HEADER DNA-RNA HYBRID 24-OCT-24 9K8N TITLE SOLUTION STRUCTURE OF A SHORT ZINC-DEPENDENT DNAZYME MINGAA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNAZYME MINGAA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DNAZYME, RNA CLEAVAGE, ZINC-DEPENDENT, DNA-RNA HYBRID EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.YAMASAKI,T.YAMASAKI,K.TAKEUCHI REVDAT 1 29-OCT-25 9K8N 0 JRNL AUTH K.YAMASAKI,R.INOMATA,T.YAMASAKI,T.KUBOTA,N.MIYASHITA, JRNL AUTH 2 K.TAKEUCHI,M.MIYAGISHI JRNL TITL A MINIMAL ZN2+-DEPENDENT RNA-CLEAVING DNAZYME AND ITS JRNL TITL 2 B-DNA-LIKE CRYSTAL AND SOLUTION STRUCTURES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3, CNS 1.3 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9K8N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300052942. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 11 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.44 MM NA DNAZYME MINGAA, 10 MM REMARK 210 DEUTERATED TRIS-D11, 1 MM NA REMARK 210 ZNCL2, 0.1 MM NA DSS, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36699 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF A SHORT ZINC-DEPENDENT DNAZYME MINGAA DBREF 9K8N A 1 26 PDB 9K8N 9K8N 1 26 SEQRES 1 A 26 DG DG DA DT DC DA DC DC DC DG DC DG DA SEQRES 2 A 26 DA DG DC DG OMG A A DG DG DA DT DC DC HET OMG A 18 37 HET ZN A 101 1 HETNAM OMG O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION FORMUL 1 OMG C11 H16 N5 O8 P FORMUL 2 ZN ZN 2+ LINK O3' DG A 17 P OMG A 18 1555 1555 1.61 LINK O3' OMG A 18 P A A 19 1555 1555 1.61 LINK N7 DG A 21 ZN ZN A 101 1555 1555 2.30 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 512 537 CONECT 537 512 538 539 540 CONECT 538 537 CONECT 539 537 CONECT 540 537 541 CONECT 541 540 542 561 562 CONECT 542 541 543 544 563 CONECT 543 542 549 CONECT 544 542 545 546 564 CONECT 545 544 574 CONECT 546 544 547 549 565 CONECT 547 546 548 CONECT 548 547 566 567 568 CONECT 549 543 546 550 569 CONECT 550 549 551 560 CONECT 551 550 552 570 CONECT 552 551 553 CONECT 553 552 554 560 CONECT 554 553 555 556 CONECT 555 554 CONECT 556 554 557 571 CONECT 557 556 558 559 CONECT 558 557 572 573 CONECT 559 557 560 CONECT 560 550 553 559 CONECT 561 541 CONECT 562 541 CONECT 563 542 CONECT 564 544 CONECT 565 546 CONECT 566 548 CONECT 567 548 CONECT 568 548 CONECT 569 549 CONECT 570 551 CONECT 571 556 CONECT 572 558 CONECT 573 558 CONECT 574 545 CONECT 653 832 CONECT 832 653 MASTER 76 0 2 0 0 0 0 6 539 1 41 2 END