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(-) Description

Title :  STRUCTURE OF SDA1 NUCLEASE APOPROTEIN AS AN EGFP FIXED-ARM FUSION
 
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 :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Beta-Beta-Alpha Metal Finger Nuclease, Sequence Nonspecific Dna Binding, Metal Binding Protein, Dna Binding Protein, Metal Binding (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 - GREEN FLUORESCENT PROTEIN,EXTRACELLULAR STREPTODORNASE D
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32BEGFPX
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GFP, SDA1, SDAD2, HKU360_01468, SD90_06600
    Organism Common: JELLYFISH
    Organism Scientific: AEQUOREA VICTORIA, STREPTOCOCCUS PYOGENES
    Organism Taxid: 6100, 1314
    Synonym: PHAGE-ENCODED EXTRACELLULAR STREPTODORNASE D,PHAGE-ENCODED STREPTODORNASE,STREPTODORNASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CR21Mod. Amino Acid{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3EDO4Ligand/Ion1,2-ETHANEDIOL
4SO46Ligand/IonSULFATE ION
Biological Unit 1 (4, 15)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CR21Mod. Amino Acid{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3EDO4Ligand/Ion1,2-ETHANEDIOL
4SO46Ligand/IonSULFATE ION
Biological Unit 2 (4, 30)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2CR22Mod. Amino Acid{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3EDO8Ligand/Ion1,2-ETHANEDIOL
4SO412Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:1179 , ARG A:1208 , ASN A:1215 , HOH A:1755binding site for residue SO4 A 1401
02AC2SOFTWARELYS A:1130 , ASP A:1185 , ARG A:1186 , HOH A:1667binding site for residue SO4 A 1402
03AC3SOFTWAREGLY A:1188 , ALA A:1191 , ASP A:1192 , ASN A:1211 , EDO A:1409 , HOH A:1657 , HOH A:1745binding site for residue SO4 A 1403
04AC4SOFTWARELYS A:41 , TYR A:1102 , SER A:1251 , GLN A:1374 , EDO A:1407binding site for residue SO4 A 1404
05AC5SOFTWAREVAL A:1351 , HIS A:1382 , THR A:1385binding site for residue SO4 A 1405
06AC6SOFTWAREVAL A:55 , PRO A:56 , TRP A:57 , PRO A:58 , HIS A:139 , HOH A:1540 , HOH A:1575 , HOH A:1593 , HOH A:1607binding site for residue SO4 A 1406
07AC7SOFTWARETYR A:39 , LYS A:41 , SO4 A:1404binding site for residue EDO A 1407
08AC8SOFTWARETYR A:1072 , ARG A:1073binding site for residue EDO A 1408
09AC9SOFTWARELYS A:1130 , ASP A:1192 , GLY A:1196 , ARG A:1197 , PRO A:1198 , SO4 A:1403binding site for residue EDO A 1409
10AD1SOFTWAREHIS A:77 , ASN A:1067 , LYS A:1243binding site for residue EDO A 1410
11AD2SOFTWAREHIS A:148 , PHE A:165 , LYS A:166 , HOH A:1524 , HOH A:1683binding site for residue ACT A 1411
12AD3SOFTWAREALA A:231 , ALA A:232 , ARG A:1274 , HOH A:1585binding site for residue ACT A 1412
13AD4SOFTWAREASN A:1166 , ARG A:1186 , HOH A:1514 , HOH A:1667binding site for residue ACT A 1413
14AD5SOFTWARELYS A:1168 , TYR A:1182binding site for residue ACT A 1414

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Met A:88 -Pro A:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FGU)

