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(-) Description

Title :  STRUCTURE OF THE PERIPLASMIC BINDING PROTEIN M117N-NOCT FROM A. TUMEFACIENS IN COMPLEX WITH OCTOPINE
 
Authors :  A. Vigouroux, S. Morera
Date :  17 Mar 16  (Deposition) - 30 Nov 16  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Periplasmic Binding Protein, Opine, Octopine, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Lang, A. Vigouroux, A. El Sahili, A. Kwasiborski, M. Aumont-Nicaise, Y. Dessaux, J. A. Shykoff, S. Morera, D. Faure
Fitness Costs Restrict Niche Expansion By Generalist Niche-Constructing Pathogens.
Isme J V. 11 374 2017
PubMed-ID: 27801902  |  Reference-DOI: 10.1038/ISMEJ.2016.137

(-) Compounds

Molecule 1 - NOPALINE-BINDING PERIPLASMIC PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NOCT, ATU6027, AGR_PTI_67
    Organism Scientific: AGROBACTERIUM FABRUM (STRAIN C58 / ATCC 33970)
    Organism Taxid: 176299

 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  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
26DB2Ligand/IonOCTOPINE
3EDO3Ligand/Ion1,2-ETHANEDIOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5TOE2Ligand/Ion2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL
Biological Unit 1 (5, 6)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
26DB1Ligand/IonOCTOPINE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5TOE2Ligand/Ion2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
26DB1Ligand/IonOCTOPINE
3EDO2Ligand/Ion1,2-ETHANEDIOL
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
5TOE-1Ligand/Ion2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:103 , LYS A:104 , GLU A:145 , GLN A:182 , ILE A:183 , SER A:184 , THR A:185 , LYS A:245 , HOH A:430binding site for residue PEG A 301
2AC2SOFTWARELYS A:212 , ARG A:229 , TYR A:277binding site for residue EDO A 302
3AC3SOFTWAREILE A:81 , GLN A:99 , ALA A:101 , PRO A:144 , GLY A:167 , THR A:168 , GLU A:171 , ALA A:172 , GLN A:176 , HOH A:440binding site for residue 1PE A 303
4AC4SOFTWAREGLU A:36 , TYR A:39 , TYR A:42 , TRP A:77 , ALA A:94 , ALA A:95 , GLY A:97 , ARG A:102 , ASN A:117 , GLN A:165 , THR A:168 , SER A:169 , HIS A:170 , SER A:207 , VAL A:239 , HOH A:436binding site for residue 6DB A 304
5AC5SOFTWARETHR A:85 , ALA A:86 , GLY A:87 , PRO A:126 , THR A:130 , ARG A:244 , HOH A:423binding site for residue TOE A 305
6AC6SOFTWAREASP A:78 , GLY A:79 , ASP A:151 , THR A:154 , LYS A:155 , SER A:180binding site for residue TOE A 306
7AC7SOFTWAREILE A:52 , TRP A:274 , PRO B:218 , ASP B:219 , LYS B:221 , ASP B:222binding site for residue EDO B 302
8AC8SOFTWAREGLU B:36 , TYR B:39 , TYR B:42 , ASN B:43 , TRP B:77 , ALA B:94 , ALA B:95 , GLY B:97 , ARG B:102 , ASN B:117 , GLN B:165 , THR B:168 , SER B:169 , HIS B:170 , SER B:207binding site for residue 6DB B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ITO)

(-) 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 5ITO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ITO)

(-) Exons   (0, 0)

(no "Exon" information available for 5ITO)

(-) 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.....eehhhhhhhhhhhhhhh.eeeeee....hhhhhhhh....ee......hhhhhh..ee........eeeeee..hhhhhh.....eee....hhhhhhhhhhhhhhh....eeee..hhhhhhhhhhh....eeee.hhhhhhhhhhh....eeeeehhhhhhhhhhhhhh.eeeeeeeeehhhhh.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ito A  27 DYKSITIATEGSYAPYNFKDAGGKLIGFDIDLGNDLCKRMNIECKFVEQAWDGIIPSLTAGRYDAIMAAMGIQPAREKVIAFSRPYLLTPNTFLTTADSPLLKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQMMPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMFGPRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFGYDASP 281
                                    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     


Chain B from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........ee.....eehhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhh....ee........hhhhh.ee........eeeeee..hhhhhh.....eee....hhhhhhhhhhhhhhh....eeee..hhhhhhhhhhh....eeee.hhhhhhhhhhh....eeeeehhhhhhhhhhhhhh.eeeeeeeeehhhhh.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ito B  28 YKSITIATEGSYAPYNFKDAGGKLIGFDIDLGNDLCKRMNIECKFVEQAWDGIIPSLTAGRYDAIMAAMGIQPAREKVIAFSRPYLLTPNTFLTTADSPLLKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQMMPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMFGPRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFGYDASPK 282
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277
   Legend:   → Mismatch (orange background)
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  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 5ITO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ITO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ITO)

(-) 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: 4p0i 4pow 4pox 4pp0 5itp

(-) Related Entries Specified in the PDB File

4p0i 4P0I CONTAINS THE FREE-LIGANDED PROTEIN 4POX CONTAINS THE SAME PROTEIN COMPLEXED WITH NOPALINE 4P0W CONTAINS THE SAME PROTEIN COMPLEXES WITH PYRONOPALINE 4PP0 CONTAINS A POINT MUTANT COMPLEXED WITH PYRONOPALINE