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(-) Description

Title :  CRYSTAL STRUCTURE OF MOXIFLOXACIN, DNA, AND A. BAUMANNII TOPO IV (PARE-PARC FUSION TRUNCATE)
 
Authors :  A. Wohlkonig, P. F. Chan, A. P. Fosberry, P. Homes, J. Huang, M. Kranz, V. T. J. Miles, N. D. Pearson, R. L. Perera, A. J. Shillings, M. N. Gwynn, B.
Date :  08 Jul 10  (Deposition) - 01 Sep 10  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym./Biol. Unit :  A,C,E,F
Keywords :  Isomerase-Dna-Antibiotic Complex, Type Iia Topoisomerase, Quinolone, Antibacterial Agent (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Wohlkonig, P. F. Chan, A. P. Fosberry, P. Homes, J. Huang, M. Kranz, V. R. Leydon, T. J. Miles, N. D. Pearson, R. L. Perera, A. J. Shillings, M. N. Gwynn, B. D. Bax
Structural Basis Of Quinolone Inhibition Of Type Iia Topoisomerases And Target-Mediated Resistance
Nat. Struct. Mol. Biol. V. 17 1152 2010
PubMed-ID: 20802486  |  Reference-DOI: 10.1038/NSMB.1892

(-) Compounds

Molecule 1 - TOPOISOMERASE IV
    ChainsA, C
    EC Number5.99.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentPARE SUBUNIT C-TERMINAL 28KDA DOMAIN, RESIDUES 370-627, PARC SUBUNIT N-TERMINAL 58KDA DOMAIN, RESIDUES 1 TO 503
    Organism ScientificACINETOBACTER BAUMANNII
    Organism Taxid470
    Other DetailsTHE CONSTRUCT IS A FUSION OF THE TOPO IV, PARE AND PARC SUBUNITS. RESIDUE 604 OF PARE IS LINKED TO RESIDUES 996 OF PARC
    StrainEUROFINS MEDINET
 
Molecule 2 - DNA
    ChainsE
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    Other DetailsDNA CLEAVED INTO 2, COMPLEX TRAPPED BY MFX
    SyntheticYES
 
Molecule 3 - DNA
    ChainsF
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    Other DetailsDNA CLEAVED INTO 2, COMPLEX TRAPPED BY MFX
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ACEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1MFX2Ligand/Ion1-CYCLOPROPYL-6-FLUORO-8-METHOXY-7-[(4AS,7AS)-OCTAHYDRO-6H-PYRROLO[3,4-B]PYRIDIN-6-YL]-4-OXO-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID
2MG4Ligand/IonMAGNESIUM ION
3PTR2Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2003 , MFX F:1100 , HOH F:2003 , HOH F:2004 , HOH F:2005BINDING SITE FOR RESIDUE MG A1504
2AC2SOFTWAREASP A:467 , ASP A:469 , HOH A:2001 , HOH A:2002 , HOH E:2001BINDING SITE FOR RESIDUE MG A2487
3AC3SOFTWAREHOH C:2014 , MFX E:1100 , HOH E:2003 , HOH E:2004 , HOH F:2001BINDING SITE FOR RESIDUE MG C1504
4AC4SOFTWAREASP C:467 , ASP C:469 , HOH C:2002 , HOH C:2006 , HOH C:2009BINDING SITE FOR RESIDUE MG C2488
5AC5SOFTWAREPTR A:1124 , MG C:1504 , DT E:19 , DA E:20 , HOH E:2003 , HOH E:2004 , DT F:15 , DA F:16 , HOH F:2001BINDING SITE FOR RESIDUE MFX E1100

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XKK)

(-) Exons   (0, 0)

(no "Exon" information available for 2XKK)

(-) 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:692
 aligned with B0VP98_ACIBS | B0VP98 from UniProtKB/TrEMBL  Length:739

    Alignment length:692
                                                                                                                                                                                               1       9                                          10                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -   |     7 |       -         -         -         -     |  14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       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       484  
        B0VP98_ACIBS      - -------------------------------------------------------------------------------------------------------------------------------------------------------------------MTSLAHHAT-------------------------------------------ENRSVAEFTEQAYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLIEGQGNWGSPDDPKSFAAMRYTEAKLSAYSELLLSELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVKGTIALIRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLKIQTTGRGSYRMRAVYTIEKNEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDVRDESDHENPTRLVIVLRSNRIDAEAVMSHLFATTDLESSYRVNLNMIGEDGRPQVKSIRRILLEWIEIRKKTVTRRLQYHLNRIEKRLHILAGLLIAYLDIDTVIRIIREEDQPKPVLMEHFNIDEIQAEAILELKLRHLAKLEEMEIRHEQDELSAKAAIIREQLENPESLKNLIISELKEDAKKFGDERRSPIVA  486
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhh.hhhhhhhhhhhh......hhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....eeeee..eeeee.hhhhhhhhhh.......ee..hhhhhhhhhhhhhhh......eee....hhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh.........eehhhhhhhhhhhh....hhhhhhhhhhhhh........eeee.......hhhhh......eeee...hhhhhh........ee........ee.......hhhhhh..eee....eee....hhhhhhhhhhhhhhh...hhhhhh............ee..hhhhhhhhhhhheeeeeee.eeeee..eeeeee.....hhhhhhhhhhhhhhhh....eeeeee.........eeeee.....hhhhhhhhhhh....eeeeeee.eee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xkk A  373 ALPGKLTREESELFIVEGDSAGGSAKQARDKNFQAIMPIRGKILNTWEVSSDEVLASQEVHDIAIAIGVDPGSDDLSELRYGKICILADADSDGLHIATLLCALFVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYALDDEELETILKNVKNPQITRFKGLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGLLDKLLAKKRAADRKQWLEQKENRSVAEFTEQAYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLIEGQGNWGSPDDPKSFAAMRyTEAKLSAYSELLLSELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVKGTIALIRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLKIQTTGRGSYRMRAVYTIEKNEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDVRDESDHENPTRLVIVLRSNRIDAEAVMSHLFATTDLESSYRVNLNMIGEDGRPQVKSIRRILLEWIEIRKKTVTRRLQYHLNRIEKRLHILAGLLIAYLDIDTVIRIIREEDQPKPVLMEHFNIDEIQAEAILELKLRHLAKLEEMEIRHEQDELSAKAAIIREQLENPESLKNLIISELKEDAKKFGDERRSPIVA 1486
                                 ||388       398       408       418       428       438       448       458       468       478       488       498       508       518       528|      541       551       561       571       581       591    ||1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1314      1324      1334      1344      1354      1364      1374      1384      1394      1404      1414      1424      1434      1444      1454      1464      1474      1484  
                               378|                                                                                                                                            528|                                                             596|                                                                                                              1124-PTR                                                                                                                                                                                                                                                                                                                                                                      
                                385                                                                                                                                             532                                                             1010                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            

