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(-) Description

Title :  STRUCTURE OF AMPPCP-BOUND DNAA FROM AQUIFEX AEOLICUS
 
Authors :  J. P. Erzberger, M. L. Mott, J. M. Berger
Date :  15 Jun 06  (Deposition) - 25 Jul 06  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.51
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Aaa+ Atpase, Helix-Turn-Helix, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. P. Erzberger, M. L. Mott, J. M. Berger
Structural Basis For Atp-Dependent Dnaa Assembly And Replication-Origin Remodeling.
Nat. Struct. Mol. Biol. V. 13 676 2006
PubMed-ID: 16829961  |  Reference-DOI: 10.1038/NSMB1115

(-) Compounds

Molecule 1 - CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSV272
    Expression System StrainBL21-RIL
    Expression System Taxid562
    Expression System Vector TypeMODIFIED PET VECTOR
    GeneDNAA
    Organism ScientificAQUIFEX AEOLICUS
    Organism Taxid63363

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1ACP4Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG4Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:126 , ASP A:180 , ASP A:181 , ACP A:700BINDING SITE FOR RESIDUE MG A 400
2AC2SOFTWARETHR B:126 , ASP B:181 , ACP B:700BINDING SITE FOR RESIDUE MG B 401
3AC3SOFTWARELYS C:125 , THR C:126 , ASP C:181 , ACP C:700BINDING SITE FOR RESIDUE MG C 402
4AC4SOFTWARELYS D:125 , THR D:126 , ASP D:180 , ASP D:181 , ACP D:700BINDING SITE FOR RESIDUE MG D 403
5AC5SOFTWARETYR A:83 , PHE A:88 , ILE A:89 , ASN A:94 , VAL A:121 , GLY A:122 , THR A:123 , GLY A:124 , LYS A:125 , THR A:126 , HIS A:127 , ASP A:181 , VAL A:276 , ARG A:277 , GLU A:280 , MG A:400 , ARG D:230BINDING SITE FOR RESIDUE ACP A 700
6AC6SOFTWAREARG A:230 , TYR B:83 , ASN B:87 , PHE B:88 , ILE B:89 , ASN B:94 , VAL B:121 , GLY B:122 , THR B:123 , GLY B:124 , LYS B:125 , THR B:126 , HIS B:127 , ASP B:181 , LYS B:253 , VAL B:276 , ARG B:277 , GLU B:280 , MG B:401BINDING SITE FOR RESIDUE ACP B 700
7AC7SOFTWAREARG B:230 , ASN C:87 , PHE C:88 , ILE C:89 , ASN C:94 , VAL C:121 , GLY C:122 , THR C:123 , GLY C:124 , LYS C:125 , THR C:126 , HIS C:127 , ASP C:181 , LYS C:253 , VAL C:276 , ARG C:277 , GLU C:280 , MG C:402BINDING SITE FOR RESIDUE ACP C 700
8AC8SOFTWAREARG C:230 , PHE D:88 , ILE D:89 , ASN D:94 , VAL D:121 , GLY D:122 , THR D:123 , GLY D:124 , LYS D:125 , THR D:126 , HIS D:127 , ASP D:181 , LYS D:253 , VAL D:276 , ARG D:277 , GLU D:280 , MG D:403BINDING SITE FOR RESIDUE ACP D 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HCB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HCB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HCB)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNAAPS01008 DnaA protein signature.DNAA_AQUAE354-373
 
 
 
  4A:354-373
B:354-373
C:354-373
D:354-373

(-) Exons   (0, 0)

(no "Exon" information available for 2HCB)

