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(-) Description

Title :  THE ZINC ION BOUND FORM OF CRYSTAL STRUCTURE OF E.COLI EXOI-SSDNA COMPLEX
 
Authors :  R. Qiu, J. Wei, T. Lou, M. Liu, C. Ji, W. Gong
Date :  29 Sep 12  (Deposition) - 09 Oct 13  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.96
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Dnaq Family, Exonuclease C-Terminal Family, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Qiu, T. Lou, J. Wei, M. Liu, S. Gu, R. Tang, C. Ji, W. Gong
The Structures Of Escherichia Coli Exonuclease I In Complex With The Single Strand Dna
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - EXODEOXYRIBONUCLEASE I
    Chains: A, B
    EC Number: 3.1.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B2011, CPEA, JW1993, SBCB, XONA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 668369
    Strain: DH5ALPHA
    Synonym: EXONUCLEASE I, DNA DEOXYRIBOPHOSPHODIESTERASE, DRPASE
 
Molecule 2 - DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
    Chains: C, D
    Engineered: YES
    Other Details: THE SSDNA SAMPLES WERE SYNTHESIZED WITH 3'-PHOSPHORYL MODIFICATION (PAGE PURIFIED)
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1IPA3Ligand/IonISOPROPYL ALCOHOL
2PO42Ligand/IonPHOSPHATE ION
3SO47Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1IPA1Ligand/IonISOPROPYL ALCOHOL
2PO41Ligand/IonPHOSPHATE ION
3SO43Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1IPA2Ligand/IonISOPROPYL ALCOHOL
2PO41Ligand/IonPHOSPHATE ION
3SO44Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:414 , PHE A:415 , PRO A:416 , GLY A:417BINDING SITE FOR RESIDUE SO4 A 501
02AC2SOFTWAREARG A:106 , MET A:235 , LYS A:299BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWARELEU A:419 , ASP A:420 , TYR A:421 , SER B:178 , ASN B:179BINDING SITE FOR RESIDUE SO4 A 503
04AC4SOFTWAREASP A:15 , GLU A:17 , ASP A:186 , PO4 C:101BINDING SITE FOR RESIDUE ZN A 504
05AC5SOFTWAREGLU A:17 , THR A:18 , PO4 C:101BINDING SITE FOR RESIDUE IPA A 505
06AC6SOFTWARELYS A:214 , HIS A:215 , ARG A:256 , LYS B:214 , HIS B:215 , ARG B:256BINDING SITE FOR RESIDUE SO4 B 501
07AC7SOFTWAREHIS A:430 , GLN A:433 , VAL A:434 , GLU B:438BINDING SITE FOR RESIDUE SO4 B 502
08AC8SOFTWAREARG B:106 , SER B:233 , MET B:235 , LYS B:299 , HOH B:602BINDING SITE FOR RESIDUE SO4 B 503
09AC9SOFTWAREASP A:332 , PHE B:11 , LYS B:198 , PHE B:205 , ASP B:206 , PHE B:209BINDING SITE FOR RESIDUE SO4 B 504
10BC1SOFTWAREASP B:15 , GLU B:17 , ASP B:186 , PO4 D:101BINDING SITE FOR RESIDUE ZN B 505
11BC2SOFTWAREGLY A:442 , TYR A:443 , GLU A:446 , GLU B:446BINDING SITE FOR RESIDUE IPA B 506
12BC3SOFTWARETHR B:18 , PO4 D:101BINDING SITE FOR RESIDUE IPA B 507
13BC4SOFTWAREASP A:15 , GLU A:17 , HIS A:181 , ASP A:186 , ZN A:504 , IPA A:505 , DA C:12BINDING SITE FOR RESIDUE PO4 C 101
14BC5SOFTWAREASP B:15 , GLU B:17 , HIS B:181 , ASP B:186 , ZN B:505 , IPA B:507 , DA D:12BINDING SITE FOR RESIDUE PO4 D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HCC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HCC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HCC)

(-) 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:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.........eeeeeeeee.....eeeeeeeee.........hhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh....hhhhhhhhheeeehhhhhhhhhhhh.............hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.........eeee.hhhhhhhh.eeeeeeeee......eeeeee....hhhhhhhhhhhhhhhhh.............eeeee.....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhh.hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hcc A   7 QQSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENLPSFRLEHLTKANGIEHSNAHDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEPFTPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYADEIVH 476
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156||     169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349   ||  361       371       381       391       401       411       421       431       441       451       461       471     
                                                                                                                                                                                157|                                                                                                                                                                                             353|                                                                                                                        
                                                                                                                                                                                 161                                                                                                                                                                                              356                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.........eeeeeeeee.....eeeeeeeeeee.......hhhhhhhhh.hhhhhhhheeehhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh....hhhhhhhhheeeehhhhhhhhhhhh.............hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.........eeee.hhhhhhhh.eeeeeeeee......eeeeee....hhhhhhhhhhhhhhhhhhhhhhh.......eeeee.....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hcc B   8 QSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENLPSFRLEHLTKANGIEHSNAHDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEFTPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYADEIVH 476
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157|      170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350  ||   363       373       383       393       403       413       423       433       443       453       463       473   
                                                                                                                                                                               157|                                                                                                                                                                                             353|                                                                                                                       
                                                                                                                                                                                161                                                                                                                                                                                              357                                                                                                                       


Chain C from PDB  Type:DNA  Length:10
                                          
                 4hcc C   1 AAAAAAAAAA  12
                                ||  12
                                5|    
                                 8    


Chain D from PDB  Type:DNA  Length:10
                                          
                 4hcc D   1 AAAAAAAAAA  12
                                ||  12
                                5|    
                                 8
   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 4HCC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

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        EX1_ECOLI | P04995: 1fxx 2qxf 3c94 3c95 3hl8 3hp9 4hcb 4jrp 4jrq 4js4 4js5

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4hcb