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(-) Description

Title :  STRUCTURE OF SDA1 NUCLEASE WITH BOUND ZINC ION
 
Authors :  A. F. Moon, J. M. Krahn, L. Xun, M. J. Cuneo, L. C. Pedersen
Date :  21 Dec 15  (Deposition) - 30 Mar 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Beta-Beta-Alpha Metal Finger Nuclease, Sequence Nonspecific Dna Binding, Metal Binding, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. F. Moon, J. M. Krahn, X. Lu, M. J. Cuneo, L. C. Pedersen
Structural Characterization Of The Virulence Factor Sda1 Nuclease From Streptococcus Pyogenes.
Nucleic Acids Res. V. 44 3946 2016
PubMed-ID: 26969731  |  Reference-DOI: 10.1093/NAR/GKW143

(-) Compounds

Molecule 1 - EXTRACELLULAR STREPTODORNASE D
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEXM
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 37-294
    Gene: SDA1, SDAD2, HKU360_01468, SD90_06600
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314
    Synonym: PHAGE-ENCODED EXTRACELLULAR STREPTODORNASE D,PHAGE-ENCODED STREPTODORNASE,STREPTODORNASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 42)

Asymmetric Unit (5, 42)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2CL5Ligand/IonCHLORIDE ION
3EDO3Ligand/Ion1,2-ETHANEDIOL
4NA2Ligand/IonSODIUM ION
5ZN26Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO-1Ligand/Ion1,2-ETHANEDIOL
4NA-1Ligand/IonSODIUM ION
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO-1Ligand/Ion1,2-ETHANEDIOL
4NA-1Ligand/IonSODIUM ION
5ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO1Ligand/Ion1,2-ETHANEDIOL
4NA-1Ligand/IonSODIUM ION
5ZN-1Ligand/IonZINC ION
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4NA-1Ligand/IonSODIUM ION
5ZN-1Ligand/IonZINC ION

(-) Sites  (42, 42)

