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(-) Description

Title :  STRUCTURE OF A TRAPPED ENDONUCLEASE III-DNA COVALENT INTERMEDIATE: ESTRANGED-ADENINE COMPLEX
 
Authors :  J. C. Fromme, G. L. Verdine
Date :  14 Mar 03  (Deposition) - 15 Jul 03  (Release) - 31 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Repair, Dna Glycosylase, [4Fe-4S] Cluster, Iron-Sulfur Cluster, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. C. Fromme, G. L. Verdine
Structure Of A Trapped Endonuclease Iii-Dna Covalent Intermediate
Embo J. V. 22 3461 2003
PubMed-ID: 12840008  |  Reference-DOI: 10.1093/EMBOJ/CDG311
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*AP*AP*GP*AP*CP*AP*TP*GP*GP*AP*C)-3'
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 2 - 5'-D(*GP*TP*CP*CP*AP*(PED)P*GP*TP*CP*T)-3'
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 3 - ENDONUCLEASE III
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21(C41)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneNTH
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2PED1Mod. NucleotidePENTANE-3,4-DIOL-5-PHOSPHATE
3SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:113 , LEU A:115 , VAL A:118 , DC C:21 , HOH C:34BINDING SITE FOR RESIDUE NA A 224
2AC2SOFTWARELEU A:149 , PHE A:184 , CYS A:189 , CYS A:196 , CYS A:199 , CYS A:205 , GLY A:208BINDING SITE FOR RESIDUE SF4 A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ORP)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d1orpa_ A: Endonuclease III                                                                                                                                                                                           SCOP domains
               CATH domains -1orpA02             1orpA01 A:22-133 Hypothetical protein; domain 2                                                                 1orpA02 A:2-21,A:134-213                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..........hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh......hhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1orp A   1 MLTKQQIRYCLDEMAKMFPDAHCELVHRNPFELLIAVVLSAQCTDALVNKVTKRLFEKYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKTANVVVSVAFGVPAIAVDTHVERVSKRLGFCRWDDSVLEVEKTLMKIIPKEEWSITHHRMIFFGRYHCKAQSPQCPSCPLLHLCREGKKRMR 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

Chain B from PDB  Type:DNA  Length:11
                                           
                 1orp B   1 AAGACATGGAC  11
                                    10 

Chain C from PDB  Type:DNA  Length:10
                                          
                 1orp C  13 GTCCAxGTCT  22
                                 |  22
                                18-PED

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ORP)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1ORP)

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 Related Entries

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(-) Related Entries Specified in the PDB File

1orn STRUCTURE OF A TRAPPED ENDONUCLEASE III - DNA COVALENT INTERMEDIATE: ESTRANGED-GUANINE COMPLEX
2abk STRUCTURE OF E. COLI ENDONUCLEASE III WITHOUT DNA