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(-) Description

Title :  STRUCTURE OF E. COLI YBAB
 
Authors :  R. Kniewel, J. Buglino, T. Chadna, C. D. Lima, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  24 Jun 03  (Deposition) - 08 Jul 03  (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 :  Nysgxrc T5, Unknown Function, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Kniewel, J. Buglino, T. Chadna, C. D. Lima
Structure Of E. Coli Ybab
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL UPF0133 PROTEIN YBAB
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET T7
    Expression System Strain: B834 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YBAB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: YBAB;
YPOTHETICAL PROTEIN YBAB

 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 1PUG)

(-) Sites  (0, 0)

(no "Site" information available for 1PUG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PUG)

(-) 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:94
 aligned with YBAB_ECOLI | P0A8B5 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:94
                                    20        30        40        50        60        70        80        90       100    
           YBAB_ECOLI    11 MKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLEDDKEMLEDLVAAAFNDAARRIEETQKEKMASVSSGMQLPPG 104
               SCOP domains d1puga_ A: Hypothetical upf0133 protein YbaB                                                   SCOP domains
               CATH domains 1pugA00 A:11-104  [code=3.30.1310.10, no name defined]                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.eeeeeehhh.eeeeee....eeeeee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 1pug A  11 MKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLEDDKEMLEDLVAAAFNDAARRIEETQKEKMASVSSGMQLPPG 104
                                    20        30        40        50        60        70        80        90       100    


Chain B from PDB  Type:PROTEIN  Length:74
 aligned with YBAB_ECOLI | P0A8B5 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:74
                                    27        37        47        57        67        77        87    
           YBAB_ECOLI    18 QEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLEDDKEMLEDLVAAAFNDAARRIEETQKEK  91
               SCOP domains d1pugb_ B: Hypothetical upf0133 protein YbaB                               SCOP domains
               CATH domains 1pugB00 B:18-91  [code=3.30.1310.10, no name defined]                      CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhheeeeeehhh.eeeeee....eeeeee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 1pug B  18 QEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLEDDKEMLEDLVAAAFNDAARRIEETQKEK  91
                                    27        37        47        57        67        77        87    


Chain C from PDB  Type:PROTEIN  Length:80
 aligned with YBAB_ECOLI | P0A8B5 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:80
                                    25        35        45        55        65        75        85        95
           YBAB_ECOLI    16 QMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLEDDKEMLEDLVAAAFNDAARRIEETQKEKMASV  95
               SCOP domains d1pugc_ C: Hypothetical upf0133 protein YbaB                                     SCOP domains
               CATH domains 1pugC00 C:16-95  [code=3.30.1310.10, no name defined]                            CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhheeeeee....eeeeee....eeeeee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 1pug C  16 QMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLEDDKEMLEDLVAAAFNDAARRIEETQKEKMASV  95
                                    25        35        45        55        65        75        85        95


Chain D from PDB  Type:PROTEIN  Length:75
 aligned with YBAB_ECOLI | P0A8B5 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:75
                                    30        40        50        60        70        80        90     
           YBAB_ECOLI    21 MQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLEDDKEMLEDLVAAAFNDAARRIEETQKEKMASV  95
               SCOP domains d1pugd_ D: Hypothetical upf0133 protein YbaB                                SCOP domains
               CATH domains 1pugD00 D:21-95  [code=3.30.1310.10, no name defined]                       CATH domains
           Pfam domains (1) YbaB_DNA_bd-1pugD01 D:21-95                                                 Pfam domains (1)
           Pfam domains (2) YbaB_DNA_bd-1pugD02 D:21-95                                                 Pfam domains (2)
           Pfam domains (3) YbaB_DNA_bd-1pugD03 D:21-95                                                 Pfam domains (3)
           Pfam domains (4) YbaB_DNA_bd-1pugD04 D:21-95                                                 Pfam domains (4)
         Sec.struct. author .hhhhhhhhhheeeee.....eeeeee....eeeeee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 1pug D  21 MQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLEDDKEMLEDLVAAAFNDAARRIEETQKEKMASV  95
                                    30        40        50        60        70        80        90
   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, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: YbaB_DNA_bd] (2)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (YBAB_ECOLI | P0A8B5)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
cellular component
    GO:0043590    bacterial nucleoid    The region of a bacterial cell to which the DNA is confined.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0009295    nucleoid    The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.

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