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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF DSBB C41S BY JOINT CALCULATION WITH SOLID-STATE NMR AND X-RAY DATA
 
Authors :  M. Tang, L. J. Sperling, C. D. Schwieters, A. E. Nesbitt, R. B. Gennis, C. M. Rienstra
Date :  30 May 12  (Deposition) - 27 Feb 13  (Release) - 22 May 13  (Revision)
Method :  SOLID-STATE NMR
Resolution :  NOT APPLICABLE
Chains :  Asym. Unit :  A,B,C,D,E,F  (10x)
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Membrane Protein, Oxidoreductase, Disulfide Bond, Redox-Active Center, Cell Inner Membrane, Cell Membrane, Chaperone, Electron Transport, Membrane, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Tang, A. E. Nesbitt, L. J. Sperling, D. A. Berthold, C. D. Schwieters R. B. Gennis, C. M. Rienstra
Structure Of The Disulfide Bond Generating Membrane Protein Dsbb In The Lipid Bilayer.
J. Mol. Biol. V. 425 1670 2013
PubMed-ID: 23416557  |  Reference-DOI: 10.1016/J.JMB.2013.02.009

(-) Compounds

Molecule 1 - DISULFIDE BOND FORMATION PROTEIN B
    ChainsA, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPQE70
    GeneB1185, DSBB, JW5182, ROXB, YCGA
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12
    SynonymDISULFIDE OXIDOREDUCTASE
 
Molecule 2 - FAB FRAGMENT LIGHT CHAIN
    ChainsB, E
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsFAB FRAGMENT IS OBTAINED BY PAPAIN DIGESTION OF A SELECTED MONOCLONAL ANTIBODY
 
Molecule 3 - FAB FRAGMENT HEAVY CHAIN
    ChainsC, F
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsFAB FRAGMENT IS OBTAINED BY PAPAIN DIGESTION OF A SELECTED MONOCLONAL ANTIBODY

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit (10x)ABCDEF
Biological Unit 1 (1x)ABC   
Biological Unit 2 (1x)   DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1UQ12Ligand/IonUBIQUINONE-1
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1UQ11Ligand/IonUBIQUINONE-1
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1UQ11Ligand/IonUBIQUINONE-1

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:29 , LEU A:38 , PRO A:40 , SER A:41 , CYS A:44 , GLU A:47 , ARG A:48 , HIS A:91 , MET A:142 , PRO A:143BINDING SITE FOR RESIDUE UQ1 A 201
2AC2SOFTWARELEU D:38 , PRO D:40 , CYS D:44BINDING SITE FOR RESIDUE UQ1 D 201

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:104 -A:130
2B:43 -B:114
3B:159 -B:219
4B:239 -C:134
5C:22 -C:96
6C:146 -C:201
7D:104 -D:130
8E:43 -E:114
9E:159 -E:219
10E:239 -F:134
11F:22 -F:96
12F:146 -F:201

(-) Cis Peptide Bonds  (9, 90)

Asymmetric Unit
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10Ser B:27 -Pro B:28
21, 2, 3, 4, 5, 6, 7, 8, 9, 10Tyr B:165 -Pro B:166
31, 2, 3, 4, 5, 6, 7, 8, 9, 10Phe C:152 -Pro C:153
41, 2, 3, 4, 5, 6, 7, 8, 9, 10Glu C:154 -Pro C:155
51, 2, 3, 4, 5, 6, 7, 8, 9, 10Ser E:27 -Pro E:28
61, 2, 3, 4, 5, 6, 7, 8, 9, 10Arg E:53 -Thr E:54
71, 2, 3, 4, 5, 6, 7, 8, 9, 10Tyr E:165 -Pro E:166
81, 2, 3, 4, 5, 6, 7, 8, 9, 10Phe F:152 -Pro F:153
91, 2, 3, 4, 5, 6, 7, 8, 9, 10Glu F:154 -Pro F:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2LTQ)

