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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OUTER MEMBRANE LIPOPROTEIN RECEPTOR, LOLB
 
Authors :  K. Takeda, H. Miyatake, N. Yokota, S. Matsuyama, H. Tokuda, K. Miki
Date :  17 May 02  (Deposition) - 15 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Unclosed Beta Barrel, Lipoprotein, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Takeda, H. Miyatake, N. Yokota, S. Matsuyama, H. Tokuda, K. Miki
Crystal Structures Of Bacterial Lipoprotein Localization Factors, Lola And Lolb.
Embo J. V. 22 3199 2003
PubMed-ID: 12839983  |  Reference-DOI: 10.1093/EMBOJ/CDG324
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OUTER MEMBRANE LIPOPROTEIN LOLB
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PYKT102
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:21 , ARG A:135 , GLN A:160 , PRO A:161 , ALA A:162 , HOH A:259BINDING SITE FOR RESIDUE SO4 A 191
2AC2SOFTWAREARG A:34 , ARG A:49 , HOH A:226 , HOH A:255 , HOH A:361BINDING SITE FOR RESIDUE SO4 A 192
3AC3SOFTWAREHIS B:21 , ARG B:135 , GLN B:160 , PRO B:161 , ALA B:162BINDING SITE FOR RESIDUE SO4 B 193
4AC4SOFTWAREARG B:34 , ARG B:49BINDING SITE FOR RESIDUE SO4 B 194

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IWM)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:160 -Pro A:161
2Gln B:160 -Pro B:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IWM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IWM)

(-) Exons   (0, 0)

(no "Exon" information available for 1IWM)

(-) 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:177
 aligned with LOLB_ECOLI | P61320 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:177
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
           LOLB_ECOLI    31 GKSPDSPQWRQHQQDVRNLNQYQTRGAFAYISDQQKVYARFFWQQTGQDRYRLLLTNPLGSTELELNAQPGNVQLVDNKGQRYTADDAEEMIGKLTGMPIPLNSLRQWILGLPGDATDYKLDDQYRLSEITYSQNGKNWKVVYGGYDTKTQPAMPANMELTDGGQRIKLKMDNWIVK 207
               SCOP domains d1iwma_ A: Outer membrane lipoprotein receptor LolB                                                                                                                               SCOP domains
               CATH domains 1iwmA00 A:10-186 outer membrane lipoprotein receptor (LolB), chain A                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..eeeeeeeeeee....eeeeeeeeeee...eeeeeee.....eeeeeeee..eeeee.....eeee.hhhhhhhhhhh...hhhhhhhhh.........eee.....eeeeeee....eeeeee..ee......ee.eeeee....eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iwm A  10 GKSPDSPQWRQHQQDVRNLNQYQTRGAFAYISDQQKVYARFFWQQTGQDRYRLLLTNPLGSTELELNAQPGNVQLVDNKGQRYTADDAEEMIGKLTGMPIPLNSLRQWILGLPGDATDYKLDDQYRLSEITYSQNGKNWKVVYGGYDTKTQPAMPANMELTDGGQRIKLKMDNWIVK 186
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with LOLB_ECOLI | P61320 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:177
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
           LOLB_ECOLI    31 GKSPDSPQWRQHQQDVRNLNQYQTRGAFAYISDQQKVYARFFWQQTGQDRYRLLLTNPLGSTELELNAQPGNVQLVDNKGQRYTADDAEEMIGKLTGMPIPLNSLRQWILGLPGDATDYKLDDQYRLSEITYSQNGKNWKVVYGGYDTKTQPAMPANMELTDGGQRIKLKMDNWIVK 207
               SCOP domains d1iwmb_ B: Outer membrane lipoprotein receptor LolB                                                                                                                               SCOP domains
               CATH domains 1iwmB00 B:10-186 outer membrane lipoprotein receptor (LolB), chain A                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..eeeeeeeeeee....eeeeeeeeeee...eeeeeee.....eeeeeeee..eeeee.....eeee.hhhhhhhhhhh...hhhhhhhhh.........eee.....eeeeeeee..eeeeeee..ee......ee.eeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iwm B  10 GKSPDSPQWRQHQQDVRNLNQYQTRGAFAYISDQQKVYARFFWQQTGQDRYRLLLTNPLGSTELELNAQPGNVQLVDNKGQRYTADDAEEMIGKLTGMPIPLNSLRQWILGLPGDATDYKLDDQYRLSEITYSQNGKNWKVVYGGYDTKTQPAMPANMELTDGGQRIKLKMDNWIVK 186
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
   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  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IWM)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LOLB_ECOLI | P61320)
molecular function
    GO:0071723    lipopeptide binding    Interacting selectively and non-covalently with a lipopeptide, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds and containing a nonprotein group consisting of a lipid or lipids.
    GO:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
    GO:0010876    lipid localization    Any process in which a lipid is transported to, or maintained in, a specific location.
    GO:0044874    lipoprotein localization to outer membrane    A process in which a lipoprotein is transported to, or maintained in, a specific location in an outer membrane.
    GO:0042157    lipoprotein metabolic process    The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
    GO:0051668    localization within membrane    Any process in which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a membrane.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LOLB_ECOLI | P61320: 1iwn

(-) Related Entries Specified in the PDB File

1iwl 1IWL CONTAINS CRYSTAL STRUCTURE OF THE LIPOPROTEIN LOCALIZATION FACTOR, LOLA
1iwn 1IWN CONTAINS CRYSTAL STRUCTURE OF THE SAME PROTEIN COMPLEXED WITH PG5