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(-) Description

Title :  ION SELECTIVITY OF OMPF PORIN SOAKED IN 0.3M KBR
 
Authors :  D. Balasundaresan, L. Blachowicz, B. Roux
Date :  22 Jul 13  (Deposition) - 23 Oct 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Porin, Outer Membrane Protein, Beta-Barrel, Ion Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Dhakshnamoorthy, B. K. Ziervogel, L. Blachowicz, B. Roux
A Structural Study Of Ion Permeation In Ompf Porin From Anomalous X-Ray Diffraction And Molecular Dynamics Simulations.
J. Am. Chem. Soc. V. 135 16561 2013
PubMed-ID: 24106986  |  Reference-DOI: 10.1021/JA407783A

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN F
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPR272
    Expression System Strain: K12
    Expression System Taxid: 83333
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 23-362
    Gene: B0929, CMLB, COA, CRY, JW0912, OMPF, TOLF
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: OUTER MEMBRANE PROTEIN 1A, OUTER MEMBRANE PROTEIN B, OUTER MEMBRANE PROTEIN IA, PORIN OMPF

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 34)

Asymmetric/Biological Unit (5, 34)
No.NameCountTypeFull Name
1BR9Ligand/IonBROMIDE ION
2C8E4Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
3GOL4Ligand/IonGLYCEROL
4MG8Ligand/IonMAGNESIUM ION
5PEG9Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (32, 32)

Asymmetric Unit (32, 32)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:121 , HOH A:652BINDING SITE FOR RESIDUE PEG A 401
02AC2SOFTWAREASP A:113 , MET A:114 , ARG A:270 , HOH A:666BINDING SITE FOR RESIDUE PEG A 402
03AC3SOFTWARELEU A:227 , ALA A:228 , VAL A:260BINDING SITE FOR RESIDUE C8E A 403
04AC4SOFTWAREARG A:82 , ASP A:113 , ARG A:132BINDING SITE FOR RESIDUE GOL A 404
05AC5SOFTWAREVAL A:11BINDING SITE FOR RESIDUE GOL A 405
06AC6SOFTWAREGLU A:201 , GLN A:203 , GLY A:206BINDING SITE FOR RESIDUE MG A 406
07AC7SOFTWAREASN A:316 , ILE A:318 , SER A:328 , HOH A:557 , HOH A:595BINDING SITE FOR RESIDUE MG A 407
08AC8SOFTWARESER A:125 , ARG A:167BINDING SITE FOR RESIDUE BR A 408
09AC9SOFTWAREHOH A:514BINDING SITE FOR RESIDUE BR A 409
10BC1SOFTWARETYR A:102 , GLY A:103 , VAL A:104 , TYR A:106 , PHE A:129 , VAL A:130 , GLY A:131BINDING SITE FOR RESIDUE BR A 410
11BC2SOFTWAREMET A:114 , LEU A:115 , PRO A:116 , GLN A:262 , SER A:272BINDING SITE FOR RESIDUE BR A 411
12BC3SOFTWAREGLN A:66 , GLY A:67 , ASN A:68 , ASN A:69 , SER A:70 , ALA A:75 , ASN A:79 , LYS C:80 , THR C:81 , ARG C:100BINDING SITE FOR RESIDUE PEG A 412
13BC4SOFTWARELYS A:80 , THR A:81 , ARG A:100 , GLN B:66 , ASN B:69 , SER B:70 , GLU B:71 , ALA B:75 , ASN B:79 , HOH B:503BINDING SITE FOR RESIDUE PEG B 401
14BC5SOFTWAREHOH B:639 , HOH B:646BINDING SITE FOR RESIDUE PEG B 402
15BC6SOFTWAREARG B:140 , ASN B:141 , SER B:142 , PHE B:153 , SER B:177 , SER B:179 , HOH B:656BINDING SITE FOR RESIDUE PEG B 403
16BC7SOFTWAREPHE B:267 , TYR B:301 , TYR C:313BINDING SITE FOR RESIDUE C8E B 404
17BC8SOFTWARELEU B:259 , ILE B:273BINDING SITE FOR RESIDUE C8E B 405
18BC9SOFTWAREARG B:82 , ASP B:113 , ARG B:132BINDING SITE FOR RESIDUE GOL B 406
19CC1SOFTWAREGLU B:201 , GLN B:203 , GLY B:206 , HOH B:601 , HOH B:673BINDING SITE FOR RESIDUE MG B 407
20CC2SOFTWAREASN B:316 , ILE B:318 , SER B:328 , HOH B:600 , HOH C:663BINDING SITE FOR RESIDUE MG B 408
21CC3SOFTWARESER B:125 , ARG B:167BINDING SITE FOR RESIDUE BR B 410
22CC4SOFTWAREILE B:51BINDING SITE FOR RESIDUE BR B 411
23CC5SOFTWARETYR C:98 , GLY C:159 , GLY C:173 , HOH C:586BINDING SITE FOR RESIDUE C8E C 401
24CC6SOFTWAREASN C:207 , ASN C:236 , ASN C:252 , HOH C:588 , HOH C:593BINDING SITE FOR RESIDUE MG C 402
25CC7SOFTWAREHOH B:532 , ASN C:69 , ASP C:74 , HOH C:636BINDING SITE FOR RESIDUE MG C 403
26CC8SOFTWAREGLU C:201 , GLN C:203 , GLY C:206 , HOH C:606 , HOH C:676BINDING SITE FOR RESIDUE MG C 404
27CC9SOFTWAREASN C:316 , ILE C:318 , SER C:328BINDING SITE FOR RESIDUE MG C 405
28DC1SOFTWAREASP C:126 , ASP C:127 , PHE C:128 , GLY C:134 , ARG C:163 , ARG C:167 , ARG C:168 , SER C:169 , ASN C:170 , GLN C:200BINDING SITE FOR RESIDUE PEG C 406
29DC2SOFTWARELYS B:80 , THR B:81 , GLN C:66 , ASN C:69 , SER C:70 , GLU C:71 , ALA C:75 , ASN C:79 , HOH C:504BINDING SITE FOR RESIDUE PEG C 407
30DC3SOFTWAREASP C:113 , ARG C:132 , HOH C:640BINDING SITE FOR RESIDUE GOL C 409
31DC4SOFTWARELYS C:16 , HOH C:506 , HOH C:600BINDING SITE FOR RESIDUE BR C 410
32DC5SOFTWARESER C:125 , ARG C:167BINDING SITE FOR RESIDUE BR C 411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LSI)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:26 -Asn A:27
2Asn B:27 -Gly B:28

