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(-) Description

Title :  CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA OCCD3 (OPDP)
 
Authors :  B. Van Den Berg, E. Eren
Date :  16 Jul 11  (Deposition) - 08 Feb 12  (Release) - 08 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Beta-Barrel, Channel, Bacterial Outer Membrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Eren, J. Vijayaraghavan, J. Liu, B. R. Cheneke, D. S. Touw, B. W. Lepore, M. Indic, L. Movileanu, B. Van Den Berg
Substrate Specificity Within A Family Of Outer Membrane Carboxylate Channels.
Plos Biol. V. 10 01242 2012
PubMed-ID: 22272184  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1001242

(-) Compounds

Molecule 1 - GLYCINE-GLUTAMATE DIPEPTIDE PORIN OPDP
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 26-484
    Gene: OPDP, PA4501
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1C8E3Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1C8E3Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1C8E6Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2SO44Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:38 , THR A:94 , GLN A:95 , THR A:97BINDING SITE FOR RESIDUE SO4 A 468
2AC2SOFTWAREGLY A:34 , ALA A:35 , TYR A:93 , ARG A:149BINDING SITE FOR RESIDUE SO4 A 469
3AC3SOFTWARESER A:247 , HIS A:248 , ASN A:254BINDING SITE FOR RESIDUE C8E A 470
4AC4SOFTWARETYR A:256 , LEU A:258 , GLY A:279BINDING SITE FOR RESIDUE C8E A 471
5AC5SOFTWAREASN A:50 , HIS A:262 , ILE A:264 , LEU A:273 , LEU A:450 , SER A:452 , PHE A:454BINDING SITE FOR RESIDUE C8E A 472

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SYB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SYB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SYB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SYB)

(-) Exons   (0, 0)

(no "Exon" information available for 3SYB)

(-) 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:408
 aligned with Q9HVS0_PSEAE | Q9HVS0 from UniProtKB/TrEMBL  Length:484

    Alignment length:452
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482  
         Q9HVS0_PSEAE    33 PAPDNPSYAAEVQSIPSVAKPIKGQAGATGLVEGQSLTLTTRNFYSRENMKDSFTFRIPKAGGGSQRIHQRNAWVQGTVLKYSSGYTQGTVGFGFDVAAFNEIALERGKGRIGGGGNRTLANSDGEALGEWSKLGVANIRLRASNTEFKAGRFLVNTPVFSYIDNRALPSSFTGFAVTSEELDNLSLQAGSFRKVSPRTGSGDEDMTTEYGTRQVKGDRLNYLGGNYKPLDGLEISLYGSHFQDVWNQYYLGVTHDIGDLENGIALRTAFNGYHTGDTGAREAGYIDNDTWSLAFTLGHRAHALTLAYQQVDGNEYFDYVHETSAIFLANSMLADYNSPNEKSAQIRYETDWSYYGVPGLSTGVWYVKGWDIDGTHYDGDRNGAYGNYAEVRAQDGEKHHELGLMAAYKVQNGPIKDSTFKLTYMMHKASQNQIDGSVNELRLVSTFPFNLL 484
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh.hhhhhh...hhhhh.......eeeeeeeeeeeeee--------------------.eeeeeeeeeeeee.......eeeeeeeeeeeeee.-----------------------.eeeeeeeeeeeeee..eeeeeeee..ee..ee.........eeeeeeeeeeee..eeeeeeeeeeee.......................eeeeeeeeeee..eeeeeeeeee...eeeeeeeeeeee.-.....eeeeeeeeeeeee.........eeeeeeeeeeeee..eeeeeeeeeee.............................eeeeeeeeee.hhhh...eeeeeeeeeeeeee......hhhhh...hhhhhh.eeeeeeeeeeeeeee.........eeeeeeeeeee........eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3syb A   8 PAPDNPSYAAEVQSIPSVAKPIKGQAGATGLVEGQSLTLTTRNFYSREN--------------------QRNAWVQGTVLKYSSGYTQGTVGFGFDVAAFNEIAL-----------------------GEWSKLGVANIRLRASNTEFKAGRFLVNTPVFSYIDNRALPSSFTGFAVTSEELDNLSLQAGSFRKVSPRTGSGDEDMTTEYGTRQVKGDRLNYLGGNYKPLDGLEISLYGSHFQDVWNQYYLGVTHDIG-LENGIALRTAFNGYHTGDTGAREAGYIDNDTWSLAFTLGHRAHALTLAYQQVDGNEYFDYVHETSAIFLANSMLADYNSPNEKSAQIRYETDWSYYGVPGLSTGVWYVKGWDIDGTHYDGDRNGAYGNYAEVRAQDGEKHHELGLMAAYKVQNGPIKDSTFKLTYMMHKASQNQIDGSVNELRLVSTFPFNLL 459
                                    17        27        37        47        |-         -        77        87        97       107    |    -         -       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457  
                                                                           56                   77                                112                     136                                                                                                                              265 |                                                                                                                                                                                                
                                                                                                                                                                                                                                                                                             267
   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 3SYB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SYB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SYB)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9HVS0_PSEAE | Q9HVS0)
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: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: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.

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 Related Entries

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(-) Related Entries Specified in the PDB File

3sy7 3sy9 3sys 3szd 3szv 3t0s 3t20 3t24