSRRLWGKEG 236
                                   |13       | -         -|       43        53       |63        73        83        93       103      |113       123       133       143  |    153       163       173       183       193       203       213 |     223       233   
                                  11-MSE    21           34       43-MSE    53      61                                              110-MSE                             146-MSE                                      191-MSE                 215-MSE

Chain B from PDB  Type:PROTEIN  Length:214
 aligned with YIIM_ECOLI | P32157 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:232
                                   1                                                                                                                                                                                                                            224 
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223| 
           YIIM_ECOLI     - -------MRYPVDVYTGKIQAYPEGKPSAIAKIQVDGELMLTELGLEGDEQAEKKVHGGPDRALCHYPREHYLYWAREFPEQAELFVAPAFGENLSTDGLTESNVYMGDIFRWGEALIQVSQPRSPCYKLNYHFDISDIAQLMQNTGKVGWLYSVIAPGKVSADAPLELVSRVSDVTVQEAAAIAWHMPFDDDQYHRLLSAAGLSKSWTRTMQKRRLSGKIEDFSRRLWGK-   -
               SCOP domains d1o67b_ B: Hypoth             etical protein YiiM                                                                                                                                                                                        SCOP domains
               CATH domains 1o67B00 B:4-235 P             K beta-barrel domain     -like                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.ee..eeee.-------------..ee...eeeee..ee....-----...hhhhheeeeehhhhhhhhhhhhhhhhhh........eee............eeee..eeeeeeee....hhhhhhh...hhhhhhhhhh...eeeeeee.eeee....eeeee.....hhhhhhhhhhh...hhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------MOSC  PDB: B:36-173 UniProt: 26-163                                                                                                       -------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o67 B   4 FLVEREQmRYPVDVYTG-------------AKIQVDGELmLTELGLEGDE-----VHGGPDRALCHYPREHYLYWAREFPEQAELFVAPAFGENLSTDGLTESNVYmGDIFRWGEALIQVSQPRSPCYKLNYHFDISDIAQLmQNTGKVGWLYSVIAPGKVSADAPLELVSRVSDVTVQEAAAIAWHmPFDDDQYHRLLSAAGLSKSWTRTmQKRRLSGKIEDFSRRLWGKE 235
                                   |13      |  -         -|       43        53     |  63        73        83        93       103      |113       123       133       143  |    153       163       173       183       193       203       213 |     223       233  
                                  11-MSE   20            34       43-MSE    53    59                                                110-MSE                             146-MSE                                      191-MSE                 215-MSE

Chain C from PDB  Type:PROTEIN  Length:210
 aligned with YIIM_ECOLI | P32157 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:229
                                  1                                                                                                                                                                                                                              
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214         
           YIIM_ECOLI     - ------MRYPVDVYTGKIQAYPEGKPSAIAKIQVDGELMLTELGLEGDEQAEKKVHGGPDRALCHYPREHYLYWAREFPEQAELFVAPAFGENLSTDGLTESNVYMGDIFRWGEALIQVSQPRSPCYKLNYHFDISDIAQLMQNTGKVGWLYSVIAPGKVSADAPLELVSRVSDVTVQEAAAIAWHMPFDDDQYHRLLSAAGLSKSWTRTMQKRRLSGKIEDFSRRLWG 223
               SCOP domains d1o67c_ C: Hypot             hetical protein YiiM                                                                                                                                                                                     SCOP domains
               CATH domains 1o67C00 C:5-233              PK beta-barrel domain-      like                                                                                                                                                                         CATH domains
           Pfam domains (1) ----------------             -------------MOSC-1o67      C04 C:47-172                                                                                                   -----3-alpha-1o67C01 C:178-224                      --------- Pfam domains (1)
           Pfam domains (2) ----------------             -------------MOSC-1o67      C05 C:47-172                                                                                                   -----3-alpha-1o67C02 C:178-224                      --------- Pfam domains (2)
           Pfam domains (3) ----------------             -------------MOSC-1o67      C06 C:47-172                                                                                                   -----3-alpha-1o67C03 C:178-224                      --------- Pfam domains (3)
         Sec.struct. author .hhhhh.ee..eeee.-------------..eee..eeeee..ee......------hhhhheeeeehhhhhhhhhhhhhhhhhh........eee............eeee..eeeeeeee....hhhhhhhh..hhhhhhhhhh...eeeeeee.eeee....eeeee.....hhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------MOSC  PDB: C:36-173 UniProt: 26-163                                                                                                       ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o67 C   5 LVEREQmRYPVDVYTG-------------AKIQVDGELmLTELGLEGDEQA------GPDRALCHYPREHYLYWAREFPEQAELFVAPAFGENLSTDGLTESNVYmGDIFRWGEALIQVSQPRSPCYKLNYHFDISDIAQLmQNTGKVGWLYSVIAPGKVSADAPLELVSRVSDVTVQEAAAIAWHmPFDDDQYHRLLSAAGLSKSWTRTmQKRRLSGKIEDFSRRLWG 233
                                  | 14     |   -        34        44        54|      |64        74        84        94       104     | 114       124       134       144 |     154       164       174       184      |194       204       214|      224         
                                 11-MSE   20            34       43-MSE      55     62                                             110-MSE                             146-MSE                                      191-MSE                 215-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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PK beta-barrel domain-like (31)

Superfamily: PK beta-barrel domain-like (31)

Family: MOSC (MOCO sulphurase C-terminal) domain (3)

Protein domain: Hypothetical protein YiiM (2)

Escherichia coli [TaxId: 562] (2)

1a	d1o67a_	A:
1b	d1o67b_	B:
1c	d1o67c_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: M1 Pyruvate Kinase; Domain 3 (24)

Homologous Superfamily: PK beta-barrel domain-like (3)

Escherichia coli. Organism_taxid: 562. (2)

1a	1o67C00	C:5-233
1b	1o67A00	A:4-236
1c	1o67B00	B:4-235

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: 3-alpha] (2)

Family: 3-alpha (2)

Escherichia coli (strain K12) (2)

1a	3-alpha-1o67C01	C:178-224
1b	3-alpha-1o67C02	C:178-224
1c	3-alpha-1o67C03	C:178-224

Clan: no clan defined [family: MOSC] (3)

Family: MOSC (3)

Escherichia coli (strain K12) (2)

2a	MOSC-1o67C04	C:47-172
2b	MOSC-1o67C05	C:47-172
2c	MOSC-1o67C06	C:47-172

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (YIIM_ECOLI | P32157)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0030151	molybdenum ion binding	Interacting selectively and non-covalently with molybdenum (Mo) ions.
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
	GO:0009636	response to toxic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Sites
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	Cis Peptide Bonds
		Ala A:91 - Pro A:92	[ RasMol ]
		Ala B:91 - Pro B:92	[ RasMol ]
		Ala C:91 - Pro C:92	[ RasMol ]

Biological Units
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	1o67
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	YIIM_ECOLI \| P32157	:	1o65

(no "Related Entries Specified in the PDB File" available for 1O67)

Description

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Ligands, Modified Residues, Ions (1, 18)

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Cis Peptide Bonds (3, 3)

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