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(-) Description

Title :  SGRAI WITH COGNATE DNA AND CALCIUM BOUND
 
Authors :  P. W. Dunten, N. C. Horton, E. J. Little
Date :  18 Jul 08  (Deposition) - 19 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
Keywords :  Restriction Enzyme/Dna Complex, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. W. Dunten, E. J. Little, M. T. Gregory, V. M. Manohar, M. Dalton, D. Hough, J. Bitinaite, N. C. Horton
The Structure Of Sgrai Bound To Dna; Recognition Of An 8 Base Pair Target.
Nucleic Acids Res. V. 36 5405 2008
PubMed-ID: 18701646  |  Reference-DOI: 10.1093/NAR/GKN510
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SGRAIR RESTRICTION ENZYME
    Chains: A, B, C, D
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A_SGRAIR
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SGRAIR
    Mutation: YES
    Organism Scientific: STREPTOMYCES GRISEUS
    Organism Taxid: 1911
 
Molecule 2 - DNA (5'- D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP* DAP*DCP*DTP*DC)-3')
    Chains: E, F, G, H
    Engineered: YES
    Other Details: INCLUDES THE SGRAI RECOGNITION SEQUENCE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB  EF  
Biological Unit 2 (1x):   CD  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1CA8Ligand/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  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:188 , PHE A:241 , HOH A:530 , HOH A:531 , DC F:8 , HOH F:746BINDING SITE FOR RESIDUE CA A 340
2AC2SOFTWAREGLU A:103 , ASN A:149 , LEU A:150 , HOH A:442 , HOH A:515 , HOH A:532 , HOH A:533BINDING SITE FOR RESIDUE CA A 341
3AC3SOFTWAREASP B:188 , PHE B:241 , HOH B:493 , HOH B:494 , DC E:8 , HOH E:46BINDING SITE FOR RESIDUE CA B 340
4AC4SOFTWAREGLU B:103 , ASN B:149 , LEU B:150 , HOH B:495 , HOH B:496BINDING SITE FOR RESIDUE CA B 341
5AC5SOFTWAREASP C:188 , PHE C:241 , HOH C:499 , HOH C:500 , DC H:8 , HOH H:760BINDING SITE FOR RESIDUE CA C 340
6AC6SOFTWAREGLU C:103 , ASN C:149 , LEU C:150 , HOH C:501BINDING SITE FOR RESIDUE CA C 341
7AC7SOFTWAREASP D:188 , PHE D:241 , HOH D:496 , HOH D:497 , DC G:8 , HOH G:47BINDING SITE FOR RESIDUE CA D 340
8AC8SOFTWAREGLU D:103 , ASN D:149 , LEU D:150 , ASP D:188 , HOH D:498BINDING SITE FOR RESIDUE CA D 341

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gln A:129 -Pro A:130
2Gln B:129 -Pro B:130
3Gln C:129 -Pro C:130
4Gln D:129 -Pro D:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DVO)

(-) 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:334
 aligned with Q9F6L0_STRGR | Q9F6L0 from UniProtKB/TrEMBL  Length:339

    Alignment length:338
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331        
         Q9F6L0_STRGR     2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMNYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAEGRSAVHRAIRELYVPPTAADLARRFFAFLNERMELVNG 339
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh.hhhhh.eee............eeehhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh..........eeeee.hhhhh.hhhhhh.....hhhhhhhhhhhhhhhh...hhh.eeeeeee....hhhhhhhhhhhhhhhhhhhhhh.......eeee......hhhhhhh...hhhhhhh----.......ee...hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dvo A   2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMDYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAE----VHRAIRELYVPPTAADLARRFFAFLNERMELVNG 339
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301    |  311       321       331        
                                                                                                                                                                                                                                                                                                                                     301  306                                 


Chain B from PDB  Type:PROTEIN  Length:336
 aligned with Q9F6L0_STRGR | Q9F6L0 from UniProtKB/TrEMBL  Length:339