(-) 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    
   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:317
 aligned with DNAA_AQUAE | O66659 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:323
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396   
           DNAA_AQUAE    77 DFLNPKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIELDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTKNVREIEGKIKLIKLKGFEGLERKERKERDKLMQIVEFVANYYAVKVEDILSDKRNKRTSEARKIAMYLCRKVCSASLIEIARAFKRKDHTTVIHAIRSVEEEKKKDRKFKHLVGFLEKQAFDKIC 399
               SCOP domains d2hcba2 A:77-289 Chromosomal replication initiation factor DnaA                                                                                                                                                      d2hcba1 A:290-399 Chromosomal replicati  on initiation factor DnaA C-  terminal domain IV                      SCOP domains
               CATH domains 2hcbA01 A:77-243 P-loop containing nucleotide triphosphate hydrolases                                                                                                  2hcbA02 A:244-290                              2hcbA03 A:291-399  [code=1.10.1750.10,   no name defined]                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.....hhhhhhhhhhhh.........eeeee....hhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.hhhhhhhhhhh..eeeeehhhhhh..hhhhhhhhhhhhhhhhh..eeeeee..hhhhh...hhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhh....--....hhhhhhhhhhhh...hhhhhhh..--..hhhhhhhhhhhhhh..--..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNAA  PDB: A:354-373-------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hcb A  77 DFLNPKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIELDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTKNVREIEGKIKLIKLKGFEGLERKERKERDKLMQIVEFVANYYAVKVEDILSDKR--RTSEARKIAMYLCRKVCSASLIEIARAF--KDHTTVIHAIRSVEEEKK--RKFKHLVGFLEKQAFDKIC 399
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326 |  |  336       346       356 |  |  366       376 |  |  386       396   
                                                                                                                                                                                                                                                                                     328  |                        358  |              378  |                  
                                                                                                                                                                                                                                                                                        331                           361                 381                  

Chain B from PDB  Type:PROTEIN  Length:318
 aligned with DNAA_AQUAE | O66659 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:323
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396   
           DNAA_AQUAE    77 DFLNPKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIELDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTKNVREIEGKIKLIKLKGFEGLERKERKERDKLMQIVEFVANYYAVKVEDILSDKRNKRTSEARKIAMYLCRKVCSASLIEIARAFKRKDHTTVIHAIRSVEEEKKKDRKFKHLVGFLEKQAFDKIC 399
               SCOP domains d2hcbb2 B:77-289 Chromosomal replication initiation factor DnaA                                                                                                                                                      d2hcbb1 B:290-399 Chromosomal replicat ion initiation factor DnaA C-te  rminal domain IV                       SCOP domains
               CATH domains 2hcbB01 B:77-243 P-loop containing nucleotide triphosphate hydrolases                                                                                                  2hcbB02 B:244-290                              2hcbB03 B:291-399  [code=1.10.1750.10 , no name defined]                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.....hhhhhhhhhhh..........eeee.....hhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhh.hhhhhhhhhhh..eeeeehhhhhh..hhhhhhhhhhhhhhhhh..eeeeee..hhhhh...hhhhhhhhh..eeee...hhhhhhhhhhhhh.......hhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhh.........hhhhhh...hhhhh...-.hhhhhhhhhhhhhhhhh...hhhhhh....--.hhhhhhhhhhhhhh..--..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNAA  PDB: B:354-373-------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hcb B  77 DFLNPKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIELDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTKNVREIEGKIKLIKLKGFEGLERKERKERDKLMQIVEFVANYYAVKVEDILSDK-NKRTSEARKIAMYLCRKVCSASLIEIARAFK--DHTTVIHAIRSVEEEKK--RKFKHLVGFLEKQAFDKIC 399
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326| |    336       346       356  |  | 366       376 |  |  386       396   
                                                                                                                                                                                                                                                                                    327 |                           359  |             378  |                  
                                                                                                                                                                                                                                                                                      329                              362                381                  

