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(-) Description

Title :  STRUCTURE OF THE PERIPLASMIC BINDING PROTEIN 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 :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Periplasmic Binding Protein, Opine, 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
    Organism Taxid: 358

 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  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
16DB2Ligand/IonOCTOPINE
2EDO7Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
16DB1Ligand/IonOCTOPINE
2EDO7Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
16DB1Ligand/IonOCTOPINE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:36 , TYR A:39 , TYR A:42 , TRP A:77 , ALA A:94 , ALA A:95 , GLY A:97 , ARG A:102 , MET A:117 , GLN A:165 , THR A:168 , SER A:169 , HIS A:170 , SER A:207 , VAL A:239 , HOH A:416binding site for residue 6DB A 301
02AC2SOFTWARELYS A:104 , THR A:143 , PRO A:144 , GLU A:145 , HOH A:409binding site for residue EDO A 302
03AC3SOFTWARELYS A:104 , LYS A:175 , HOH A:459binding site for residue EDO A 303
04AC4SOFTWAREILE A:81 , PRO A:144 , HOH A:409 , HOH A:449binding site for residue EDO A 304
05AC5SOFTWAREPRO A:138 , ASN A:141 , THR A:143 , GLN A:146 , HOH A:512binding site for residue EDO A 305
06AC6SOFTWAREALA A:133 , ILE A:134 , GLU A:135 , ASN A:136 , EDO A:307 , HOH A:451binding site for residue EDO A 306
07AC7SOFTWARETYR A:186 , ASP A:187 , ASN A:191 , EDO A:306binding site for residue EDO A 307
08AC8SOFTWAREALA A:86 , GLY A:87 , HOH A:455binding site for residue EDO A 308
09AC9SOFTWARELEU A:114 , THR A:115 , THR A:231 , GLY A:238 , HOH A:433 , HOH A:474 , HOH A:486binding site for residue PEG A 309
10AD1SOFTWAREGLU B:36 , TYR B:39 , TYR B:42 , TRP B:77 , ALA B:94 , ALA B:95 , GLY B:97 , ARG B:102 , MET B:117 , GLN B:165 , THR B:168 , SER B:169 , HIS B:170 , SER B:207 , VAL B:239 , HOH B:415binding site for residue 6DB B 301

(-) SS Bonds  (0, 0)

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

(-) 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 5ITP)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ITP)

(-) 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:254
                                                                                                                                                                                                                                                                                              
               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
                 5itp A  28 YKSITIATEGSYAPYNFKDAGGKLIGFDIDLGNDLCKRMNIECKFVEQAWDGIIPSLTAGRYDAIMAAMGIQPAREKVIAFSRPYLLTPMTFLTTADSPLLKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQMMPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMFGPRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFGYDASP 281
                                    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    


Chain B from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               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....hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeee.hhhhhhhhhhh....eeeeehhhhhhhhhhhhhh.eeeeeeeeehhhhh.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5itp B  28 YKSITIATEGSYAPYNFKDAGGKLIGFDIDLGNDLCKRMNIECKFVEQAWDGIIPSLTAGRYDAIMAAMGIQPAREKVIAFSRPYLLTPMTFLTTADSPLLKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQMMPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMFGPRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFGYDASP 281
                                    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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  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 5ITP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 5ito

(-) 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