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(-) Description

Title :  CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA OCCK2 (OPDF)
 
Authors :  B. Van Den Berg, E. Eren
Date :  18 Jul 11  (Deposition) - 08 Feb 12  (Release) - 08 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
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 - PORIN
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 25-421
    Gene: PA0240
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x):  B
Biological Unit 2 (1x): A 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
13PE1Ligand/Ion1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
2C8E5Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
3SO47Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
13PE-1Ligand/Ion1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
2C8E3Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
3SO45Ligand/IonSULFATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
13PE1Ligand/Ion1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
2C8E2Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
3SO42Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:314 , C8E A:407 , LEU B:308 , TYR B:310 , THR B:326 , ARG B:327 , ARG B:348BINDING SITE FOR RESIDUE C8E B 406
02AC2SOFTWARETYR B:310 , PHE B:312 , SO4 B:413BINDING SITE FOR RESIDUE C8E B 407
03AC3SOFTWARETYR A:354 , HIS B:25 , ASN B:27 , ASN B:370 , ASP B:384 , GLU B:385 , ASN B:386BINDING SITE FOR RESIDUE C8E B 408
04AC4SOFTWAREPHE B:9 , THR B:53 , GLN B:54BINDING SITE FOR RESIDUE SO4 B 409
05AC5SOFTWAREARG B:161 , ASN B:162 , HOH B:498 , HOH B:504BINDING SITE FOR RESIDUE SO4 B 410
06AC6SOFTWAREARG B:97BINDING SITE FOR RESIDUE SO4 B 411
07AC7SOFTWAREARG B:235 , HOH B:451BINDING SITE FOR RESIDUE SO4 B 412
08AC8SOFTWAREHIS B:263 , PHE B:312 , LEU B:317 , C8E B:407BINDING SITE FOR RESIDUE SO4 B 413
09AC9SOFTWAREGLY A:8 , PHE A:9 , LEU A:10 , THR A:53 , GLN A:54BINDING SITE FOR RESIDUE 3PE A 406
10BC1SOFTWAREHIS A:263 , PHE A:312 , PHE A:324 , C8E B:406BINDING SITE FOR RESIDUE C8E A 407
11BC2SOFTWARELEU A:66 , TYR A:67 , GLY A:96 , ARG A:97 , ARG A:235 , ARG A:250 , VAL A:252BINDING SITE FOR RESIDUE C8E A 408
12BC3SOFTWAREGLN A:54 , GLY A:55BINDING SITE FOR RESIDUE SO4 A 409
13BC4SOFTWAREARG A:161BINDING SITE FOR RESIDUE SO4 A 410

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp B:72 -Gly B:73
2Gly A:6 -Gln A:7

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SZD)

(-) 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:368
 aligned with Q9I6P8_PSEAE | Q9I6P8 from UniProtKB/TrEMBL  Length:421

    Alignment length:392
                                    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       359       369       379       389       399       409       419  
         Q9I6P8_PSEAE    30 GQGFLEDAKASLTARNFHLHRNFVGDASQGKAEEWTQSFILDARSGFTQGSVGFGLDVLGLYSLKLDGGKGTAGTQLLPIHDDGRPADDFGRLAVAGKLRVSNSELKIGEWMPVLPILRSDDGRSLPQTFRGGQLSANEIAGLTLYAGQFRGNSPRNDASMQDMSLFGRPAATSDRFDFAGGEYRFNGERSLLGLWNAELKDIYRQQYLQLQHSQPLGDWLLGANLGGFRGRDAGSARAGKLDNRTVSALFSARYGLHTLYLGLQKVSGDDGWMRVNGTSGGTLANDSYNASYDNPGERSWQLRYDFDFVGLGLPGLTFMTRYLHGDHVRLAGVTDDGSEWGRESELGYTLQSGAFKRLNVRWRNSSQRRDWGSNTRFDENRLIVSYPLSLL 421
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeeeeeee..----.eeeeeeeeeeeeee.......eeeeeeeeeeeeee....-----------------..eeeeeeeeeeeee..eeeeeeee..ee..ee.........eeeeeeeeeeee..eeeeeeeeeeee.........eee..eeeeee..eeeeeeeeee....eeeeeeeeee...eeeeeeeeeeeeee..eeeeeeeeeeeeee.........eeeeeeeeeeeee..eeeeeeeeeee..............................eeeeeeeeee........eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee.........eeeeeeeeeee...---.eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3szd A   6 GQGFLEDAKASLTARNFHLHRNFVG----GKAEEWTQSFILDARSGFTQGSVGFGLDVLGLYSLKLDGG-----------------ADDFGRLAVAGKLRVSNSELKIGEWMPVLPILRSDDGRSLPQTFRGGQLSANEIAGLTLYAGQFRGNSPRNDASMQDMSLFGRPAATSDRFDFAGGEYRFNGERSLLGLWNAELKDIYRQQYLQLQHSQPLGDWLLGANLGGFRGRDAGSARAGKLDNRTVSALFSARYGLHTLYLGLQKVSGDDGWMRVNGTSGGTLANDSYNASYDNPGERSWQLRYDFDFVGLGLPGLTFMTRYLHGDHVRLAGVTDDGSEWGRESELGYTLQSGAFKRLNVRWRNSSQRRDWG---RFDENRLIVSYPLSLL 397
                                    15        25    |   35        45        55        65        |-         -      | 95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375  |   |385       395  
                                                   30   35                                     74                92                                                                                                                                                                                                                                                                                           378 382               


