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(-) Description

Title :  STRUCTURE OF THE PBP NOCT
 
Authors :  A. Vigouroux, S. Morera
Date :  21 Feb 14  (Deposition) - 22 Oct 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Periplasmic Binding Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Lang, A. Vigouroux, S. Planamente, A. El Sahili, P. Blin, M. Aumont-Nicaise, Y. Dessaux, S. Morera, D. Faure
Agrobacterium Uses A Unique Ligand-Binding Mode For Trappin Opines And Acquiring A Competitive Advantage In The Niche Construction On Plant Host.
Plos Pathog. V. 10 04444 2014
PubMed-ID: 25299655  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1004444

(-) Compounds

Molecule 1 - NOPALINE-BINDING PERIPLASMIC PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 26-283
    Gene: NOCT, ATU6027, AGR_PTI_67
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 176299
    Strain: C58 / ATCC 33970

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:122 , LYS A:197 , ASP A:222 , HOH A:430 , HOH A:441binding site for residue EDO A 301
2AC2SOFTWAREGLU A:36 , TRP A:77 , EDO A:303 , EDO A:304binding site for residue PEG A 302
3AC3SOFTWAREGLU A:36 , SER A:38 , TYR A:39 , PEG A:302binding site for residue EDO A 303
4AC4SOFTWAREGLN A:283 , PEG A:302binding site for residue EDO A 304
5AC5SOFTWAREHOH A:585binding site for residue EDO A 305
6AC6SOFTWARELYS B:50 , LEU B:51 , PHE B:72 , HOH B:482 , HOH B:494 , HOH B:495binding site for residue EDO B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P0I)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:40 -Pro A:41
2Ala B:40 -Pro B:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P0I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P0I)

(-) Exons   (0, 0)

(no "Exon" information available for 4P0I)

(-) 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:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........ee.....eehhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh....ee......hhhhhh..ee........eeeeee..hhhhhh.....eee....hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeee.hhhhhhhhhhh....eeeeehhhhhhhhhhhhhh.eeeeeeeeehhhhh.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p0i A  29 KSITIATEGSYAPYNFKDAGGKLIGFDIDLGNDLCKRMNIECKFVEQAWDGIIPSLTAGRYDAIMAAMGIQPAREKVIAFSRPYLLTPMTFLTTADSPLLKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQMMPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMFGPRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFGYDASPKQ 283
                                    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     


Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee........ee.....eehhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh....ee......hhhhhh..ee........eeeeee..hhhhhh.....eee....hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhh.....eeee.hhhhhhhhhhh....eeeeehhhhhhhhhhhhhh.eeeeeeeeehhhhh.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p0i B  27 DYKSITIATEGSYAPYNFKDAGGKLIGFDIDLGNDLCKRMNIECKFVEQAWDGIIPSLTAGRYDAIMAAMGIQPAREKVIAFSRPYLLTPMTFLTTADSPLLKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQMMPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMFGPRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFGYDASPK 282
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276
   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  (0, 0)

(no "SCOP Domain" information available for 4P0I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P0I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P0I)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NOCT_AGRFC | P35120: 4pow 4pox 4pp0 5ito 5itp

(-) Related Entries Specified in the PDB File

4pow 4pox 4pp0