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(-) Description

Title :  THE CRYSTAL STRUCTURES OF PORCINE PATHOGEN APH87_TBPB
 
Authors :  C. Calmettes, T. F. Moraes
Date :  26 Nov 10  (Deposition) - 02 Feb 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Lipoprotein, Transferrin Receptor, Iron Acquisition, Vaccine Candidate, Beta Barrel, Transferrin Binding, Transferrin, Outermembrane, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Calmettes, R. H. Yu, L. P. Silva, D. Curran, D. C. Schriemer, A. B. Schryvers, T. F. Moraes
Structural Variations Within The Transferrin Binding Site O Transferrin-Binding Protein B, Tbpb.
J. Biol. Chem. V. 286 12683 2011
PubMed-ID: 21297163  |  Reference-DOI: 10.1074/JBC.M110.206102

(-) Compounds

Molecule 1 - TRANSFERRIN-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TFBA
    Organism Common: HAEMOPHILUS PLEUROPNEUMONIAE
    Organism Scientific: ACTINOBACILLUS PLEUROPNEUMONIAE
    Organism Taxid: 715
    Strain: H87

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric/Biological Unit (2, 16)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION
2GOL15Ligand/IonGLYCEROL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:170 , ARG A:190 , LYS A:219 , ARG A:221 , THR A:243 , GOL A:533 , HOH A:683BINDING SITE FOR RESIDUE GOL A 3968
02AC2SOFTWAREASP A:297 , LEU A:379 , ARG A:383 , ASN A:492 , GLY A:493 , TYR A:496 , HOH A:564 , HOH A:572 , HOH A:735 , HOH A:741 , HOH A:821 , HOH A:1003BINDING SITE FOR RESIDUE GOL A 529
03AC3SOFTWAREGLN A:208 , LEU A:210 , GLU A:218 , THR A:238 , ALA A:239 , THR A:240 , LYS A:242 , HOH A:771 , HOH A:870BINDING SITE FOR RESIDUE GOL A 530
04AC4SOFTWARETHR A:100 , LYS A:101 , SER A:102 , GLY A:103 , SER A:104 , ASN A:105BINDING SITE FOR RESIDUE GOL A 531
05AC5SOFTWAREASN A:168 , PRO A:169 , PRO A:245 , ILE A:246 , HOH A:693 , HOH A:747 , GOL A:3968BINDING SITE FOR RESIDUE GOL A 533
06AC6SOFTWAREGLU A:76 , HIS A:135 , GLU A:310 , GOL A:543 , HOH A:645 , HOH A:728BINDING SITE FOR RESIDUE GOL A 534
07AC7SOFTWAREGLU A:225 , ASN A:227 , ARG A:234 , GLY A:235 , LYS A:236 , HOH A:684 , HOH A:865BINDING SITE FOR RESIDUE GOL A 535
08AC8SOFTWAREARG A:36 , ALA A:330 , SER A:354 , LEU A:356 , LYS A:360 , HOH A:937 , HOH A:985BINDING SITE FOR RESIDUE GOL A 536
09AC9SOFTWAREGLN A:34 , HIS A:273 , HOH A:783 , HOH A:889BINDING SITE FOR RESIDUE GOL A 537
10BC1SOFTWARELYS A:300 , LYS A:345 , MET A:347 , GOL A:540 , HOH A:848 , HOH A:1000BINDING SITE FOR RESIDUE GOL A 538
11BC2SOFTWAREASN A:206 , GLU A:225 , HOH A:867 , HOH A:868 , HOH A:935 , HOH A:997BINDING SITE FOR RESIDUE GOL A 539
12BC3SOFTWARELYS A:300 , GOL A:538 , HOH A:960BINDING SITE FOR RESIDUE GOL A 540
13BC4SOFTWAREGLU A:31 , TYR A:395 , HOH A:647BINDING SITE FOR RESIDUE GOL A 541
14BC5SOFTWARESER A:104 , ASN A:105 , THR A:106 , MET A:107 , ASN A:108 , LYS A:284BINDING SITE FOR RESIDUE GOL A 542
15BC6SOFTWAREHIS A:135 , PRO A:136 , LYS A:138 , PRO A:261 , GLU A:310 , ASN A:312 , GOL A:534BINDING SITE FOR RESIDUE GOL A 543
16BC7SOFTWAREASN A:316 , ASN A:318 , GLU A:357 , TYR A:358 , GLU A:382 , HOH A:743 , HOH A:937BINDING SITE FOR RESIDUE CAC A 532

