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(-) Description

Title :  CRYSTAL STRUCTURE OF UNKNOWN CONSERVED YBAA PROTEIN FROM SHIGELLA FLEXNERI
 
Authors :  G. Minasov, I. I. Vorontsov, L. Shuvalova, J. S. Brunzelle, O. Kiryukhina, F. R. Collart, A. Joachimiak, W. F. Anderson, Midwest Center For Structural Genomics (Mcsg)
Date :  17 Jan 07  (Deposition) - 06 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (2x),B (2x)
Keywords :  Crystal Structure, Ybaa Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, I. I. Vorontsov, L. Shuvalova, J. S. Brunzelle, O. Kiryukhina, F. R. Collart, A. Joachimiak, W. F. Anderson
Crystal Structure Of Unknown Conserved Ybaa Protein From Shigella Flexneri
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YBAA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YBAA
    Organism Scientific: SHIGELLA FLEXNERI
    Organism Taxid: 623

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): A (2x)B (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:84 , HOH A:122 , ASN B:-1 , MET B:1 , PRO B:74 , HOH B:123BINDING SITE FOR RESIDUE NA A 118
2AC2SOFTWAREASP A:48 , GLY A:49 , ASP A:53 , MET A:56 , HOH A:143 , HOH A:155BINDING SITE FOR RESIDUE NA A 119

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OKQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OKQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OKQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OKQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2OKQ)

(-) 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:127
 aligned with YBAA_SHIFL | P0AAQ9 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:127
                                      1                                                                                                                    
                                     -|       10        20        30        40        50        60        70        80        90       100       110       
           YBAA_SHIFL     - ----------MKYVDGFVVAVPADKKDAYREMAAKAAPLFKEFGALRIVECWASDVPDGKVTDFRMAVKAEENEEVVFSWIEYPSKEVRDAANQKMMSDPRMKEFGESMPFDGKRMIYGGFESIIDE 117
               SCOP domains ----------d2okqa1 A:1-117 Hypothetical protein YbaA                                                                             SCOP domains
               CATH domains 2okqA00 A:-9-117  [code=3.30.70.900, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeeeeee.......hhhhhh.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh...........eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2okq A  -9 TENLYFQSNAMKYVDGFVVAVPADKKDAYREMAAKAAPLFKEFGALRIVECWASDVPDGKVTDFRMAVKAEENEEVVFSWIEYPSKEVRDAANQKMMSDPRMKEFGESMPFDGKRMIYGGFESIIDE 117
                                     0        10        20        30        40        50        60        70        80        90       100       110       


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with YBAA_SHIFL | P0AAQ9 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:126
                                     1                                                                                                                    
                                     1        11        21        31        41        51        61        71        81        91       101       111      
           YBAA_SHIFL     - ---------MKYVDGFVVAVPADKKDAYREMAAKAAPLFKEFGALRIVECWASDVPDGKVTDFRMAVKAEENEEVVFSWIEYPSKEVRDAANQKMMSDPRMKEFGESMPFDGKRMIYGGFESIIDE 117
               SCOP domains d2okqb_ B: Hypothetical protein YbaA                                                                                           SCOP domains
               CATH domains 2okqB00 B:-8-117  [code=3.30.70.900, no name defined]                                                                          CATH domains
           Pfam domains (1) ----------DUF1428-2okqB01 B:2-104                                                                                ------------- Pfam domains (1)
           Pfam domains (2) ----------DUF1428-2okqB02 B:2-104                                                                                ------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeeeeee.......hhhhhh.....eeeeeeeeee.hhhhhhhhhhhhhhh..--------.......eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2okq B  -8 ENLYFQSNAMKYVDGFVVAVPADKKDAYREMAAKAAPLFKEFGALRIVECWASDVPDGKVTDFRMAVKAEENEEVVFSWIEYPSKEVRDAANQKMMSDPR--------PFDGKRMIYGGFESIIDE 117
                                     1        11        21        31        41        51        61        71        81        91       101       111      
                                                                                                                              91      100
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: DUF1428] (1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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