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(-) Description

Title :  ION SELECTIVITY OF OMPF PORIN SOAKED IN 0.2M NABR
 
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 :  2.10
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  (4, 20)

Asymmetric/Biological Unit (4, 20)
No.NameCountTypeFull Name
1BR8Ligand/IonBROMIDE ION
2C8E2Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
3MG6Ligand/IonMAGNESIUM ION
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:16BINDING SITE FOR RESIDUE BR A 401
02AC2SOFTWAREGLN A:66 , ASN A:68 , HOH A:582 , HOH A:607BINDING SITE FOR RESIDUE BR A 402
03AC3SOFTWARESER A:125 , ARG A:167BINDING SITE FOR RESIDUE BR A 403
04AC4SOFTWAREMET A:38 , THR A:39 , TYR A:40BINDING SITE FOR RESIDUE BR A 404
05AC5SOFTWAREHOH A:696BINDING SITE FOR RESIDUE MG A 405
06AC6SOFTWAREASN A:207 , ASN A:236 , ASN A:252BINDING SITE FOR RESIDUE MG A 406
07AC7SOFTWARETYR A:32 , HOH A:696BINDING SITE FOR RESIDUE PEG A 407
08AC8SOFTWAREALA A:228 , ALA A:261BINDING SITE FOR RESIDUE C8E A 408
09AC9SOFTWAREASP A:126 , ARG A:168 , SER B:70 , GLU B:71 , GLY B:72BINDING SITE FOR RESIDUE BR B 401
10BC1SOFTWARELYS B:16 , HOH B:516BINDING SITE FOR RESIDUE BR B 402
11BC2SOFTWAREPEG B:404BINDING SITE FOR RESIDUE MG B 403
12BC3SOFTWARETYR B:32 , ASP B:121 , MG B:403BINDING SITE FOR RESIDUE PEG B 404
13BC4SOFTWAREVAL B:174BINDING SITE FOR RESIDUE C8E B 405
14BC5SOFTWAREPHE B:45 , LYS C:16 , ALA C:17 , ARG C:42BINDING SITE FOR RESIDUE BR B 406
15BC6SOFTWAREASN B:207 , ASN B:236 , ASN B:252 , HOH B:572 , HOH B:609 , HOH B:622BINDING SITE FOR RESIDUE MG B 407
16BC7SOFTWAREASN C:207 , ASN C:236 , ASN C:252 , HOH C:617 , HOH C:625BINDING SITE FOR RESIDUE MG C 401
17BC8SOFTWAREARG C:168 , ASN C:170 , HOH C:703 , HOH C:704BINDING SITE FOR RESIDUE MG C 403
18BC9SOFTWAREALA C:166 , ARG C:167 , SER C:248 , GLY C:249BINDING SITE FOR RESIDUE PEG C 404
19CC1SOFTWARETYR C:22 , GLU C:117 , HOH C:706BINDING SITE FOR RESIDUE PEG C 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LSE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LSE)

(-) 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:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4lsea_ A: Porin                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeeeeeeeeeeeee............ee..eeeeeeeeeee....eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeee..hhhhhhhhh..................eeeeeeeeeee........eeeeeeee..............eeeeeeeeee..eeeeeeeeeee.hhhhhhh......eeeeeeeeeeeee..eeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee....eeeeeeeeee..............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lse A   1 AEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 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


Chain B from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4lseb_ B: Porin                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeeeeeeeeeeeee............ee..eeeeeeeeeeeee..eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeee..hhhhhh.....................eeeeeeeeee.hhhhh...eeeeeeee......hhhhh...eeeeeeeeee..eeeeeeeeeee.hhhhhh.......eeeeeeeeeeeee..eeeeeeeeeee...eeee....eeee..eeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee....eeeeeeeeee..............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lse B   1 AEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 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


Chain C from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4lsec_ C: Porin                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeeeeeeeeeeeee............ee..eeeeeeeeeee....eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeee..hhhhhhhhh..................eeeeeeeeeee.hhhh...eeeeeeee..............eeeeeeeeee..eeeeeeeeeee.hhhhhhh......eeeeeeeeeeeee..eeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee....eeeeeeeeee..............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lse C   1 AEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 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
   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 4LSE)

(-) Pfam Domains  (0, 0)

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

(-) 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 4lsf 4lsh 4lsi

(-) Related Entries Specified in the PDB File

4lsf 4lsh 4lsi