    Alignment length:338
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331        
         Q9F6L0_STRGR     2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMNYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAEGRSAVHRAIRELYVPPTAADLARRFFAFLNERMELVNG 339
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.eee............eeehhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh..........eeeee.hhhhh.hhhhhh.....hhhhhhhhhhhhhhhh...hhh.eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.........eeeeeee...hhhhhhh...hhhhhhhh--.......eee...hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dvo B   2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMDYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAEG--AVHRAIRELYVPPTAADLARRFFAFLNERMELVNG 339
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301|  |   311       321       331        
                                                                                                                                                                                                                                                                                                                                      302  |                                  
                                                                                                                                                                                                                                                                                                                                         305                                  


Chain C from PDB  Type:PROTEIN  Length:334
 aligned with Q9F6L0_STRGR | Q9F6L0 from UniProtKB/TrEMBL  Length:339

    Alignment length:338
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331        
         Q9F6L0_STRGR     2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMNYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAEGRSAVHRAIRELYVPPTAADLARRFFAFLNERMELVNG 339
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.eee............eeehhhhhhhhhh........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhhh...........eeeee.hhhhh.hhhhhh.....hhhhhhhhhhhhhhh....hhh.eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.........eeeeeee...hhhhhhh...hhhhhh----.......eee...hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dvo C   2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMDYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLA----AVHRAIRELYVPPTAADLARRFFAFLNERMELVNG 339
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        |-   |   311       321       331        
                                                                                                                                                                                                                                                                                                                                    300  305                                  


Chain D from PDB  Type:PROTEIN  Length:336
 aligned with Q9F6L0_STRGR | Q9F6L0 from UniProtKB/TrEMBL  Length:339

    Alignment length:338
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331        
         Q9F6L0_STRGR     2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMNYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAEGRSAVHRAIRELYVPPTAADLARRFFAFLNERMELVNG 339
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.eee............eeehhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhhh...........eeeee.hhhhh.hhhhhh.....hhhhhhhhhhhhhhhh...hhh.eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.....eeee......hhhhhhh...hhhhhhhh--.......eee...hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dvo D   2 PFTYSIEATRNLATTERCIQDIRNAPVRNRSTQFQLAQQNMLAYTFGEVIPGFASAGINGMDYRDVIGRPVENAVTEGTHFFRDDFRVDSNAKAKVAGDIFEIVSSAVMWNCAARWNSLMVGEGWRSQPRYSRPTLSPSPRRQVAVLNLPRSFDWVSLLVPESQEVIEEFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREEIAGLTRPNQILLSGAYQRLQGRVQPGEISLAVAFKRSLRSDRLYQPLYEANVMQLLLEGKLGAPKVEFEVHTLAPEGTNAFVTYEAASLYGLAEG--AVHRAIRELYVPPTAADLARRFFAFLNERMELVNG 339
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301|  |   311       321       331        
                                                                                                                                                                                                                                                                                                                                      302  |                                  
                                                                                                                                                                                                                                                                                                                                         305                                  


Chain E from PDB  Type:DNA  Length:18
                                                  
                 3dvo E   1 GAGTCCACCGGTGGACTC  18
                                    10        


Chain F from PDB  Type:DNA  Length:18
                                                  
                 3dvo F   1 GAGTCCACCGGTGGACTC  18
                                    10        


Chain G from PDB  Type:DNA  Length:18
                                                  
                 3dvo G   1 GAGTCCACCGGTGGACTC  18
                                    10        


Chain H from PDB  Type:DNA  Length:18
                                                  
                 3dvo H   1 GAGTCCACCGGTGGACTC  18
                                    10
   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 3DVO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9F6L0_STRGR | Q9F6L0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0009036    Type II site-specific deoxyribonuclease activity    Catalysis of the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates and 3' hydroxyls. Cleavage is dependent on the presence in the DNA of a specific recognition site; cleavage occurs at or very near this recognition site.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009307    DNA restriction-modification system    A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.

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  3dvo
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  3.1.21.4
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 Related Entries

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

UniProtKB/TrEMBL
        Q9F6L0_STRGR | Q9F6L0: 3dpg 3dw9 3mq6 3mqy 3n78 3n7b 4c3g

(-) Related Entries Specified in the PDB File

3dpg SGRAI WITH NONCOGNATE DNA AND CALCIUM BOUND