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(-) Description

Title :  CRYSTAL STRUCTURE OF A POTF MUTANT COMPLEXED WITH SPERMIDINE
 
Authors :  U. Scheib, S. Shanmugaratnam, J. A. Farias-Rico, B. Hocker
Date :  25 Feb 13  (Deposition) - 10 Jul 13  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym./Biol. Unit :  A
Keywords :  Periplasmic Binding Protein-Like Ii, Polyamine Receptor, Spermidine Binding Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Scheib, S. Shanmugaratnam, J. A. Farias-Rico, B. Hocker
Change In Protein-Ligand Specificity Through Binding Pocket Grafting.
J. Struct. Biol. V. 185 186 2014
PubMed-ID: 23792166  |  Reference-DOI: 10.1016/J.JSB.2013.06.002

(-) Compounds

Molecule 1 - PUTRESCINE-BINDING PERIPLASMIC PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL-21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B0854, JW0838, POTF
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SPD1Ligand/IonSPERMIDINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:37 , THR A:38 , GLU A:39 , TYR A:40 , GLU A:185 , TRP A:244 , TRP A:276 , ASP A:278 , HOH A:849 , HOH A:850 , HOH A:863 , HOH A:873BINDING SITE FOR RESIDUE SPD A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JDF)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JDF)

(-) 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    
   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:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4jdfa_ A: automated matches                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhh.eeeeeee.hhhhhhhhhhhh.....ee..hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeehhhhhhhhh.......hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.ee..hhhhhhhhh....eeeeehhhhhhhhhhhhhhh....eeee.....eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhhhhhhhhhh......hhhhhh.ee.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jdf A  29 QKTLHIYNWTEYIAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSAYFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHDPDNKFAMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVSFLDDPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAIGWAGSVWQASNRAKEAKNGVNVSFSIPKEGAMAWFDVFAMPADAKNKDEAYQFLNYLLRPDVVAHISDHVFYANANKAATPLVSAEVRENPGIYPPADVRAKLFTQKVQDPKIDRVRTRAWTKVKSG 369
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368
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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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  4jdf
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  POTF_ECOLI | P31133
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 Related Entries

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

UniProtKB/Swiss-Prot
        POTF_ECOLI | P31133: 1a99

(-) Related Entries Specified in the PDB File

1a99