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:352 -A:353

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:25 -Val A:26
2Cys A:352 -Cys A:353
3Asp A:475 -Ser A:476
4Ser A:476 -Gly A:477

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PQS)

(-) 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:504
 aligned with Q44167_ACTPL | Q44167 from UniProtKB/TrEMBL  Length:547

    Alignment length:504
                                    53        63        73        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       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543    
         Q44167_ACTPL    44 KVNYTDEETQKRKKEELDKLMEPALGYVTKIPVNIPSVRKTEISEIDTVTDESLSLVPNEDKLRTIANENYGSVVTKSGSNTMNFVRSGYTIDVDHYGLRDKGYVYYKGVHPSKELPKGNIIVYQGEWDFTSNADLDAKRPNYNPEFNGYGAGQRVGVTSADAKERTYISKFNIDFSNKKLNGQLLTKTKENQEKLRYTVEANISGNRFRGKATATDKTDPILGKDSEHLEGGLYGPKSEELAGKFVAHDKSLFAVFSGKRGNDVLETVKIIDASKIDLTTFESSELNNFGNANVLIIDGQKIDLAGADFKNRKTVDINGKTMVAIACCSNLEYMKFGQLWQKEGEQTKDNSLFLQGERTATDKIPVGGNYKYVGTWDALVSKGTNWVAEADNNRESGYRSEFDVNFGDKKVSGKLFDKGGIVPVFMINADIKGNGFTGTANTTDTGFALDSGSSQHGNAVFSDIKVNGGFYGPTAGELGGQFHHKSDNGSVGAVFGAKRQIEK 547
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains Lipoprotein_5-3pqsA01 A:25-525                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       --- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh.....eeeee.........ee....eeee.........hhhhhhhhhhhh...eeee........eeeeeeee.........eeeeeee.....eee...eeeeeeeeeeee.ee.......................hhhhh..eeeeeeeeee....eeeeeeeeee....eeeeeeeeeeee..eeeeeeee...........eeeeeeeee.....eeeeeee.....eeeeeeeee......eee.eeeeeee.....eee........eeee..eeee......eeeeeeee..eeeeeeee......eeeeeeeeee..eeeeeeeeeeee..hhhhh....eeeeeeeeeeeee...eeee..........eeeeeee....eeeeee.........eeeeeeee..eeeeeee.....ee.........ee....eeeeeeee.....eeeeeeee.....eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pqs A  25 KVNYTDEETQKRKKEELDKLMEPALGYVTKIPVNIPSVRKTEISEIDTVTDESLSLVPNEDKLRTIANENYGSVVTKSGSNTMNFVRSGYTIDVVHYGLRDKGYVYYKGVHPSKELPKGNIIVYQGEWDFTSNADLDAKRPNYNPEFNGYGAGQRVGVTSADAKERTYISKFNIDFSNKKLNGQLLTKTKENQEKLRYTVEANISGNRFRGKATATDKTDPILGKDSEHLEGGLYGPKSEELAGKFVAHDKSLFAVFSGKRGNDVLETVKIIDASKIDLTTFESSELNNFGNANVLIIDGQKIDLAGADFKNRKTVDINGKTMVAIACCSNLEYMKFGQLWQKEGEQTKDNSLFLQGERTATDKIPVGGNYKYVGTWDALVSKGTNWVAEADNNRESGYRSEFDVNFGDKKVSGKLFDKGGIVPVFMINADIKGNGFTGTANTTDTGFALDSGSSQHGNAVFSDIKVNGGFYGPTAGELGGQFHHKSDNGSVGAVFGAKRQIEK 528
                                    34        44        54        64        74        84        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       394       404       414       424       434       444       454       464       474       484       494       504       514       524
   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 3PQS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Lipoprotein_5] (2)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q44167_ACTPL | Q44167)
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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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UniProtKB/TrEMBL
        Q44167_ACTPL | Q44167: 4o3y 4o3z 4o49

(-) Related Entries Specified in the PDB File

3pqu