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(-) Description

Title :  CRYSTAL STRUCTURE OF A COMPUTATIONALLY DESIGNED SSPB HETERODIMER
 
Authors :  D. N. Bolon, R. A. Grant, T. A. Baker, R. T. Sauer
Date :  25 May 05  (Deposition) - 23 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  A (2x),B (2x),C (2x)
Keywords :  Protein Design, Aaa, Adaptor, Specificity, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. N. Bolon, R. A. Grant, T. A. Baker, R. T. Sauer
Specificity Versus Stability In Computational Protein Design.
Proc. Natl. Acad. Sci. Usa V. 102 12724 2005
PubMed-ID: 16129838  |  Reference-DOI: 10.1073/PNAS.0506124102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STRINGENT STARVATION PROTEIN B HOMOLOG
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21, PACYCDUET1
    Expression System Strain: BLR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SSPB
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
 
Molecule 2 - STRINGENT STARVATION PROTEIN B HOMOLOG
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BLR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SSPB
    Mutation: YES
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
 
Molecule 3 - STRINGENT STARVATION PROTEIN B HOMOLOG
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYCDUET1
    Expression System Strain: BLR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SSPB
    Mutation: YES
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC
Biological Unit 3 (2x): A (2x)B (2x)C (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:56 , THR A:59 , GLN C:70 , GLU C:81BINDING SITE FOR RESIDUE MG A 1001
2AC2SOFTWAREGLN A:70 , GLU A:81 , ALA B:56 , THR B:59BINDING SITE FOR RESIDUE MG B 1002
3AC3SOFTWAREALA C:56 , THR C:59BINDING SITE FOR RESIDUE MG C 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZSZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZSZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZSZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZSZ)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZSZ)

(-) 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:106
 aligned with SSPB_HAEIN | P45206 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:106
                                    14        24        34        44        54        64        74        84        94       104      
           SSPB_HAEIN     5 SSPKRPYLLRAYYDWLVDNSFTPYLVVDATYLGVNVPVEYVKDGQIVLNLSASATGNLQLTNDFIQFNARFKGVSRELYIPMGAALAIYARENGDGVMFEPEEIYD 110
               SCOP domains d1zsza1 A:5-110 Stringent starvation protein B, SspB                                                       SCOP domains
               CATH domains 1zszA00 A:5-110 Stringent starvation protein B, SspB                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeeeee........hhhhh...eeeee......eeeee...eeeeeeee..eeeeeeee...eeeeee.....eee...hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1zsz A   5 SSPKRPYLLRAYYDWLVDNSFTPYLVVDATYLGVNVPVEYVKDGQIVLNLSASATGNLQLTNDFIQFNARFKGVSRELYIPMGAALAIYARENGDGVMFEPEEIYD 110
                                    14        24        34        44        54        64        74        84        94       104      


Chain B from PDB  Type:PROTEIN  Length:106
 aligned with SSPB_HAEIN | P45206 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:106
                                    14        24        34        44        54        64        74        84        94       104      
           SSPB_HAEIN     5 SSPKRPYLLRAYYDWLVDNSFTPYLVVDATYLGVNVPVEYVKDGQIVLNLSASATGNLQLTNDFIQFNARFKGVSRELYIPMGAALAIYARENGDGVMFEPEEIYD 110
               SCOP domains d1zszb1 B:5-110 Stringent starvation protein B, SspB                                                       SCOP domains
               CATH domains 1zszB00 B:5-110 Stringent starvation protein B, SspB                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeeeee........hhhhh...eeeee......eeeee...eeeeeeee..eeeeeeee...eeeeee.....eee...hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1zsz B   5 SSPKRPYLLRSLYDWLVDNSFTPYLVVDATYLGVNVPVEYVKDGQIVLNLSASATGNLQLTNDFIQFNARFKGVSRELYIPMGAALAIYARENGDGAMFEPEEIYD 110
                                    14        24        34        44        54        64        74        84        94       104      


Chain C from PDB  Type:PROTEIN  Length:109
 aligned with SSPB_HAEIN | P45206 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:109
                                    14        24        34        44        54        64        74        84        94       104         
           SSPB_HAEIN     5 SSPKRPYLLRAYYDWLVDNSFTPYLVVDATYLGVNVPVEYVKDGQIVLNLSASATGNLQLTNDFIQFNARFKGVSRELYIPMGAALAIYARENGDGVMFEPEEIYDELN 113
               SCOP domains d1zszc1 C:5-113 Stringent starvation protein B, SspB                                                          SCOP domains
               CATH domains 1zszC00 C:5-113 Stringent starvation protein B, SspB                                                          CATH domains
           Pfam domains (1) SspB-1zszC01 C:5-113                                                                                          Pfam domains (1)
           Pfam domains (2) SspB-1zszC02 C:5-113                                                                                          Pfam domains (2)
           Pfam domains (3) SspB-1zszC03 C:5-113                                                                                          Pfam domains (3)
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeeeee........hhhhh...eeeee.hhhhheeeee...eeeeeeee..eeeeeeee...eeeeee.....eee...hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1zsz C   5 SSPKRPYYLRGFYDWLVDNSFTPYLVVDATYLGVNVPVEYVKDGQIVLNLSASATGNLQLTNDFIQFNQRFKGVSRELYIPMGAALAIYARENGDGMMFEPEEIYDELN 113
                                    14        24        34        44        54        64        74        84        94       104
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: SspB] (10)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1ZSZ)

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  1zsz
    Family and Domain Information: ProDom | SYSTERS
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  SSPB_HAEIN | P45206
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 Related Entries

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

UniProtKB/Swiss-Prot
        SSPB_HAEIN | P45206: 1ou8 1ou9 1oul 1twb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1ZSZ)