Asymmetric Unit (42, 42)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:294 , ASN B:211 , HOH B:430 , HOH B:431 , HOH B:436binding site for residue ZN A 301
02AC2SOFTWAREASN A:211 , HOH A:426 , HOH A:436 , HOH A:441 , SER B:294binding site for residue ZN A 302
03AC3SOFTWAREHIS A:51 , HIS A:56 , HOH A:454 , HOH A:487 , HOH A:493binding site for residue ZN A 303
04AC4SOFTWARESER A:120 , GLU A:125 , ASP A:192 , HOH A:401 , HOH A:419 , HOH A:423 , HOH A:464binding site for residue ZN A 304
05AC5SOFTWAREGLU A:125 , HOH A:409 , HOH A:435 , HOH A:485 , HOH A:495binding site for residue ZN A 305
06AC6SOFTWAREHIS A:95 , HOH A:492 , HIS D:95binding site for residue ZN A 306
07AC7SOFTWAREHIS A:231 , HOH A:486 , HOH A:490 , HOH A:497binding site for residue ZN A 307
08AC8SOFTWAREHIS A:239 , TYR A:241 , SER A:265 , HOH A:489 , HOH A:496binding site for residue ZN A 308
09AC9SOFTWAREGLY A:281binding site for residue CL A 309
10AD1SOFTWAREASP A:64 , LYS A:243binding site for residue CL A 310
11AD2SOFTWAREASN A:283 , LEU A:292 , SER A:293 , SER A:294 , HOH A:406 , HOH A:418 , TRP B:127 , ARG B:186binding site for residue ACT A 311
12AD3SOFTWARETRP A:127 , ARG A:186 , HOH A:404 , ASN B:283 , LEU B:292 , SER B:293 , SER B:294binding site for residue ACT A 312
13AD4SOFTWAREHIS B:51 , HIS B:56 , ACT B:310 , HOH B:490binding site for residue ZN B 301
14AD5SOFTWARESER B:120 , GLU B:125 , ASP B:192 , HOH B:412 , HOH B:413 , HOH B:448binding site for residue ZN B 302
15AD6SOFTWAREGLU B:125 , HOH B:406 , HOH B:467 , HOH B:479binding site for residue ZN B 303
16AD7SOFTWAREHIS B:155 , HOH D:477binding site for residue ZN B 304
17AD8SOFTWAREHIS B:231 , HOH B:441 , HOH B:493 , HOH B:495binding site for residue ZN B 305
18AD9SOFTWAREHIS B:239 , TYR B:241binding site for residue ZN B 306
19AE1SOFTWAREGLU B:76 , HOH B:483binding site for residue ZN B 307
20AE2SOFTWAREASP B:152 , HOH B:487 , HOH B:499binding site for residue ZN B 308
21AE3SOFTWAREASP B:64binding site for residue CL B 309
22AE4SOFTWAREHIS B:51 , HIS B:56 , ZN B:301binding site for residue ACT B 310
23AE5SOFTWAREGLU B:132 , ARG B:186 , HOH B:475 , HOH B:485binding site for residue NA B 311
24AE6SOFTWARESER C:294 , ASN D:211 , HOH D:429 , HOH D:442 , HOH D:447binding site for residue ZN C 301
25AE7SOFTWAREASN C:211 , HOH C:433 , HOH C:447 , HOH C:449 , SER D:294binding site for residue ZN C 302
26AE8SOFTWAREASP C:192 , HOH C:402 , HOH C:419binding site for residue ZN C 303
27AE9SOFTWAREHIS C:51 , HIS C:56 , ACT C:310 , HOH C:504binding site for residue ZN C 304
28AF1SOFTWAREHIS C:231 , HOH C:498 , HOH C:505 , HOH C:508binding site for residue ZN C 305
29AF2SOFTWAREHIS C:239 , TYR C:241 , HOH C:512binding site for residue ZN C 306
30AF3SOFTWAREASP C:100 , SER C:105 , TYR C:248 , HOH C:412 , HOH C:425binding site for residue EDO C 307
31AF4SOFTWARETRP C:127binding site for residue CL C 308
32AF5SOFTWAREGLU C:125 , GLU C:128 , ARG C:197 , HOH C:461binding site for residue ACT C 309
33AF6SOFTWAREHIS C:51 , HIS C:56 , ZN C:304binding site for residue ACT C 310
34AF7SOFTWAREHIS D:51 , HIS D:56 , ACT D:308 , HOH D:501binding site for residue ZN D 301
35AF8SOFTWAREHOH B:446 , HOH B:486 , HIS D:155binding site for residue ZN D 302
36AF9SOFTWAREHIS D:231 , HOH D:503 , HOH D:505 , HOH D:507 , HOH D:508binding site for residue ZN D 303
37AG1SOFTWAREHIS D:239 , TYR D:241 , HOH D:504binding site for residue ZN D 304
38AG2SOFTWARETHR D:149 , ASP D:152binding site for residue EDO D 305
39AG3SOFTWARESER C:294 , GLY D:188 , ILE D:190 , ASP D:192 , ARG D:197 , ASN D:202 , HOH D:405binding site for residue EDO D 306
40AG4SOFTWAREASP D:64binding site for residue CL D 307
41AG5SOFTWAREHIS D:51 , HIS D:56 , ZN D:301binding site for residue ACT D 308
42AG6SOFTWAREGLU D:125 , HOH D:423binding site for residue NA D 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FGW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FGW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FGW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FGW)

(-) Exons   (0, 0)

(no "Exon" information available for 5FGW)