Chain C from PDB  Type:PROTEIN  Length:317
 aligned with DNAA_AQUAE | O66659 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:323
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396   
           DNAA_AQUAE    77 DFLNPKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIELDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTKNVREIEGKIKLIKLKGFEGLERKERKERDKLMQIVEFVANYYAVKVEDILSDKRNKRTSEARKIAMYLCRKVCSASLIEIARAFKRKDHTTVIHAIRSVEEEKKKDRKFKHLVGFLEKQAFDKIC 399
               SCOP domains d2hcbc2 C:77-289 Chromosomal replication initiation factor DnaA                                                                                                                                                      d2hcbc1 C:290-399 Chromosomal replicat ion initiation factor DnaA C-t   erminal domain IV                      SCOP domains
               CATH domains 2hcbC01 C:77-243 P-loop containing nucleotide triphosphate hydrolases                                                                                                  2hcbC02 C:244-290                              2hcbC03 C:291-399  [code=1.10.1750.10 , no name defined]                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.....hhhhhhhhhhh.........eeeee.....hhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhh.hhhhhhhhhh..eeeeehhhhhh..hhhhhhhhhhhhhhhhh..eeeeee..hhhhh...hhhhhhhhhhheeee....hhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhh...hhhhhh...-.....hhhhhhhhhhhhh...hhhhhh...---.hhhhhhhhhhhh....--.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNAA  PDB: C:354-373-------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hcb C  77 DFLNPKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIELDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTKNVREIEGKIKLIKLKGFEGLERKERKERDKLMQIVEFVANYYAVKVEDILSDK-NKRTSEARKIAMYLCRKVCSASLIEIARAF---DHTTVIHAIRSVEEEKK--RKFKHLVGFLEKQAFDKIC 399
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326| |    336       346       356 |   | 366       376 |  |  386       396   
                                                                                                                                                                                                                                                                                    327 |                          358 362             378  |                  
                                                                                                                                                                                                                                                                                      329                                                 381                  

Chain D from PDB  Type:PROTEIN  Length:320
 aligned with DNAA_AQUAE | O66659 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:323
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396   
           DNAA_AQUAE    77 DFLNPKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIELDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTKNVREIEGKIKLIKLKGFEGLERKERKERDKLMQIVEFVANYYAVKVEDILSDKRNKRTSEARKIAMYLCRKVCSASLIEIARAFKRKDHTTVIHAIRSVEEEKKKDRKFKHLVGFLEKQAFDKIC 399
               SCOP domains d2hcbd2 D:77-289 Chromosomal replication initiation factor DnaA                                                                                                                                                      d2hcbd1 D:290-399 Chromosomal replicat ion initiation factor DnaA C-terminal domain IV                         SCOP domains
               CATH domains 2hcbD01 D:77-243 P-loop containing nucleotide triphosphate hydrolases                                                                                                  2hcbD02 D:244-290                              2hcbD03 D:291-399  [code=1.10.1750.10 , no name defined]                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.....hhhhhhhhhhh..........eeeee....hhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh..hhhhhhhhhhhhhhhhh..eeeeee..hhhhh...hhhhhhhhhhheeeee...hhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.........hhhhhhh..-hhhhhhhhhhhhhhhhhh...hhhhhhh......hhhhhhhhhhhhh...--.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNAA  PDB: D:354-373-------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hcb D  77 DFLNPKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIELDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTKNVREIEGKIKLIKLKGFEGLERKERKERDKLMQIVEFVANYYAVKVEDILSDK-NKRTSEARKIAMYLCRKVCSASLIEIARAFKRKDHTTVIHAIRSVEEEKK--RKFKHLVGFLEKQAFDKIC 399
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326| |    336       346       356       366       376 |  |  386       396   
                                                                                                                                                                                                                                                                                    327 |                                              378  |                  
                                                                                                                                                                                                                                                                                      329                                                 381                  

   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  (2, 8)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 12)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HCB)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (DNAA_AQUAE | O66659)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003688    DNA replication origin binding    Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006270    DNA replication initiation    The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
    GO:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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        DNAA_AQUAE | O666591l8q 3r8f

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