HEADER DNA 21-FEB-20 6M0C TITLE SOLUTION NMR STRUCTURES OF DNA MINIDUMBBELL FORMED BY 5'-CTTG CATG-3'. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*TP*TP*GP*CP*AP*TP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS DNA STRUCTURE, MINIDUMBBELL, TYPE II TETRALOOP, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.K.NGAI,P.GUO REVDAT 2 08-JUL-20 6M0C 1 JRNL REVDAT 1 17-JUN-20 6M0C 0 JRNL AUTH C.K.NGAI,S.L.LAM,H.K.LEE,P.GUO JRNL TITL HIGH-RESOLUTION STRUCTURES OF DNA MINIDUMBBELLS COMPRISING JRNL TITL 2 TYPE II TETRALOOPS WITH A PURINE MINOR GROOVE RESIDUE. JRNL REF J.PHYS.CHEM.B V. 124 5131 2020 JRNL REFN ISSN 1089-5647 JRNL PMID 32484672 JRNL DOI 10.1021/ACS.JPCB.0C03163 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6M0C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1300015760. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 1 NAPI REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM DNA (5' REMARK 210 -D(*CP*TP*TP*GP*CP*AP*TP*G)-3'), REMARK 210 1 MM SODIUM PHOSPHATE, 0.02 MM REMARK 210 DSS, 99.96% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-COSY; 2D REMARK 210 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER, TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DT A 2 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 2 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 1 DA A 6 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DT A 2 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 DT A 2 C3' - O3' - P ANGL. DEV. = 10.9 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC A 5 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 DT A 2 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 3 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DC A 5 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 3 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 DT A 2 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 4 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 DC A 5 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 4 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 5 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 5 DT A 2 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 DT A 2 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 5 DT A 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 5 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 5 DC A 5 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 5 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 6 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 6 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 6 DT A 2 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 6 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 6 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 6 DC A 5 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 6 DC A 5 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 6 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 6 DA A 6 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 6 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 7 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 7 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 7 DT A 2 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 151 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DT A 2 0.07 SIDE CHAIN REMARK 500 3 DA A 6 0.06 SIDE CHAIN REMARK 500 4 DC A 1 0.06 SIDE CHAIN REMARK 500 4 DT A 2 0.06 SIDE CHAIN REMARK 500 5 DA A 6 0.09 SIDE CHAIN REMARK 500 9 DT A 2 0.10 SIDE CHAIN REMARK 500 10 DT A 2 0.06 SIDE CHAIN REMARK 500 11 DC A 1 0.06 SIDE CHAIN REMARK 500 11 DT A 2 0.10 SIDE CHAIN REMARK 500 11 DA A 6 0.05 SIDE CHAIN REMARK 500 13 DT A 2 0.08 SIDE CHAIN REMARK 500 14 DT A 2 0.06 SIDE CHAIN REMARK 500 16 DT A 2 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 103 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 2 OP1 REMARK 620 2 DT A 2 O5' 52.1 REMARK 620 3 DT A 2 O4' 110.0 58.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 106 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 2 O2 REMARK 620 2 DA A 6 OP1 132.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 104 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 2 O4 REMARK 620 2 DT A 7 OP1 82.7 REMARK 620 3 DG A 8 OP1 127.2 85.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 3 OP2 REMARK 620 2 DT A 3 O5' 56.4 REMARK 620 3 DG A 4 OP1 151.1 95.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 105 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 5 OP1 REMARK 620 2 DA A 6 OP2 118.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 7 OP2 REMARK 620 2 DG A 8 OP1 89.6 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 107 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36315 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURES OF DNA MINIDUMBBELL FORMED BY 5'-CTTG CATG- REMARK 900 3'. DBREF 6M0C A 1 8 PDB 6M0C 6M0C 1 8 SEQRES 1 A 8 DC DT DT DG DC DA DT DG HET NA A 101 1 HET NA A 102 1 HET NA A 103 1 HET NA A 104 1 HET NA A 105 1 HET NA A 106 1 HET NA A 107 1 HETNAM NA SODIUM ION FORMUL 2 NA 7(NA 1+) LINK OP1 DT A 2 NA NA A 103 1555 1555 2.47 LINK O5' DT A 2 NA NA A 103 1555 1555 3.07 LINK O4' DT A 2 NA NA A 103 1555 1555 2.74 LINK O2 DT A 2 NA NA A 106 1555 1555 2.72 LINK O4 DT A 2 NA NA A 104 1555 1555 2.67 LINK OP2 DT A 3 NA NA A 101 1555 1555 2.59 LINK O5' DT A 3 NA NA A 101 1555 1555 2.65 LINK OP1 DG A 4 NA NA A 101 1555 1555 2.51 LINK OP2 DG A 4 NA NA A 107 1555 1555 2.46 LINK OP1 DC A 5 NA NA A 105 1555 1555 2.48 LINK OP1 DA A 6 NA NA A 106 1555 1555 2.57 LINK OP2 DA A 6 NA NA A 105 1555 1555 2.50 LINK OP1 DT A 7 NA NA A 104 1555 1555 2.54 LINK OP2 DT A 7 NA NA A 102 1555 1555 2.49 LINK OP1 DG A 8 NA NA A 102 1555 1555 2.50 LINK OP1 DG A 8 NA NA A 104 1555 1555 2.61 SITE 1 AC1 2 DT A 3 DG A 4 SITE 1 AC2 2 DT A 7 DG A 8 SITE 1 AC3 2 DT A 2 DA A 6 SITE 1 AC4 3 DT A 2 DT A 7 DG A 8 SITE 1 AC5 2 DC A 5 DA A 6 SITE 1 AC6 2 DT A 2 DA A 6 SITE 1 AC7 1 DG A 4 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