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(-) Description

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 :  2.33
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)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1O65)

(-) Sites  (0, 0)

(no "Site" information available for 1O65)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O65)

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O65)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MOSCPS51340 MOSC domain profile.YIIM_ECOLI26-163
 
 		  3A:36-173
B:36-173
C:36-173
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MOSCPS51340 MOSC domain profile.YIIM_ECOLI26-163
 
 		  1A:36-173
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MOSCPS51340 MOSC domain profile.YIIM_ECOLI26-163
 
 		  1-
B:36-173
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MOSCPS51340 MOSC domain profile.YIIM_ECOLI26-163
 
 		  1-
-
C:36-173

(-) Exons   (0, 0)

(no "Exon" information available for 1O65)

(-) Sequences/Alignments

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:218
 aligned with YIIM_ECOLI | P32157 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:233
                                    1                                                                                                                                                                                                                            224 
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 | 
           YIIM_ECOLI     - --------MRYPVDVYTGKIQAYPEGKPSAIAKIQVDGELMLTELGLEGDEQAEKKVHGGPDRALCHYPREHYLYWAREFPEQAELFVAPAFGENLSTDGLTESNVYMGDIFRWGEALIQVSQPRSPCYKLNYHFDISDIAQLMQNTGKVGWLYSVIAPGKVSADAPLELVSRVSDVTVQEAAAIAWHMPFDDDQYHRLLSAAGLSKSWTRTMQKRRLSGKIEDFSRRLWGK-   -
               SCOP domains d1o65a_ A: Hypothet            ical protein YiiM                                                                                                                                                                                          SCOP domains
               CATH domains 1o65A00 A:3-235 PK             beta-barrel domain-lik   e                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.ee..eeee..------------..eee..eeeee..ee......---..hhhhhheeeeehhhhhhhhhhhhhhhhhh........eee............eeee..eeeeeeee....hhhhhhh...hhhhhhhhhh...eeeeeee.eeee....eeeee.....hhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------MOSC  PDB: A:36-173 UniProt: 26-163                                                                                                       -------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o65 A   3 KFLVEREQMRYPVDVYTGK------------AKIQVDGELMLTELGLEGDEQA---VHGGPDRALCHYPREHYLYWAREFPEQAELFVAPAFGENLSTDGLTESNVYMGDIFRWGEALIQVSQPRSPCYKLNYHFDISDIAQLMQNTGKVGWLYSVIAPGKVSADAPLELVSRVSDVTVQEAAAIAWHMPFDDDQYHRLLSAAGLSKSWTRTMQKRRLSGKIEDFSRRLWGKE 235
                                    12        |-         - |      42        52  |   | 62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   
                                             21           34                   55  59                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with YIIM_ECOLI | P32157 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:231
                                    1                                                                                                                                                                                                                              
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 
           YIIM_ECOLI     - --------MRYPVDVYTGKIQAYPEGKPSAIAKIQVDGELMLTELGLEGDEQAEKKVHGGPDRALCHYPREHYLYWAREFPEQAELFVAPAFGENLSTDGLTESNVYMGDIFRWGEALIQVSQPRSPCYKLNYHFDISDIAQLMQNTGKVGWLYSVIAPGKVSADAPLELVSRVSDVTVQEAAAIAWHMPFDDDQYHRLLSAAGLSKSWTRTMQKRRLSGKIEDFSRRLWG 223
               SCOP domains d1o65b_ B: Hypothet           ical protein YiiM                                                                                                                                                                                         SCOP domains
               CATH domains 1o65B00 B:3-233 PK            beta-barrel domain-like                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.ee..eeee..-----------...eee..eeee............---..hhhhheeeeehhhhhhhhhhhhhhhhhh........eee............eeee..eeeeeeee....hhhhhhh...hhhhhhhhhh...eeeeeee.eeee....eeeee.....hhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------MOSC  PDB: B:36-173 UniProt: 26-163                                                                                                       ------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o65 B   3 KFLVEREQMRYPVDVYTGK-----------IAKIQVDGELMLTELGLEGDEQAE---HGGPDRALCHYPREHYLYWAREFPEQAELFVAPAFGENLSTDGLTESNVYMGDIFRWGEALIQVSQPRSPCYKLNYHFDISDIAQLMQNTGKVGWLYSVIAPGKVSADAPLELVSRVSDVTVQEAAAIAWHMPFDDDQYHRLLSAAGLSKSWTRTMQKRRLSGKIEDFSRRLWG 233
                                    12        |-         -|       42        52   |   |62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
                                             21          33                     56  60                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:217
 aligned with YIIM_ECOLI | P32157 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:235
                                    1                                                                                                                                                                                                                            224   
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 |   
           YIIM_ECOLI     - --------MRYPVDVYTGKIQAYPEGKPSAIAKIQVDGELMLTELGLEGDEQAEKKVHGGPDRALCHYPREHYLYWAREFPEQAELFVAPAFGENLSTDGLTESNVYMGDIFRWGEALIQVSQPRSPCYKLNYHFDISDIAQLMQNTGKVGWLYSVIAPGKVSADAPLELVSRVSDVTVQEAAAIAWHMPFDDDQYHRLLSAAGLSKSWTRTMQKRRLSGKIEDFSRRLWGK---   -
               SCOP domains d1o65c_ C: Hypothet           ical protein YiiM                                                                                                                                                                                             SCOP domains
               CATH domains 1o65C00 C:3-237 PK            beta-barrel domain-lik       e                                                                                                                                                                                CATH domains
           Pfam domains (1) -------------------           --------------MOSC-1o6       5C04 C:47-172                                                                                                  -----3-alpha-1o65C01 C:178-224                      ------------- Pfam domains (1)
           Pfam domains (2) -------------------           --------------MOSC-1o6       5C05 C:47-172                                                                                                  -----3-alpha-1o65C02 C:178-224                      ------------- Pfam domains (2)
           Pfam domains (3) -------------------           --------------MOSC-1o6       5C06 C:47-172                                                                                                  -----3-alpha-1o65C03 C:178-224                      ------------- Pfam domains (3)
         Sec.struct. author .hhhhhhh.ee..eeee..-----------...ee...eeeee..ee.....-------hhhhheeeeehhhhhhhhhhhhhhhhhh........eee............eeee..eeeeeeee....hhhhhhhh..hhhhhhhhhh...eeeeeee.eeee....eeeee.....hhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------MOSC  PDB: C:36-173 UniProt: 26-163                                                                                                       ---------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o65 C   3 KFLVEREQMRYPVDVYTGK-----------IAKIQVDGELMLTELGLEGDEQ-------GPDRALCHYPREHYLYWAREFPEQAELFVAPAFGENLSTDGLTESNVYMGDIFRWGEALIQVSQPRSPCYKLNYHFDISDIAQLMQNTGKVGWLYSVIAPGKVSADAPLELVSRVSDVTVQEAAAIAWHMPFDDDQYHRLLSAAGLSKSWTRTMQKRRLSGKIEDFSRRLWGKEGG 237
                                    12        |-         -|       42        52 |      62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     
                                             21          33                   54      62
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 6)

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

(-) Gene Ontology  (5, 5)

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.

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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 ]  
 
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  1o65
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  YIIM_ECOLI | P32157
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        YIIM_ECOLI | P32157: 1o67

(-) Related Entries Specified in the PDB File

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