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(-) Description

Title :  HIGH RESOLUTION XRAY STRUCTURE OF OMP32
 
Authors :  K. Zeth, U. Zachariae, H. Engelhardt
Date :  22 Dec 05  (Deposition) - 31 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Omp32 Porin Outer Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Zachariae, T. Kluhspies, S. De, H. Engelhardt, K. Zeth
High Resolution Crystal Structures And Molecular Dynamics Studies Reveal Substrate Binding In The Porin Omp32
J. Biol. Chem. V. 281 7413 2006
PubMed-ID: 16434398  |  Reference-DOI: 10.1074/JBC.M510939200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OUTER MEMBRANE PORIN PROTEIN 32
    Chains: A
    Mutation: YES
    Organism Scientific: DELFTIA ACIDOVORANS
    Organism Taxid: 80866
    Synonym: OMP32
 
Molecule 2 - PAP
    Chains: B
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO46Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:29 , ASP A:64 , ASN A:136 , GLU A:158 , GLY A:309 , HOH A:627BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWAREGLY A:70 , PHE A:71 , HOH A:893BINDING SITE FOR RESIDUE CA A 502
3AC3SOFTWAREARG A:76 , THR A:78 , SER A:80 , HOH A:721BINDING SITE FOR RESIDUE CA A 503
4AC4SOFTWAREGLU A:254 , LYS A:256 , ARG A:329 , HOH A:669 , HOH A:729 , HOH A:947 , HOH A:967BINDING SITE FOR RESIDUE SO4 A 600
5AC5SOFTWAREARG A:38 , HOH A:659 , HOH A:747BINDING SITE FOR RESIDUE SO4 A 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FGR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FGR)

(-) 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:332
 aligned with OMP32_DELAC | P24305 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:332
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349  
          OMP32_DELAC    20 QSSVTLFGIVDTNVAYVNKDAAGDSRYGLGTSGASTSRLGLRGTEDLGGGLKAGFWLEGEIFGDDGNASGFNFKRRSTVSLSGNFGEVRLGRDLVPTSQKLTSYDLFSATGIGPFMGFRNWAAGQGADDNGIRANNLISYYTPNFGGFNAGFGYAFDEKQTIGTADSVGRYIGGYVAYDNGPLSASLGLAQQKTAVGGLATDRDEITLGASYNFGVAKLSGLLQQTKFKRDIGGDIKTNSYMLGASAPVGGVGEVKLQYALYDQKAIDSKAHQITLGYVHNLSKRTALYGNLAFLKNKDASTLGLQAKGVYAGGVQAGESQTGVQVGIRHAF 351
               SCOP domains d2fgra_ A: automated matches                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2fgrA00 A:1-332 Porin                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeee........eeeeee......eeeeeeeeeee..eeeeeeeeee...............eeeeeeee..eeeee..eehhhhhhhhhhh...........................ee..eeeee......eeeeeeee...............eeeeeeeee...eeeeeeeeeeeeee..eeeeeeeeeeeeeee....eeeeeeeeeeeee....eeeeeeeeeeeeeee...eeeeeeeeeeee.hhheeeeeeeeeeeee....eeeeeeeeeeee......................eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fgr A   1 ESSVTLFGIVDTNVAYVNKDAAGDSRYGLGTSGASTSRLGLRGTEDLGGGLKAGFWLEGEIFGDDGNASGFNFKRRSTVSLSGNFGEVRLGRDLVPTSQKLTSYDLFSATGIGPFMGFRNWAAGQGADDNGIRANNLISYYTPNFGGFNAGFGYAFDEKQTIGTADSVGRYIGGYVAYDNGPLSASLGLAQQKTAVGGLATDRDEITLGASYNFGVAKLSGLLQQTKFKRDIGGDIKTNSYMLGASAPVGGVGEVKLQYALYDQKAIDSKAHQITLGYVHNLSKRTALYGNLAFLKNKDASTLGLQAKGVYAGGVQAGESQTGVQVGIRHAF 332
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330  


Chain B from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 2fgr B 401 DNWQNGTS 408
   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 Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (OMP32_DELAC | P24305)
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.
biological process
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        OMP32_DELAC | P24305: 1e54 2fgq

(-) Related Entries Specified in the PDB File

1e54 2fgq