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(-) Description

Title :  STRUCTURE OF THE XYLO-OLIGOSACCHARIDE SPECIFIC SOLUTE BINDING PROTEIN FROM BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS BL-04 IN COMPLEX WITH ARABINOXYLOBIOSE
 
Authors :  F. Fredslund, M. Ejby, A. Vujicic-Zagar, B. Svensson, D. J. Slotboom, M. Abou Hachem
Date :  13 Aug 13  (Deposition) - 30 Oct 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Transport Protein, Solute Binding Protein, Probiotic, Prebiotic, Arabinoxylobiose, Abc Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ejby, F. Fredslund, A. Vujicic-Zagar, B. Svensson, D. J. Slotboom, M. Abou Hachem
Structural Basis For Arabinoxylo-Oligosaccharide Capture By The Probiotic Bifidobacterium Animalis Subsp. Lactis Bl-04
Mol. Microbiol. V. 90 1100 2013
PubMed-ID: 24279727  |  Reference-DOI: 10.1111/MMI.12419

(-) Compounds

Molecule 1 - SUGAR TRANSPORTER SOLUTE-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 19-425
    Organism Scientific: BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS BL-04
    Organism Taxid: 580050
    Synonym: XOS BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
11PE4Ligand/IonPENTAETHYLENE GLYCOL
2AHR1Ligand/IonALPHA-L-ARABINOFURANOSE
3XYP2Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:192 , ASP A:220 , HIS A:221 , THR A:250 , THR A:252 , GLN A:419 , ALA A:422 , GLN A:423 , HOH A:2129 , HOH A:2147BINDING SITE FOR RESIDUE 1PE A1429
2AC2SOFTWAREPRO A:86 , LYS A:102 , ILE A:105 , ASP A:106 , GLY A:108 , PRO A:324 , LYS A:325 , HOH A:2047BINDING SITE FOR RESIDUE 1PE A1430
3AC3SOFTWAREGLU A:170 , ALA A:174 , LYS A:177 , GLU A:237 , LEU A:241BINDING SITE FOR RESIDUE 1PE A1431
4AC4SOFTWAREGLU A:57 , PRO A:61 , GLY A:62 , THR A:63 , LYS A:64 , HOH A:2019BINDING SITE FOR RESIDUE 1PE A1432
5AC5SOFTWAREASN A:39 , ASN A:72 , SER A:144 , GLU A:146 , TRP A:195 , HIS A:199 , GLN A:254 , TRP A:277 , THR A:318 , TYR A:346 , TRP A:384 , ASP A:386 , HOH A:2035 , HOH A:2051 , HOH A:2058 , HOH A:2195 , HOH A:2202 , HOH A:2217 , HOH A:2219BINDING SITE FOR POLY-SACCHARIDE RESIDUES AHR A1426 THROUGH XYP A1428

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:209 -A:227

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C1U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C1U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C1U)

(-) Exons   (0, 0)

(no "Exon" information available for 4C1U)

(-) Sequences/Alignments

Asymmetric/Biological 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    
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Chain A from PDB  Type:PROTEIN  Length:396
                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhh..........hhhhhhhhhhhhh..ee..ee..eeeeeeeeeeeeehhhhhhh.......hhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......hhhhh.......hhhhhhhh..eeeeeee.hhhhhhh...........eeee..............eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh.hhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c1u A  30 DDKTITFWHNASAGEGRQYWENLAKSFEEANPGTKVEIQAIQNEDFAGKLQTAMQDPASGPDVFMSLGGAKTKEMIDAGQVMDLTDKISDTVKTDMKTTLSAATFDGKVYGVPVSVEPGGMWYSKDLFKKAGVSDVPATYEELLADAKKLKDSGTDAIALGAKDAWPAAHWYYWLVLRECSPEVYDKSVQDHDFSNACWVNAGKKLQELKDLKVFNDGFLTTTAQQGANSSAGLLANHKAAMELMGAWEPGVLKDLTPDQKPMADLGFFAFPEVAGGEGEPGALMGGVTYFCVNPKASQTSIDFVNYMGEKKNQEDYAKAFSTIPASEPARAVVTDESLKQVIEYLDKAPSMQLWMDTALGTNIGNALNAAVVNMLSGQGSPEDIVKAMQDAAQKG 425
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419
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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  (0, 0)

(no "SCOP Domain" information available for 4C1U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C1U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C1U)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

3zkk STRUCTURE OF THE XYLO-OLIGOSACCHARIDE SPECIFIC SOLUTE BINDING PROTEIN FROM BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS BL-04 IN COMPLEX WITH XYLOTETRAOSE
3zkl STRUCTURE OF THE XYLO-OLIGOSACCHARIDE SPECIFIC SOLUTE BINDING PROTEIN FROM BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS BL-04 IN COMPLEX WITH XYLOTRIOSE
4c1t STRUCTURE OF THE XYLO-OLIGOSACCHARIDE SPECIFIC SOLUTE BINDING PROTEIN FROM BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS BL-04 IN COMPLEX WITH ARABINOXYLOTRIOSE