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(-) Description

Title :  THE STRUCTURE OF PYROCOCCUS FURIOSUS SFSA IN COMPLEX WITH CA2+
 
Authors :  P. J. Baker, F. L. Allen
Date :  12 Jan 12  (Deposition) - 15 Oct 14  (Release) - 15 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ob Fold, Pd-(D/E)Xk Domain, Nuclease, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. L. Allen, J. Akerboom, S. J. Bliss, F. Blombach, S. E. Sedelnikova, J. Van Der Oost, P. J. Baker
The Structure Of Sfsa And Its Dna Complex; A Dna/Rna Nuclease With A Novel Domain Combination
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUGAR FERMENTATION STIMULATION PROTEIN HOMOLOG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PF1198, SFSA
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / VC1

 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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:117 , GLU A:130 , THR A:131 , HOH A:401 , HOH A:402 , HOH A:403BINDING SITE FOR RESIDUE CA A 301
2AC2SOFTWAREGLU A:108 , ASP A:117 , HOH A:402 , HOH A:404 , HOH A:405 , HOH A:406BINDING SITE FOR RESIDUE CA A 302
3AC3SOFTWAREASP B:117 , GLU B:130 , THR B:131 , HOH B:402 , HOH B:403 , HOH B:404 , HOH B:469BINDING SITE FOR RESIDUE CA B 301
4AC4SOFTWAREGLU B:108 , ASP B:117 , HOH B:403 , HOH B:405 , HOH B:407BINDING SITE FOR RESIDUE CA B 302

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:102 -A:122
2B:102 -B:122

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Gly A:59 -Gly A:60
3Tyr A:144 -Pro A:145
4Ser B:7 -Pro B:8
5Tyr B:144 -Pro B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DA2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DA2)

(-) Exons   (0, 0)

(no "Exon" information available for 4DA2)

(-) 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:231
 aligned with SFSA_PYRFU | Q8U1K8 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:231
                             1                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229 
           SFSA_PYRFU     - -MKLMEVSPLFPCIFLRRVNRFVGLVRIKERIERALITNTGRLNEFMIPGRIGYCTPKAGGKTRYILLGFEDHGKIAIIDTRLQGKAFEKIIEKELLPELEGCRIIKREPRVGESRLDYLLECSKGEIFVETKSAVLREGEYAMYPDCPSVRGQRHIKELIKLARDGKRAMIVFIGALPNVSKFKPYKKGDPKIAELLKEALEAGVEIRALGLHMELSGEIIYRGELGVEI 230
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....eeeeeeee....eeeeee..eeeeee...............eeeeee.......eeeeeeee..eeee.hhhhhhhhhhhhhhh..hhhhh..eeeee..ee..ee..eeee....eeeeeeee..eee..eeee....hhhhhhhhhhhhhhhhh..eeeeeeee......eeee....hhhhhhhhhhhhhhh.eeeeeeeee....eeeeeee.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4da2 A   0 AMKLMEVSPLFPCIFLRRVNRFVGLVRIKERIERALITNTGRLNEFMIPGRIGYCTPKAGGKTRYILLGFEDHGKIAIIDTRLQGKAFEKIIEKELLPELEGCRIIKREPRVGESRLDYLIECSKGEIFVETKSAVLREGEYAMYPDCPSVRGQRHIKELIKLARDGKRAMIVFIGALPNVSKFKPYKKGDPKIAELLKEALEAGVEIRALGLHMELSGEIIYRGELGVEI 230
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229 


Chain B from PDB  Type:PROTEIN  Length:231
 aligned with SFSA_PYRFU | Q8U1K8 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:231
                             1                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229 
           SFSA_PYRFU     - -MKLMEVSPLFPCIFLRRVNRFVGLVRIKERIERALITNTGRLNEFMIPGRIGYCTPKAGGKTRYILLGFEDHGKIAIIDTRLQGKAFEKIIEKELLPELEGCRIIKREPRVGESRLDYLLECSKGEIFVETKSAVLREGEYAMYPDCPSVRGQRHIKELIKLARDGKRAMIVFIGALPNVSKFKPYKKGDPKIAELLKEALEAGVEIRALGLHMELSGEIIYRGELGVEI 230
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....eeeeeeeeee..eeeeee..eeeeee...............eeeeee.......eeeeeeee..eeee.hhhhhhhhhhhhhhh..hhhhh..eeeee..ee..ee..eeee....eeeeeeee..eee..eeee....hhhhhhhhhhhhhhhhh..eeeeeeee......eeee....hhhhhhhhhhhhhhh.eeeeeeeee....eeeeeee.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4da2 B   0 AMKLMEVSPLFPCIFLRRVNRFVGLVRIKERIERALITNTGRLNEFMIPGRIGYCTPKAGGKTRYILLGFEDHGKIAIIDTRLQGKAFEKIIEKELLPELEGCRIIKREPRVGESRLDYLIECSKGEIFVETKSAVLREGEYAMYPDCPSVRGQRHIKELIKLARDGKRAMIVFIGALPNVSKFKPYKKGDPKIAELLKEALEAGVEIRALGLHMELSGEIIYRGELGVEI 230
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229
   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  (0, 0)

(no "SCOP Domain" information available for 4DA2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DA2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DA2)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4DA2)

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  SFSA_PYRFU | Q8U1K8
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 Related Entries

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

UniProtKB/Swiss-Prot
        SFSA_PYRFU | Q8U1K8: 4dav

(-) Related Entries Specified in the PDB File

4dap 4dav