(-) 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:495
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee..........hhhhh...eeeehhhhhh......eeee...ee...........eeeeehhhhhhhhh........eeeee.....eehhhhhhhh...eeeee...eeeee.....eeeee.eeeee..hhhhh...hhh.eeeeehhhhhh.....hhhhhhhhhhhhhhhhh....eeeeeeee.........eeeeeeee.....eeeeeee...............................ee..hhhhh..hhhhhhhh..ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fgu A    3 KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFgVQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGIAAAGKAQLDIKNFPELYRTTERVYKKSGQSTKPVTVSNIHYSVLDGYGRSGEAYGIITKDMIDMSASKPEPSGWYSYFFKNTNQRATESDYKHSPKNVSKISNNIKASILLSNGNVRNGYLFDRSGLIADSLGGRPFRNNLITGTRTQNVGNNDRKGGMQYIENKVLDHIKRNPKVHVYYKATPVYQGSELLPRAVLVSALSSDGFIDETVRVFNNVAGFNIDYQNGGLLSSSLQDTVYVNGQSDVYWYNKDSMEMSEQVALTRGKHHST 1385
                                    12        22        32        42        52        62 |||    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224      1060      1070      1080      1090      1100      1110      1120||    1137      1147      1157      1167      1177      1187      1197      1207      1217      1227      1237      1247      1257      1267      1277      1287      1338    ||1350      1370      1380     
                                                                                        64||                                                                                                                                                                 232|                                                          1121|                                                                                                                                                                 1294|   1343|         1359|               
                                                                                         66-CR2                                                                                                                                                              1059                                                           1129                                                                                                                                                                  1336    1346          1370               
                                                                                          68
   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 5FGU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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        GFP_AEQVI | P42212: 1b9c 1bfp 1c4f 1cv7 1ema 1emb 1emc 1eme 1emf 1emg 1emk 1eml 1emm 1f09 1f0b 1gfl 1h6r 1hcj 1huy 1jby 1jbz 1jc0 1jc1 1kp5 1kyp 1kyr 1kys 1myw 1q4a 1q4b 1q4c 1q4d 1q4e 1q73 1qxt 1qy3 1qyf 1qyo 1qyq 1rm9 1rmm 1rmo 1rmp 1rrx 1s6z 1w7s 1w7t 1w7u 1yfp 1yhg 1yhh 1yhi 1yj2 1yjf 1z1p 1z1q 2ah8 2aha 2awj 2awk 2awl 2awm 2b3p 2b3q 2due 2duf 2dug 2duh 2dui 2emd 2emn 2emo 2fwq 2fzu 2g16 2g2s 2g3d 2g5z 2g6e 2h6v 2h9w 2hcg 2hfc 2hgd 2hgy 2hjo 2hqz 2hrs 2jad 2o24 2o29 2o2b 2okw 2oky 2q57 2q6p 2qrf 2qt2 2qu1 2qz0 2wsn 2wso 2wur 2y0g 2ydz 2ye0 2ye1 2yfp 3cb9 3cbe 3cd1 3cd9 3dpw 3dpx 3dpz 3dq1 3dq2 3dq3 3dq4 3dq5 3dq6 3dq7 3dq8 3dq9 3dqa 3dqc 3dqd 3dqe 3dqf 3dqh 3dqi 3dqj 3dqk 3dql 3dqm 3dqn 3dqo 3dqu 3ed8 3ek4 3ek7 3ek8 3ekh 3ekj 3evp 3evr 3evu 3evv 3g9a 3gex 3gj1 3gj2 3i19 3k1k 3la1 3o77 3o78 3ogo 3osq 3osr 3p28 3sg2 3sg3 3sg4 3sg5 3sg6 3sg7 3sry 3ss0 3ssh 3ssk 3ssl 3ssp 3sst 3ssv 3ssy 3st0 3sv5 3svb 3svc 3svd 3sve 3u8p 3ufz 3ug0 3v3d 3vht 3w1c 3w1d 3wlc 3wld 3ztf 4anj 4ar7 4as8 4b5y 4bdu 4en1 4eul 4ges 4gf6 4h47 4h48 4ik1 4ik3 4ik4 4ik5 4ik8 4ik9 4j88 4j89 4j8a 4jfg 4jrb 4ka9 4kag 4kex 4kf5 4kw4 4kw8 4kw9 4l12 4l13 4l1i 4lqt 4lqu 4lw5 4n3d 4ndj 4ndk 4ogs 4orn 4p1q 4p7h 4pa0 4pfe 4u2v 4xbi 4xgy 4xl5 4xov 4xow 4xvp 4z4k 4z4m 4zf3 4zf4 4zf5 5aqb 5dpg 5dph 5dpi 5dpj 5dqb 5dqm 5drf 5drg 5dtx 5dty 5dtz 5du0 5ehu 5f9g 5fji 5hbd 5hge 5hw9 5hzo 5j2o 5j3n 5ktg 5t3i
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5fgw