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(-) Description

Title :  STRUCTURAL GENOMICS, 2.2A CRYSTAL STRUCTURE OF PROTEIN YKOF FROM BACILLUS SUBTILIS
 
Authors :  R. Zhang, L. Lezondra, S. Moy, I. Dementieva, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  29 Jan 04  (Deposition) - 06 Jul 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 :  Structural Genomics, Protein Ykof, Alpha-Beta-Beta-Alpha Sandwich, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, L. Lezondra, S. Moy, I. Dementieva, A. Joachimiak
2. 2A Crystal Structure Of Protein Ykof From Bacillus Subtilis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YKOF
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PDM68
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YKOF
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1S7H)

(-) Sites  (0, 0)

(no "Site" information available for 1S7H)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S7H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S7H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S7H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S7H)

(-) Exons   (0, 0)

(no "Exon" information available for 1S7H)

(-) 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:186
 aligned with YKOF_BACSU | O34911 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:186
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187      
           YKOF_BACSU     8 SRIAGFRFSLYPMTDDFISVIKSALKKTDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVMNGTFSIGCPGDTQGDTYLSKGDKRVNEDAVRGLKAEAPCQFALYPMNEPDYMGLIMEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRMAEQQTNHITMTVNLSANSPS 193
               SCOP domains d1s7ha_ A: Putative thiamin/HMP-binding protein YkoF                                                                                                                                       SCOP domains
               CATH domains 1s7hA01 A:8-87  [code=3.30.70.930, no name defined]                             ------------------------1s7hA02 A:112-193  [code=3.30.70.930, no name defined]                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee...hhhhhhhhhhhhh.....eeee....eeeeehhhhhhhhhhhhhhhhhh....eeeeeeeee...................hhhhhhh......eeeeeee....hhhhhhhhhhhhhhhh..eeeee..eeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1s7h A   8 SRIAGFRFSLYPMTDDFISVIKSALKKTDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVMNGTFSIGCPGDTQGDTYLSKGDKRVNEDAVRGLKAEAPCQFALYPMNEPDYMGLIMEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRMAEQQTNHITMTVNLSANSPS 193
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187      


Chain B from PDB  Type:PROTEIN  Length:180
 aligned with YKOF_BACSU | O34911 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:185
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188     
           YKOF_BACSU     9 RIAGFRFSLYPMTDDFISVIKSALKKTDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVMNGTFSIGCPGDTQGDTYLSKGDKRVNEDAVRGLKAEAPCQFALYPMNEPDYMGLIMEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRMAEQQTNHITMTVNLSANSPS 193
               SCOP domains d1s7hb_ B: Putative thiamin/HMP-binding protein YkoF                                                                                                                                      SCOP domains
               CATH domains 1s7hB01 B:9-87  [code=3.30.70.930, no name defined]                            ------------------------1s7hB02 B:112-193  [code=3.30.70.930, no name defined]                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...hhhhhhhhhh...hhhhheeee....eeeeehhhhhhhhhhhhhhhhhh....eeeeeeeee...........-----.hhhhhhhh.......eeeeeee....hhhhhhhhhhhhhhhh..eeeee..eeee..hhhhhhhhhhhhhhhhhh....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s7h B   9 RIAGFRFSLYPMTDDFISVIKSALKKTDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVMNGTFSIGCPGDTQGDTY-----KRVNEDAVRGLKAEAPCQFALYPMNEPDYMGLIMEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRMAEQQTNHITMTVNLSANSPS 193
                                    18        28        38        48        58        68        78        88      |  -  |    108       118       128       138       148       158       168       178       188     
                                                                                                                 95   101                                                                                            


