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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OUTER MEMBRANE PROTEIN OPDK FROM PSEUDOMONAS AERUGINOSA
 
Authors :  S. Biswas, B. Van Den Berg
Date :  02 Aug 07  (Deposition) - 24 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Outer Membrane Protein, Beta Barrel, Vanillate Transport, Porin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Biswas, M. M. Mohammad, L. Movileanu, B. Van Den Berg
Crystal Structure Of The Outer Membrane Protein Opdk From Pseudomonas Aeruginosa.
Structure V. 16 1027 2008
PubMed-ID: 18611376  |  Reference-DOI: 10.1016/J.STR.2008.04.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE PORIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: OPDK GENE WITH SHLB SIGNAL SEQUENCE CLONED INTO PB22 WITH 8 HIS TAG
    Expression System Strain: C43 E.COLI CELLS
    Expression System Vector Type: PB22
    Gene: PSEUDOMONAS AERUGINOSA
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Strain: PAO1

 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, 22)

Asymmetric Unit (1, 22)
No.NameCountTypeFull Name
1C8E22Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1C8E12Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1C8E10Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA B:182 , ALA B:184 , TYR B:186 , HIS B:260 , TYR B:307 , ARG B:344BINDING SITE FOR RESIDUE C8E B 391
02AC2SOFTWAREASN A:17 , TRP A:37 , LEU A:382BINDING SITE FOR RESIDUE C8E A 391
03AC3SOFTWARELEU B:195 , MET B:322 , ARG B:344BINDING SITE FOR RESIDUE C8E B 392
04AC4SOFTWAREPRO A:143 , TYR A:186 , ARG A:344BINDING SITE FOR RESIDUE C8E A 392
05AC5SOFTWARELEU A:195 , GLY A:321 , MET A:322 , ARG A:344BINDING SITE FOR RESIDUE C8E A 393
06AC6SOFTWAREALA A:182 , ALA A:184 , HIS A:199 , HIS A:260 , PHE A:262 , TYR A:307BINDING SITE FOR RESIDUE C8E A 394
07AC7SOFTWAREPHE A:135BINDING SITE FOR RESIDUE C8E A 395
08AC8SOFTWARELEU A:228 , TYR A:250 , LEU A:266BINDING SITE FOR RESIDUE C8E A 398
09AC9SOFTWARETRP A:37 , GLN A:39 , PHE B:41BINDING SITE FOR RESIDUE C8E A 399
10BC1SOFTWARELEU A:147 , PHE A:262 , TYR A:307BINDING SITE FOR RESIDUE C8E A 401
11BC2SOFTWAREASN B:180 , TYR B:181 , HIS B:199BINDING SITE FOR RESIDUE C8E B 393
12BC3SOFTWAREPHE B:253BINDING SITE FOR RESIDUE C8E B 394
13BC4SOFTWARELEU B:224 , GLY B:225 , SER B:254 , ALA B:255 , TYR B:263BINDING SITE FOR RESIDUE C8E B 395
14BC5SOFTWARESER B:106 , LEU B:108BINDING SITE FOR RESIDUE C8E B 396
15BC6SOFTWARETRP B:222BINDING SITE FOR RESIDUE C8E B 397
16BC7SOFTWARELEU B:142 , TRP B:303BINDING SITE FOR RESIDUE C8E B 398
17BC8SOFTWAREASN B:17 , TRP B:37BINDING SITE FOR RESIDUE C8E B 399
18BC9SOFTWARELEU B:195 , LEU B:228 , GLY B:229 , TRP B:316BINDING SITE FOR RESIDUE C8E B 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QTK)

(-) 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:371
 aligned with Q9HUR5_PSEAE | Q9HUR5 from UniProtKB/TrEMBL  Length:417

