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(-) Description

Title :  CRYSTAL STRUCTURE OF REDUCED DSBA3 FROM NEISSERIA MENINGITIDIS
 
Authors :  C. Lafaye, L. Serre
Date :  21 Jul 08  (Deposition) - 04 Aug 09  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Thiol-Oxidoreductase, Neisseria, Dsba, Disulfide Bond (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Lafaye, T. Iwema, P. Carpentier, C. Jullian-Binard, J. S. Kroll, J. F. Collet, L. Serre
Biochemical And Structural Study Of The Homologues Of The Thiol-Disulfide Oxidoreductase Dsba In Neisseria Meningitidis.
J. Mol. Biol. V. 392 952 2009
PubMed-ID: 19631659  |  Reference-DOI: 10.1016/J.JMB.2009.07.056
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOL:DISULFIDE INTERCHANGE PROTEIN DSBA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLIM01
    Expression System Strain: BL21(DE3)-CODON PLUS-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DSBA-3, NMB0407
    Organism Scientific: NEISSERIA MENINGITIDIS MC58
    Organism Taxid: 122586
    Strain: MC58 / SEROGROUP B

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:167 , PHE A:168 , ASP A:169 , HIS B:36BINDING SITE FOR RESIDUE SO4 A 196
2AC2SOFTWAREGLU A:103 , ARG A:105 , LYS A:141 , HOH A:213BINDING SITE FOR RESIDUE SO4 A 197
3AC3SOFTWARELYS A:93 , GLN A:98 , LYS A:116 , LYS B:93BINDING SITE FOR RESIDUE SO4 B 196
4AC4SOFTWAREHIS A:36 , GLY B:167 , PHE B:168 , ASP B:169BINDING SITE FOR RESIDUE SO4 B 197

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DVX)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Thr A:151 -Pro A:152
2Ala B:2 -Leu B:3
3Thr B:151 -Pro B:152
4Gly B:157 -Gly B:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DVX)

(-) 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:191
 aligned with Q9K0Z4_NEIMB | Q9K0Z4 from UniProtKB/TrEMBL  Length:214

    Alignment length:191
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208 
         Q9K0Z4_NEIMB    19 AYALTEGEDYLVLDKPIPQEQSGKIEVLEFFGYFCVHCHHFDPLLLKLGKALPSDAYLRTEHVVWQPEMLGLARMAAAVNLSGLKYQANPAVFKAVYEQKIRLENRSVAGKWALSQKGFDGKKLMRAYDSPEAAAAALKMQKLTEQYRIDSTPTVIVGGKYRVIFNNGFDGGVHTIKELVAKVREERKRQT 209
               SCOP domains d3dvxa_ A: automated matches                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee............eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee...eee...hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dvx A   0 GYALTEGEDYLVLDKPIPQEQSGKIEVLEFFGYFCVHCHHFDPLLLKLGKALPSDAYLRTEHVVWQPEmLGLARmAAAVNLSGLKYQANPAVFKAVYEQKIRLENRSVAGKWALSQKGFDGKKLmRAYDSPEAAAAALKmQKLTEQYRIDSTPTVIVGGKYRVIFNNGFDGGVHTIKELVAKVREERKRQT 190
                                     9        19        29        39        49        59        69    |   79        89        99       109       119    |  129       139       149       159       169       179       189 
                                                                                               68-MSE |                                               124-MSE        139-MSE                                               
                                                                                                     74-MSE                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:186
 aligned with Q9K0Z4_NEIMB | Q9K0Z4 from UniProtKB/TrEMBL  Length:214

    Alignment length:186
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199      
         Q9K0Z4_NEIMB    20 YALTEGEDYLVLDKPIPQEQSGKIEVLEFFGYFCVHCHHFDPLLLKLGKALPSDAYLRTEHVVWQPEMLGLARMAAAVNLSGLKYQANPAVFKAVYEQKIRLENRSVAGKWALSQKGFDGKKLMRAYDSPEAAAAALKMQKLTEQYRIDSTPTVIVGGKYRVIFNNGFDGGVHTIKELVAKVREER 205
               SCOP domains d3dvxb_ B: automated matches                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeee.......eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee..eeeee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dvx B   1 YALTEGEDYLVLDKPIPQEQSGKIEVLEFFGYFCVHCHHFDPLLLKLGKALPSDAYLRTEHVVWQPEmLGLARmAAAVNLSGLKYQANPAVFKAVYEQKIRLENRSVAGKWALSQKGFDGKKLmRAYDSPEAAAAALKmQKLTEQYRIDSTPTVIVGGKYRVIFNNGFDGGVHTIKELVAKVREER 186
                                    10        20        30        40        50        60       |70   |    80        90       100       110       120   |   130       140       150       160       170       180      
                                                                                              68-MSE |                                               124-MSE        139-MSE                                           
                                                                                                    74-MSE
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DVX)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9K0Z4_NEIMB | Q9K0Z4)
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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(-) Related Entries Specified in the PDB File

3dvw CRYSTAL STRUCTURE OF REDUCED DSBA1 FROM NEISSERIA MENINGITIDIS