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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF THE OUTER MEMBRANE PROTEIN A (OMPA) TRANSMEMBRANE DOMAIN
 
Authors :  A. Pautsch, G. E. Schulz
Date :  29 Jun 99  (Deposition) - 30 Jun 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Outer Membrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Pautsch, G. E. Schulz
High Resolution Structure Of The Ompa Membrane Domain
J. Mol. Biol. V. 298 273 2000
PubMed-ID: 10764596  |  Reference-DOI: 10.1006/JMBI.2000.3671
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN A
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3B-171
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentTRANSMEMBRANE DOMAIN
    GeneOMPA
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    PlasmidPET3B-171
    StrainBL21(DE3)

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1C8E6Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:43 , PHE A:51 , LEU A:79 , PRO A:121 , ASN A:145 , C8E A:1175BINDING SITE FOR RESIDUE C8E A1172
2AC2SOFTWARELEU A:13 , GLN A:17 , ILE A:131 , THR A:137 , LEU A:139BINDING SITE FOR RESIDUE C8E A1173
3AC3SOFTWARETYR A:48 , LEU A:83 , GLY A:84 , TYR A:85 , ILE A:93 , TYR A:94 , THR A:95BINDING SITE FOR RESIDUE C8E A1174
4AC4SOFTWAREVAL A:77 , GLY A:99 , VAL A:101 , C8E A:1172BINDING SITE FOR RESIDUE C8E A1175
5AC5SOFTWAREALA A:11 , LEU A:13 , LEU A:35 , GLY A:36 , ALA A:37 , GLY A:38 , TRP A:57 , GLY A:59 , ARG A:60 , MET A:61BINDING SITE FOR RESIDUE C8E A1176
6AC6SOFTWAREASN A:46 , THR A:95 , TRP A:143 , ASN A:145BINDING SITE FOR RESIDUE C8E A1177

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QJP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QJP)

(-) Sequences/Alignments

Asymmetric/Biological 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:137
 aligned with OMPA_ECO57 | P0A911 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:171
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 
           OMPA_ECO57    22 APKDNTWYTGAKLGWSQYHDTGFINNNGPTHENQLGAGAFGGYQVNPYVGFEMGYDWLGRMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTKSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTNNIGDAHTIGTRPDNGMLSLGVSYRFG 192
               SCOP domains d1qjpa_ A: Outer              membrane protein A (OMPA) transme       mbrane domain                                                                                         SCOP domains
               CATH domains 1qjpA00 A:1-171               [code=2.40.160.20, no name define       d]                                                                                                    CATH domains
               Pfam domains -OmpA_membrane-1q             jpA01 A:2-171                                                                                                                                 Pfam domains
         Sec.struct. author .....eeeeeeeeeee.-------------...eeeeeeeeeeeee..eeeeeeeeeeee...-------.eeeeeeeeeeeeeee....eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeee..eeeeeeeeee.--------------.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qjp A   1 APKDNTWYTGAKLGWSQ-------------HENKLGAGAFGGYQVNPYVGFEMGYDWLGRMPY-------AYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTYSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTN--------------GMLSLGVSYRFG 171
                                    10      |  -         -|       40        50        60  |      -|       80        90       100       110       120       130       140    |    -       160       170 
                                           17            31                              63      71                                                                       145            160           

Chain A from PDB  Type:PROTEIN  Length:137
 aligned with OMPA_ECOLI | P0A910 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:171
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 
           OMPA_ECOLI    22 APKDNTWYTGAKLGWSQYHDTGFINNNGPTHENQLGAGAFGGYQVNPYVGFEMGYDWLGRMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTKSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTNNIGDAHTIGTRPDNGMLSLGVSYRFG 192
               SCOP domains d1qjpa_ A: Outer              membrane protein A (OMPA) transme       mbrane domain                                                                                         SCOP domains
               CATH domains 1qjpA00 A:1-171               [code=2.40.160.20, no name define       d]                                                                                                    CATH domains
               Pfam domains -OmpA_membrane-1q             jpA01 A:2-171                                                                                                                                 Pfam domains
         Sec.struct. author .....eeeeeeeeeee.-------------...eeeeeeeeeeeee..eeeeeeeeeeee...-------.eeeeeeeeeeeeeee....eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeee..eeeeeeeeee.--------------.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qjp A   1 APKDNTWYTGAKLGWSQ-------------HENKLGAGAFGGYQVNPYVGFEMGYDWLGRMPY-------AYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTYSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTN--------------GMLSLGVSYRFG 171
                                    10      |  -         -|       40        50        60  |      -|       80        90       100       110       120       130       140    |    -       160       170 
                                           17            31                              63      71                                                                       145            160           

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: MBB (97)

(-) Gene Ontology  (16, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (OMPA_ECO57 | P0A911)
molecular function
    GO:0015288    porin activity    Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0000746    conjugation    The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0046930    pore complex    Any small opening in a membrane that allows the passage of gases and/or liquids.

Chain A   (OMPA_ECOLI | P0A910)
molecular function
    GO:0015288    porin activity    Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
    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).
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0000746    conjugation    The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
    GO:0009597    detection of virus    The series of events in which a stimulus from a virus is received and converted into a molecular signal.
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules 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.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019867    outer membrane    The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.
    GO:0046930    pore complex    Any small opening in a membrane that allows the passage of gases and/or liquids.

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 Related Entries

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

UniProtKB/Swiss-Prot
        OMPA_ECOLI | P0A9101bxw 1g90 2ge4 2jmm 3jbu 3nb3 5m2q

(-) Related Entries Specified in the PDB File

1bxw