Chain C from PDB  Type:PROTEIN  Length:711
 aligned with B0VP98_ACIBS | B0VP98 from UniProtKB/TrEMBL  Length:739

    Alignment length:711
                                                                                                                                                                                                                                         1 3      4  7             8                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -     | | -    |  | -         - |      16        26        36        46        56        66        76        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       406       416       426       436       446       456       466       476       486 
        B0VP98_ACIBS      - -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MTS------LAHH-------------ATENRSVAEFTEQAYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLIEGQGNWGSPDDPKSFAAMRYTEAKLSAYSELLLSELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVKGTIALIRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLKIQTTGRGSYRMRAVYTIEKNEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDVRDESDHENPTRLVIVLRSNRIDAEAVMSHLFATTDLESSYRVNLNMIGEDGRPQVKSIRRILLEWIEIRKKTVTRRLQYHLNRIEKRLHILAGLLIAYLDIDTVIRIIREEDQPKPVLMEHFNIDEIQAEAILELKLRHLAKLEEMEIRHEQDELSAKAAIIREQLENPESLKNLIISELKEDAKKFGDERRSPIVAR  487
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_topoisoIV-2xkkC01 C:1033-1470                                                                                                                                                                                                                                                                                                                                                                                                                     ----------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_topoisoIV-2xkkC02 C:1033-1470                                                                                                                                                                                                                                                                                                                                                                                                                     ----------------- Pfam domains (2)
         Sec.struct. author ..........................eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhh.hhhhhhhhhhhh......hhhhh....eeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....eeee....eeee..hhhhhhhhh.....eeee..hhhhhhhhhhhhhh.hhhhh.eeeee..hhhhhhhhhhhhhh..hhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh.........eehhhhhhhhhhhh...hhhhhhhhhhhhhh........eeee.......hhhhh......eeee...hhhhhh........eee......eee.......hhhhhh..eee....eee....hhhhhhhhhhhhhhh...hhhhhhhhh.........ee..hhhhhhhhhhhheeeeeee.eeeee..eeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee.....hhhhhhhhhh.....eeeeeee.eee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xkk C  364 ERKKIVSGPALPGKLADCVGQTREESELFIVEGDSAGGSAKQARDKNFQAIMPIRGKILNTWEVSSDEVLASQEVHDIAIAIGVDPGSDDLSELRYGKICILADADSDGLHIATLLCALFVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYALDDEELETILKNVKNPQITRFKGLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGLLDKLLAKKRAADRKQWLEQKGATENRSVAEFTEQAYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLIEGQGNWGSPDDPKSFAAMRyTEAKLSAYSELLLSELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVKGTIALIRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLKIQTTGRGSYRMRAVYTIEKNEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDVRDESDHENPTRLVIVLRSNRIDAEAVMSHLFATTDLESSYRVNLNMIGEDGRPQVKSIRRILLEWIEIRKKTVTRRLQYHLNRIEKRLHILAGLLIAYLDIDTVIRIIREEDQPKPVLMEHFNIDEIQAEAILELKLRHLAKLEEMEIRHEQDELSAKAAIIREQLENPESLKNLIISELKEDAKKFGDERRSPIVAR 1487
                                   373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523    || 536       546       556       566       576       586       596||    1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296      1306      1316      1326      1336      1346      1356      1366      1376      1386      1396      1406      1416      1426      1436      1446      1456      1466      1476      1486 
                                                                                                                                                                                              528|                                                              597|                                                                                                                1124-PTR                                                                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                                                               532                                                              1008                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               

Chain E from PDB  Type:DNA  Length:26
                                                           
                2xkk E    6 GGTCATGAATGACTATGCACGTAAAA   31
                                    15        25      

Chain F from PDB  Type:DNA  Length:26
                                                           
                2xkk F    5 TTTACGTGCATAGTCATTCATGACCT   30
                                    14        24      

   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 2XKK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XKK)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (15, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (B0VP98_ACIBS | B0VP98)
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:0003916    DNA topoisomerase activity    Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA.
    GO:0003918    DNA topoisomerase type II (ATP-hydrolyzing) activity    Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    GO:0006265    DNA topological change    The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
    GO:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0019897    extrinsic component of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        B0V9T6_ACIBY | B0V9T62xkj
        B0VP98_ACIBS | B0VP982xkj

(-) Related Entries Specified in the PDB File

2xkj CRYSTAL STRUCTURE OF CATALYTIC CORE OF A. BAUMANNII TOPO IV (PARE-PARC FUSION TRUNCATE)