(-) 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:148
 aligned with DSBB_ECOLI | P0A6M2 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:153
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159   
           DSBB_ECOLI    10 QGRGAWLLMAFTALALELTALWFQHVMLLKPCVLCIYERCALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMVRFPEWLPLDKWVPQVFVASGDCAERQWDFLGLEMPQWLLGIFIAYLIVAVLVVI 162
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh...........-----..............................hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ltq A  10 QGRGAWLLMAFTALALELTALWFQHVMLLKPSVLCIYERVALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMV-----LPLDKWVPQVFVASGDCAERQWDFLGLEMPQWLLGIFIAYLIVAVLVVI 162
                                    19        29        39        49        59        69        79        89        99        |-    |  119       129       139       149       159   
                                                                                                                            108   114                                                

Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.............eeeeee......eeee.............eeeee...eeeeee........eeeeeee.....ee....eeee......eeeee..hhhhhhh.eeeeeeeee.........eeee........ee...............eeeeeee.hhhhhh.eeeee..........eeeee.hhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ltq B  21 DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYNLYTFGGGTKLEIKADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 239
                                    30        40        50        60        70        80        90       100       110       120       130 ||    141       151       161       171       181       191       201       211       221       231        
                                                                                                                                         132|                                                                                                         
                                                                                                                                          134                                                                                                         

Chain C from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee...eeeeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeeeeee.....eeeeee............eeee.......eeeee..........eeeeeeeeeee.....eeee........eee.........eeeeeeeeee.........eeeeee....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ltq C   1 EVQLVESGGGLVKPGGSLKLSCAASGFAFSSYDMSWVRQTPEKRLEWVAYISSGGGSTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCARPDAMDYWGQGTSVTVSSKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGP 221
                                    10        20        30        40        50        60        70        80        90       100|      114    || 125       135       145       155       165       175       185       195       205       215      
                                                                                                                             100|           119|                                                                                                    
                                                                                                                              105            121                                                                                                    

Chain D from PDB  Type:PROTEIN  Length:148
 aligned with DSBB_ECOLI | P0A6M2 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:153
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159   
           DSBB_ECOLI    10 QGRGAWLLMAFTALALELTALWFQHVMLLKPCVLCIYERCALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMVRFPEWLPLDKWVPQVFVASGDCAERQWDFLGLEMPQWLLGIFIAYLIVAVLVVI 162
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........-----.hhhhh......................hhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ltq D  10 QGRGAWLLMAFTALALELTALWFQHVMLLKPSVLCIYERVALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMV-----LPLDKWVPQVFVASGDCAERQWDFLGLEMPQWLLGIFIAYLIVAVLVVI 162
                                    19        29        39        49        59        69        79        89        99        |-    |  119       129       139       149       159   
                                                                                                                            108   114                                                

Chain E from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........eee.eeee.............eeeeee......eeee.........................eee..hhhhh.eeeeee.....ee...ee.........eeeee..hhhhhhh.eeeeeeeeeee.........ee........eeeee.........eeeeeeeeeehhhhh...eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ltq E  21 DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYNLYTFGGGTKLEIKADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 239
                                    30        40        50        60        70        80        90       100       110       120       130 ||    141       151       161       171       181       191       201       211       221       231        
                                                                                                                                         132|                                                                                                         
                                                                                                                                          134                                                                                                         

Chain F from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...ee.....eeeeeee...hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhh.eeeeeee......eeee......ee.......eeeee..........eeeeeeeeeee.....eeee.hhh....eee.........eeeeeeeeee..........eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ltq F   1 EVQLVESGGGLVKPGGSLKLSCAASGFAFSSYDMSWVRQTPEKRLEWVAYISSGGGSTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCARPDYRSYAMDYWGQGTSVTVSSKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKK 215
                                    10        20        30        40        50        60        70        80        90       100       110       121       131       141       151       161       171       181       191       201       211    
                                                                                                                                                119|                                                                                              
                                                                                                                                                 121                                                                                              

   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 2LTQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2LTQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (DSBB_ECOLI | P0A6M2)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0022900    electron transport chain    A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DSBB_ECOLI | P0A6M22hi7 2k73 2k74 2leg 2zup 2zuq 3e9j

(-) Related Entries Specified in the PDB File

2leg SIMILAR REFINEMENT METHOD
2zuq THE SOURCE OF X-RAY DATA RELATED ID: 18493 RELATED DB: BMRB