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(-) Description

Title :  THE METAL-FREE 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 :  2.00
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, 3'-5' Exonuclease, 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  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO48Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:430 , GLN A:433 , HOH A:675 , THR B:436 , GLU B:438BINDING SITE FOR RESIDUE GOL A 501
02AC2SOFTWARELYS A:214 , HIS A:215 , ARG A:256 , LYS B:214 , HIS B:215 , ARG B:256BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWAREARG A:148 , ARG A:203 , HOH A:791BINDING SITE FOR RESIDUE SO4 A 503
04AC4SOFTWAREARG A:106 , SER A:233 , MET A:235 , LYS A:299 , HOH A:641 , HOH A:689 , HOH A:759 , HOH A:809BINDING SITE FOR RESIDUE SO4 A 504
05AC5SOFTWAREPHE A:415 , PRO A:416 , GLY A:417 , HOH A:777BINDING SITE FOR RESIDUE SO4 A 505
06AC6SOFTWAREGLU A:438 , HIS B:430 , GLN B:433 , HOH B:707 , HOH B:818 , HOH B:838BINDING SITE FOR RESIDUE GOL B 501
07AC7SOFTWAREGLN A:328 , ASP A:332 , PHE B:11 , SER B:38 , GLU B:39 , LYS B:198 , PHE B:205 , HOH B:835BINDING SITE FOR RESIDUE GOL B 502
08AC8SOFTWAREARG B:148 , ARG B:203 , ARG B:316 , HOH B:640BINDING SITE FOR RESIDUE SO4 B 503
09AC9SOFTWAREARG B:106 , SER B:233 , LYS B:299 , HOH B:779 , HOH B:824 , HOH B:825BINDING SITE FOR RESIDUE SO4 B 504
10BC1SOFTWARESER B:373 , ASP B:374 , HOH B:621 , HOH B:704BINDING SITE FOR RESIDUE SO4 B 505
11BC2SOFTWARESER A:373 , ASP A:374 , HIS B:211 , LYS B:216 , HOH B:786BINDING SITE FOR RESIDUE SO4 B 506

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HCB)

(-) 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:462
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.........eeeeeeeeee....eeeeeeeeee........hhhhhhhhh.hhhhhhhheehhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh....hhhhhhhhheeeehhhhhhhhhhhh.............hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.........eeee.hhhhhhhh.eeeeeeeee......eeeeee....hhhhhhhhhhhhhhhhh.hhhhh.......eeeee.....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhh........hhhhhhhhh..hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hcb A   7 QQSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENLPSFRLEHLTKANGIEDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAEPFTPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYADEIVH 476
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156||     169      |184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474  
                                                                                                                                                                                157|            176|                                                                                                                                                                                                                                                                                                      
                                                                                                                                                                                 161             182                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.........eeeeeeeee.....eeeeeeeee.........hhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh....hhhhhhhhheeeehhhhhhhhhhhh.............hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.........eeee.hhhhhhhh.eeeeeeeee......eeeeee....hhhhhhhhhhhhhhhhh.............eeeee.....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhh........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hcb B   8 QSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENLPSFRLEHLTKANGIEDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAEPFTPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYADEIVH 476
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157|      170     ||185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475 
                                                                                                                                                                               157|            176|                                                                                                                                                                                                                                                                                                      
                                                                                                                                                                                161             182                                                                                                                                                                                                                                                                                                      


Chain C from PDB  Type:DNA  Length:12
                                            
                 4hcb C   0 AAAAAAAAAAAA  11
                                     9  


Chain D from PDB  Type:DNA  Length:12
                                            
                 4hcb D   0 AAAAAAAAAAAA  11
                                     9
   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 4HCB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

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

(-) Related Entries Specified in the PDB File

4hcc