    Alignment length:387
                                    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       
         Q9HUR5_PSEAE    31 GFLEDAKTDLVLRNYYFNRDFRDHDAGKSLVDEWAQGFILKFSSGYTPGTVGVGLDAIGLFGVKLNSGRGTSNSELLPLHDDGRAADNYGRVGVAAKLRVSASELKIGEMLPDIPLLRYDDGRLLPQTFRGFAVVSRELPGLALQAGRFDAVSLRNSADMQDLSAWSAPTQKSDGFNYAGAEYRFNRERTQLGLWHGQLEDVYRQSYANLLHKQRVGDWTLGANLGLFVDRDDGAARAGEIDSHTVYGLFSAGIGLHTFYLGLQKVGGDSGWQSVYGSSGRSMGNDMFNGNFTNADERSWQVRYDYDFVGLGWPGLIGMVRYGHGSNATTKAGSGGKEWERDVELGYTVQSGPLARLNVRLNHASNRRSFNSDFDQTRLVVSYPLSW 417
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----2qtkA01 A:8-390 P      orin                                                                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeeeeee.------..eeeeeeeeeeeeee.......eeeeeeeeeeeeee..------........----...eeeeeeeeeeeee..eeeeeeee..ee..ee.........eeeeeeeee.....eeeeeeeeeeee......................eeeeeeee......eeeeeeeeee...eeeeeeeeeeeeee..eeeeeeeeeeeeee.........eeeeeeeeeeeee..eeeeeeeeeeee.............................eeeeeeeeee.hhhh...eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qtk A   4 GFLEDAKTDLVLRNYYFNRDF------KSLVDEWAQGFILKFSSGYTPGTVGVGLDAIGLFGVKLN------NSELLPLH----AADNYGRVGVAAKLRVSASELKIGEMLPDIPLLRYDDGRLLPQTFRGFAVVSRELPGLALQAGRFDAVSLRNSADMQDLSAWSAPTQKSDGFNYAGAEYRFNRERTQLGLWHGQLEDVYRQSYANLLHKQRVGDWTLGANLGLFVDRDDGAARAGEIDSHTVYGLFSAGIGLHTFYLGLQKVGGDSGWQSVYGSSGRSMGNDMFNGNFTNADERSWQVRYDYDFVGLGWPGLIGMVRYGHGSNATTKAGSGGKEWERDVELGYTVQSGPLARLNVRLNHASNRRSFNSDFDQTRLVVSYPLSW 390
                                    13        23|      |33        43        53        63     |   -  |     83    |   93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       
                                               24     31                                    69     76     83   88                                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:368
 aligned with Q9HUR5_PSEAE | Q9HUR5 from UniProtKB/TrEMBL  Length:417

    Alignment length:386
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411      
         Q9HUR5_PSEAE    32 FLEDAKTDLVLRNYYFNRDFRDHDAGKSLVDEWAQGFILKFSSGYTPGTVGVGLDAIGLFGVKLNSGRGTSNSELLPLHDDGRAADNYGRVGVAAKLRVSASELKIGEMLPDIPLLRYDDGRLLPQTFRGFAVVSRELPGLALQAGRFDAVSLRNSADMQDLSAWSAPTQKSDGFNYAGAEYRFNRERTQLGLWHGQLEDVYRQSYANLLHKQRVGDWTLGANLGLFVDRDDGAARAGEIDSHTVYGLFSAGIGLHTFYLGLQKVGGDSGWQSVYGSSGRSMGNDMFNGNFTNADERSWQVRYDYDFVGLGWPGLIGMVRYGHGSNATTKAGSGGKEWERDVELGYTVQSGPLARLNVRLNHASNRRSFNSDFDQTRLVVSYPLSW 417
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---2qtkB01 B:8-390 P        orin                                                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeeee.--------.eeeeeeeeeeeeee.......eeeeeeeeeeeee..------........----...eeeeeeeeeeee...eeeeeeee..ee..ee.........eeeeeeeee.....eeeeeeeeeeee......................eeeeeeeeee....eeeeeeeeee...eeeeeeeeeeeeee..eeeeeeeeeeeee..........eeeeeeeeeeeee..eeeeeeeeeeee..........hhhhh..............eeeeeeeeee.hhhh...eeeeeeeeeeeee.......eeeeeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qtk B   5 FLEDAKTDLVLRNYYFNRDF--------LVDEWAQGFILKFSSGYTPGTVGVGLDAIGLFGVKLN------NSELLPLH----AADNYGRVGVAAKLRVSASELKIGEMLPDIPLLRYDDGRLLPQTFRGFAVVSRELPGLALQAGRFDAVSLRNSADMQDLSAWSAPTQKSDGFNYAGAEYRFNRERTQLGLWHGQLEDVYRQSYANLLHKQRVGDWTLGANLGLFVDRDDGAARAGEIDSHTVYGLFSAGIGLHTFYLGLQKVGGDSGWQSVYGSSGRSMGNDMFNGNFTNADERSWQVRYDYDFVGLGWPGLIGMVRYGHGSNATTKAGSGGKEWERDVELGYTVQSGPLARLNVRLNHASNRRSFNSDFDQTRLVVSYPLSW 390
                                    14        24        34        44        54        64    |    - |      |-   |    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384      
                                              24       33                                  69     76     83   88
   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 2QTK)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9HUR5_PSEAE | Q9HUR5)
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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  2qtk
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        Q9HUR5_PSEAE | Q9HUR5: 2y2x 3sys

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