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LSI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LSI)

(-) Exons   (0, 0)

(no "Exon" information available for 4LSI)

(-) Sequences/Alignments

Asymmetric/Biological 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:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4lsia_ A: Porin                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeeeeeeeee............ee..eeeeeeeeeee....eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeee..hhhhhh.....................eeeeeeeeeehhhhhh...eeeeeeee..............eeeeeeeeee..eeeeeeeeeee.hhhhhh.......eeeeeeeeeeeee..eeeeeeeeeee...eeee....eeee..eeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee....eeeeeeeeee..............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lsi A   7 DGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 340
                                    16        26        36        46        56        66        76        86        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    


Chain B from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4lsib_ B: Porin                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeee............ee..eeeeeeeeeeeee..eeeeeeeeeeee.............eeeeeeeeeee...eeeeeee....hhhhhh.........................eeeeeehhhhhh...eeeeeeee..............eeeeeeeeee..eeeeeeeeeee.hhhhhh.......eeeeeeeeeeeee..eeeeeeeeeee...eeee....eeee..eeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee....eeeeeeeeee..............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lsi B   7 DGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 340
                                    16        26        36        46        56        66        76        86        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    


Chain C from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4lsic_ C: Porin                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeeeeeeeee............ee..eeeeeeeeeee....eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeee..hhhhhh.....................eeeeeeeeeehhhhhh...eeeeeeee..............eeeeeeeeee..eeeeeeeeeee.hhhhhh.......eeeeeeeeeeeee..eeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee..eeeeeeeeee..............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lsi C   7 DGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 340
                                    16        26        36        46        56        66        76        86        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
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LSI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LSI)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        OMPF_ECOLI | P02931: 1bt9 1gfm 1gfn 1gfo 1gfp 1gfq 1hxt 1hxu 1hxx 1mpf 1opf 2omf 2zfg 2zld 3fyx 3hw9 3hwb 3k19 3k1b 3o0e 3poq 3pou 3pox 4d5u 4gcp 4gcq 4gcs 4jfb 4lse 4lsf 4lsh

(-) Related Entries Specified in the PDB File

4lse 4lsf 4lsh