(-) 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:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....hhhhh...eeeehhhhhh......eeee................eeeeehhhhhhhhhhh.............eeeee.....eehhhhhhhh...eeeee...ee...ee.eeeee..hhhhh...hhh.eeeeehhhhhh......hhhhhhhhhhhhhhhh....eeeeeeee.........eeeeeeee.....eeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fgw A  46 WSIEQHPNYYHVEGKAQLDIKNFPELYRTTERVYKKSGQSTKPVTVSNIHYSVLDGYGRSGEAYGIITKDMIDMSAGYREKWESKPEPSGWYSYFFKNTNQRATESDYKHSPKNVSKISNNIKASRNGYLFDRSGLIADSLGGRPFRNNLITGTRTQNVGNNDRKGGMQYIENKVLDHIKRNPKVHVYYKATPVYQGSELLPRAVLVSALSSDGFIDETVRVFNNVAGFNIDYQNGGLLSS 294
                                    55        65        75        85        95       105       115       125       135       145       155       165    || 183       193       203       213       223       233       243       253       263       273       283       293 
                                                                                                                                                      170|                                                                                                                   
                                                                                                                                                       179                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....hhhhh...eeeehhhhhh....eeee...ee...........eeeeehhhhhhhhhh..............eeeee.....eehhhhhhhh...eeeee...eeeee.....eeeee.eeeee..hhhhh...hhh.eeeeehhhhhh.....hhhhhhhhhhhhhhhhh....eeeeeeee.........eeeeeeee.....eeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fgw B  46 WSIEQHPNYYHVEGKAQLDIKNFPELYRTTERVYKKSSTKPVTVSNIHYSVLDGYGRSGEAYGIITKDMIDMSAGYREKWESKPEPSGWYSYFFKNTNQRATESDYKHSPKNVSKISNNIKASILLSNGNVRNGYLFDRSGLIADSLGGRPFRNNLITGTRTQNVGNNDRKGGMQYIENKVLDHIKRNPKVHVYYKATPVYQGSELLPRAVLVSALSSDGFIDETVRVFNNVAGFNIDYQNGGLLSS 294
                                    55        65        75      ||87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       
                                                               82|                                                                                                                                                                                                                 
                                                                85                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....hhhhh...eeeehhhhhh......eeee................eeeeehhhhhhhhhhh.............eeeee.....eehhhhhhhh...eeeee...ee.....ee.eeeee..hhhhh...hhh.eeeeehhhhhh.....hhhhhhhhhhhhhhhhh....eeeeeeee.........eeeeeeee.....eeeeeee.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fgw C  46 WSIEQHPNYYHVEGKAQLDIKNFPELYRTTERVYKKSGQSTKPVTVSNIHYSVLDGYGRSGEAYGIITKDMIDMSAGYREKWESKPEPSGWYSYFFKNTNQRATESDYKHSPKNVSKISNNIKASIVRNGYLFDRSGLIADSLGGRPFRNNLITGTRTQNVGNNDRKGGMQYIENKVLDHIKRNPKVHVYYKATPVYQGSELLPRAVLVSALSSDGFIDETVRVFNNVAGFNIDYQNGGLLSS 294
                                    55        65        75        85        95       105       115       125       135       145       155       165     ||181       191       201       211       221       231       241       251       261       271       281       291   
                                                                                                                                                       171|                                                                                                                    
                                                                                                                                                        178                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee....hhhhh...eeeehhhhh....eeee...ee...........eeeeehhhhhhhhhh..............eeeee.....eehhhhhhhh...eeeee...eeeee.....eeeee.eeeee..hhhhh...hhh.eeeeehhhhhh.....hhhhhhhhhhhhhhhhh....eeeeeeee.........eeeeeeee.....eeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fgw D  45 NWSIEQHPNYYHVEGKAQLDIKNFPELYRTTERVYKKSTKPVTVSNIHYSVLDGYGRSGEAYGIITKDMIDMSAGYREKWESKPEPSGWYSYFFKNTNQRATESDYKHSPKNVSKISNNIKASILLSNGNVRNGYLFDRSGLIADSLGGRPFRNNLITGTRTQNVGNNDRKGGMQYIENKVLDHIKRNPKVHVYYKATPVYQGSELLPRAVLVSALSSDGFIDETVRVFNNVAGFNIDYQNGGLLSS 294
                                    54        64        74       |87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       
                                                                82|                                                                                                                                                                                                                
                                                                 86
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

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(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5FGW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FGW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FGW)

(-) Gene Ontology  (3, 3)

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        Q675N6_STRPY | Q675N6: 5fgu

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5fgu