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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF E.COLI YBGF
 
Authors :  A. M. Krachler, A. Sharma, C. Kleanthous
Date :  24 Nov 09  (Deposition) - 15 Sep 10  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  C,D,E  (1x)
Biol. Unit 2:  A,B,F  (1x)
Keywords :  Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Krachler, A. Sharma, A. Cauldwell, G. Papadakos, C. Kleanthous
Tola Modulates The Oligomeric Status Of Ybgf In The Bacterial Periplasm.
J. Mol. Biol. V. 403 270 2010
PubMed-ID: 20816983  |  Reference-DOI: 10.1016/J.JMB.2010.08.050

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN YBGF
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: N-TERMINAL DOMAIN, RESIDUES 35-109
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x):   CDE 
Biological Unit 2 (1x): AB   F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric Unit (6, 9)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2AU2Ligand/IonGOLD ION
3AUC1Ligand/IonGOLD (I) CYANIDE ION
4EDO1Ligand/Ion1,2-ETHANEDIOL
5GOL2Ligand/IonGLYCEROL
6NA1Ligand/IonSODIUM ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2AU-1Ligand/IonGOLD ION
3AUC1Ligand/IonGOLD (I) CYANIDE ION
4EDO-1Ligand/Ion1,2-ETHANEDIOL
5GOL1Ligand/IonGLYCEROL
6NA-1Ligand/IonSODIUM ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2AU-1Ligand/IonGOLD ION
3AUC-1Ligand/IonGOLD (I) CYANIDE ION
4EDO1Ligand/Ion1,2-ETHANEDIOL
5GOL1Ligand/IonGLYCEROL
6NA-1Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU C:29 , SER C:30 , GLN C:33 , GLN E:28 , ASP E:31 , ASN E:32 , HOH E:2013 , ARG F:56BINDING SITE FOR RESIDUE GOL E1069
2AC2SOFTWARELYS A:58 , GLN A:59 , LEU A:62 , GLU C:55 , GLN C:59BINDING SITE FOR RESIDUE GOL A1068
3AC3SOFTWAREVAL A:4 , VAL B:4 , VAL C:4 , GLU D:5 , VAL F:4BINDING SITE FOR RESIDUE ACT A1069
4AC4SOFTWAREGLN C:24 , GLN C:28BINDING SITE FOR RESIDUE ACT C1070
5AC5SOFTWARELEU F:61 , LEU F:62 , ILE F:64BINDING SITE FOR RESIDUE EDO F1065
6AC6SOFTWAREGLN C:57 , VAL D:53 , ARG D:56 , GLN D:57 , GLN E:57BINDING SITE FOR RESIDUE AUC D1069
7AC7SOFTWARETYR D:48 , ASN D:51 , SER E:34 , SER E:38BINDING SITE FOR RESIDUE NA E1070
8AC8SOFTWAREGLN B:57 , GLN C:33 , GLN F:52 , VAL F:53 , ARG F:56 , HOH F:2015BINDING SITE FOR RESIDUE AU F1066
9AC9SOFTWAREASN A:32 , LEU B:29 , ASN B:32 , LEU F:29 , ASN F:32BINDING SITE FOR RESIDUE AU F1067

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WZ7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly B:2 -Ser B:3
2Leu B:67 -Ser B:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WZ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WZ7)

(-) Exons   (0, 0)

(no "Exon" information available for 2WZ7)

(-) 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:66
 aligned with CPOB_ECOLI | P45955 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:66
                                    45        55        65        75        85        95      
           CPOB_ECOLI    36 GSVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQIDSL 101
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 2wz7 A   2 GSVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQIDSL  67
                                    11        21        31        41        51        61      


Chain B from PDB  Type:PROTEIN  Length:67
 aligned with CPOB_ECOLI | P45955 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:67
                                    45        55        65        75        85        95       
           CPOB_ECOLI    36 GSVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQIDSLS 102
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 2wz7 B   2 GSVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQIDSLS  68
                                    11        21        31        41        51        61       


Chain C from PDB  Type:PROTEIN  Length:67
 aligned with CPOB_ECOLI | P45955 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:67
                                    46        56        66        76        86        96       
           CPOB_ECOLI    37 SVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQIDSLSS 103
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 2wz7 C   3 SVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQIDSLSS  69
                                    12        22        32        42        52        62       


Chain D from PDB  Type:PROTEIN  Length:67
 aligned with CPOB_ECOLI | P45955 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:67
                                    45        55        65        75        85        95       
           CPOB_ECOLI    36 GSVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQIDSLS 102
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 2wz7 D   2 GSVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQIDSLS  68
                                    11        21        31        41        51        61       


Chain E from PDB  Type:PROTEIN  Length:67
 aligned with CPOB_ECOLI | P45955 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:67
                                    45        55        65        75        85        95       
           CPOB_ECOLI    36 GSVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQIDSLS 102
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 2wz7 E   2 GSVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQIDSLS  68
                                    11        21        31        41        51        61       


Chain F from PDB  Type:PROTEIN  Length:62
 aligned with CPOB_ECOLI | P45955 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:62
                                    46        56        66        76        86        96  
           CPOB_ECOLI    37 SVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQI  98
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 2wz7 F   3 SVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQI  64
                                    12        22        32        42        52        62
   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 2WZ7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WZ7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WZ7)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (CPOB_ECOLI | P45955)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0070206    protein trimerization    The formation of a protein trimer, a macromolecular structure consisting of three noncovalently associated identical or nonidentical subunits.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

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  2wz7
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  CPOB_ECOLI | P45955
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 Related Entries

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

UniProtKB/Swiss-Prot
        CPOB_ECOLI | P45955: 2xdj

(-) Related Entries Specified in the PDB File

2xdj CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF E.COLI YBGF
2xev CRYSTAL STRUCTURE OF THE TPR DOMAIN OF XANTHOMONAS CAMPESTRIS YBGF