Chain C from PDB  Type:PROTEIN  Length:182
 aligned with YKOF_BACSU | O34911 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:184
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188    
           YKOF_BACSU     9 RIAGFRFSLYPMTDDFISVIKSALKKTDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVMNGTFSIGCPGDTQGDTYLSKGDKRVNEDAVRGLKAEAPCQFALYPMNEPDYMGLIMEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRMAEQQTNHITMTVNLSANSP 192
               SCOP domains d1s7hc_ C: Putative thiamin/HMP-binding protein YkoF                                                                                                                                     SCOP domains
               CATH domains 1s7hC01 C:9-87  [code=3.30.70.930, no name defined]                            ------------------------1s7hC02 C:112-192  [code=3.30.70.930, no name defined]                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...hhhhhhhhhhhh......eeee....eeeeehhhhhhhhhhhhhhhhhh....eeeeeeeee..............--...hhhhhh.......eeeeeee....hhhhhhhhhhhhhhhh..eeeee..eeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s7h C   9 RIAGFRFSLYPMTDDFISVIKSALKKTDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVMNGTFSIGCPGDTQGDTYLSK--KRVNEDAVRGLKAEAPCQFALYPMNEPDYMGLIMEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRMAEQQTNHITMTVNLSANSP 192
                                    18        28        38        48        58        68        78        88        98  |    108       118       128       138       148       158       168       178       188    
                                                                                                                    98  |                                                                                           
                                                                                                                      101                                                                                           


Chain D from PDB  Type:PROTEIN  Length:184
 aligned with YKOF_BACSU | O34911 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:184
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188    
           YKOF_BACSU     9 RIAGFRFSLYPMTDDFISVIKSALKKTDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVMNGTFSIGCPGDTQGDTYLSKGDKRVNEDAVRGLKAEAPCQFALYPMNEPDYMGLIMEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRMAEQQTNHITMTVNLSANSP 192
               SCOP domains d1s7hd_ D: Putative thiamin/HMP-binding protein YkoF                                                                                                                                     SCOP domains
               CATH domains 1s7hD01 D:9-87  [code=3.30.70.930, no name defined]                            ------------------------1s7hD02 D:112-192  [code=3.30.70.930, no name defined]                            CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------Ykof-1s7hD01 D:114-192                                                          Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------Ykof-1s7hD02 D:114-192                                                          Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------Ykof-1s7hD03 D:114-192                                                          Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------Ykof-1s7hD04 D:114-192                                                          Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------------------------------Ykof-1s7hD05 D:114-192                                                          Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------------------------------Ykof-1s7hD06 D:114-192                                                          Pfam domains (6)
           Pfam domains (7) ---------------------------------------------------------------------------------------------------------Ykof-1s7hD07 D:114-192                                                          Pfam domains (7)
           Pfam domains (8) ---------------------------------------------------------------------------------------------------------Ykof-1s7hD08 D:114-192                                                          Pfam domains (8)
         Sec.struct. author ..eeeeeeeee...hhhhhhhhhhhhh.....eeee....eeeeehhhhhhhhhhhhhhhhhh....eeeeeeeee...................hhhhhh.......eeeeeee....hhhhhhhhhhhhhhhh..eeeee..eeee..hhhhhhhhhhhhhhhhhh....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s7h D   9 RIAGFRFSLYPMTDDFISVIKSALKKTDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVMNGTFSIGCPGDTQGDTYLSKGDKRVNEDAVRGLKAEAPCQFALYPMNEPDYMGLIMEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRMAEQQTNHITMTVNLSANSP 192
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 8)

Asymmetric Unit
(-)
Clan: MTH1187-YkoF (6)
(-)
Family: Ykof (2)
(-)
Bacillus subtilis (2)
1aYkof-1s7hD01D:114-192
1bYkof-1s7hD02D:114-192
1cYkof-1s7hD03D:114-192
1dYkof-1s7hD04D:114-192
1eYkof-1s7hD05D:114-192
1fYkof-1s7hD06D:114-192
1gYkof-1s7hD07D:114-192
1hYkof-1s7hD08D:114-192

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (YKOF_BACSU | O34911)
molecular function
    GO:0030975    thiamine binding    Interacting selectively and non-covalently with thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
biological process
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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  1s7h
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 Related Entries

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

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        YKOF_BACSU | O34911: 1s99 1sbr

(-) Related Entries Specified in the PDB File

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