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(-) Description

Title :  STRUCTURE OF OMPF PORIN
 
Authors :  W. A. Cramer, S. D. Zakharov, E. Yamashita
Date :  04 Jan 08  (Deposition) - 29 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Ompf Porin, Ordered Waters, Ion Transport, Membrane, Outer Membrane, Phage Recognition, Transmembrane, Transport, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Yamashita, M. V. Zhalnina, S. D. Zakharov, O. Sharma, W. A. Cramer
Crystal Structures Of The Ompf Porin: Function In A Colicin Translocon.
Embo J. V. 27 2171 2008
PubMed-ID: 18636093  |  Reference-DOI: 10.1038/EMBOJ.2008.137
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN F
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneOMPF, CMLB, COA, CRY, TOLF
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymPORIN OMPF, OUTER MEMBRANE PROTEIN 1A, OUTER MEMBRANE PROTEIN IA, OUTER MEMBRANE PROTEIN B

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1C8E2Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1C8E6Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:660 , HOH A:661 , HOH A:662 , HOH A:663 , HOH A:664 , HOH A:665BINDING SITE FOR RESIDUE MG A 341
2AC2SOFTWARETYR A:98 , LEU A:158 , ASP A:172 , GLY A:173 , ALA A:193 , LYS A:210BINDING SITE FOR RESIDUE C8E A 342
3AC3SOFTWAREPHE A:267 , LEU A:269 , PRO A:271 , ILE A:273 , GLY A:298BINDING SITE FOR RESIDUE C8E A 343

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GRAM_NEG_PORINPS00576 General diffusion Gram-negative porins signature.OMPF_ECOLI317-333  1A:295-311
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GRAM_NEG_PORINPS00576 General diffusion Gram-negative porins signature.OMPF_ECOLI317-333  3A:295-311

(-) Exons   (0, 0)

(no "Exon" information available for 2ZFG)

(-) 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:339
 aligned with OMPF_ECOLI | P02931 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:340
                                    32        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
           OMPF_ECOLI    23 AEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 362
               SCOP domains d2zfga_ A: Porin                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2zfgA00 A:1-340 Porin                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains -----Porin_1-2zfgA01 A:6-3 40                                                                                                                                                                                                                                                                                                                        Pfam domains
         Sec.struct. author .eeeee..eeeeeeeeeeeeeee...-........ee..eeeeeeeeeee....eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeee..hhhhhh.....................eeeeeeeeeehhhhhh...eeeeeeee..............eeeeeeeeee..eeeeeeeeeee.hhhhhh.......eeeeeeeeeeeee..eeeeeeeeeee...eeee....eeee..eeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee..eeeeeeeeee..............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GRAM_NEG_PORIN   ----------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zfg A   1 AEIYNKDGNKVDLYGKAVGLHYFSKG-GENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 340
                                    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       340
                                                    26 |                                                                                                                                                                                                                                                                                                                        
                                                      28                                                                                                                                                                                                                                                                                                                        

   Legend:   → Mismatch (orange background)
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  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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: MBB (97)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (OMPF_ECOLI | P02931)
molecular function
    GO:0042912    colicin transmembrane transporter activity    Enables the transfer of a colicin from one side of a membrane to the other. Colicins are a group of antibiotics produced by E. coli and related species that are encoded by a group of naturally occurring plasmids, e.g. Col E1.
    GO:0015238    drug transmembrane transporter activity    Enables the directed movement of a drug from one side of a membrane to the other. A drug is any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0015075    ion transmembrane transporter activity    Enables the transfer of an ion from one side of a membrane to the other.
    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:0043213    bacteriocin transport    The directed movement of a bacteriocin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Bacteriocins are a group of antibiotics produced by bacteria and are encoded by a group of naturally occurring plasmids, e.g. Col E1. Bacteriocins are toxic to bacteria closely related to the bacteriocin producing strain.
    GO:0006855    drug transmembrane transport    The process in which a drug is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    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.
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
        OMPF_ECOLI | P029311bt9 1gfm 1gfn 1gfo 1gfp 1gfq 1hxt 1hxu 1hxx 1mpf 1opf 2omf 2zld 3fyx 3hw9 3hwb 3k19 3k1b 3o0e 3poq 3pou 3pox 4d5u 4gcp 4gcq 4gcs 4jfb 4lse 4lsf 4lsh 4lsi

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2ZFG)