Chain B from PDB  Type:PROTEIN  Length:371
 aligned with Q9I6P8_PSEAE | Q9I6P8 from UniProtKB/TrEMBL  Length:421

    Alignment length:392
                                                                                                                                                                                                                                                                                                                                                                                                                                421 
                                    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       340       350       360       370       380       390       400       410       420| 
         Q9I6P8_PSEAE    31 QGFLEDAKASLTARNFHLHRNFVGDASQGKAEEWTQSFILDARSGFTQGSVGFGLDVLGLYSLKLDGGKGTAGTQLLPIHDDGRPADDFGRLAVAGKLRVSNSELKIGEWMPVLPILRSDDGRSLPQTFRGGQLSANEIAGLTLYAGQFRGNSPRNDASMQDMSLFGRPAATSDRFDFAGGEYRFNGERSLLGLWNAELKDIYRQQYLQLQHSQPLGDWLLGANLGGFRGRDAGSARAGKLDNRTVSALFSARYGLHTLYLGLQKVSGDDGWMRVNGTSGGTLANDSYNASYDNPGERSWQLRYDFDFVGLGLPGLTFMTRYLHGDHVRLAGVTDDGSEWGRESELGYTLQSGAFKRLNVRWRNSSQRRDWGSNTRFDENRLIVSYPLSLL-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeeeee..----.eeeeeeeeeeeeee........eeeeeeeeeeeee....-----------------..eeeeeeeeeeeee..eeeeeeee..ee..ee.........eeeeeeeee.....eeeeeeeeeeee.........ee.......ee..eeeeeeeeee....eeeeeeeeee...eeeeeeeeeeeeee..eeeeeeeeeeeeee.........eeeeeeeeeeeee..eeeeeeeeeee..............................eeeeeeeeee.hhhh...eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee.........eeeeeeeeeee.......eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3szd B   7 QGFLEDAKASLTARNFHLHRNFVG----GKAEEWTQSFILDARSGFTQGSVGFGLDVLGLYSLKLDGG-----------------ADDFGRLAVAGKLRVSNSELKIGEWMPVLPILRSDDGRSLPQTFRGGQLSANEIAGLTLYAGQFRGNSPRNDASMQDMSLFGRPAATSDRFDFAGGEYRFNGERSLLGLWNAELKDIYRQQYLQLQHSQPLGDWLLGANLGGFRGRDAGSARAGKLDNRTVSALFSARYGLHTLYLGLQKVSGDDGWMRVNGTSGGTLANDSYNASYDNPGERSWQLRYDFDFVGLGLPGLTFMTRYLHGDHVRLAGVTDDGSEWGRESELGYTLQSGAFKRLNVRWRNSSQRRDWGSNTRFDENRLIVSYPLSLLG 398
                                    16        26   |    36        46        56        66       | -         -     |  96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396  
                                                  30   35                                     74                92
   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 3SZD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9I6P8_PSEAE | Q9I6P8)
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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        Q9I6P8_PSEAE | Q9I6P8: 4fms

(-) Related Entries Specified in the PDB File

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