HEADER DNA 04-JAN-19 6J37 TITLE DNA MINIDUMBBELL STRUCTURE OF TWO CTTG REPEATS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*TP*TP*GP*CP*TP*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 MINIDUMBBELL, REVERSE WOBBLE TT MISPAIR, HYDROPHOBIC INTERACTION, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.L.LAM,P.GUO REVDAT 4 22-APR-20 6J37 1 JRNL REMARK REVDAT 3 12-JUN-19 6J37 1 JRNL REVDAT 2 05-JUN-19 6J37 1 JRNL REVDAT 1 29-MAY-19 6J37 0 JRNL AUTH P.GUO,S.L.LAM JRNL TITL UNPRECEDENTED HYDROPHOBIC STABILIZATIONS FROM A REVERSE JRNL TITL 2 WOBBLE T·T MISPAIR IN DNA MINIDUMBBELL. JRNL REF J.BIOMOL.STRUCT.DYN. V. 38 1946 2020 JRNL REFN ESSN 1538-0254 JRNL PMID 31107180 JRNL DOI 10.1080/07391102.2019.1621211 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 6J37 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1300010165. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 1 MM NO LABELING DNA, 10 MM NO REMARK 210 LABELING SODIUM PHOSPHATE, 0.02 REMARK 210 MM NO LABELING DSS, 99.96% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY 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 : TOPSPIN REMARK 210 METHOD USED : NOT APPLICABLE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 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 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. = 3.1 DEGREES REMARK 500 1 DT A 2 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT A 2 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 1 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 2 DT A 2 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT A 2 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DC A 1 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 3 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 3 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 DT A 2 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 3 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 3 DG A 4 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 3 DT A 6 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 3 DT A 7 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES REMARK 500 3 DG A 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DT A 2 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 DT A 2 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 4 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 4 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 4 DG A 4 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 4 DT A 6 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 4 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 5 DT A 2 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 5 DT A 2 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 5 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 5 DG A 4 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 207 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 DC A 1 0.10 SIDE CHAIN REMARK 500 1 DG A 4 0.20 SIDE CHAIN REMARK 500 1 DT A 6 0.06 SIDE CHAIN REMARK 500 1 DT A 7 0.07 SIDE CHAIN REMARK 500 2 DC A 1 0.11 SIDE CHAIN REMARK 500 2 DT A 2 0.06 SIDE CHAIN REMARK 500 2 DT A 3 0.06 SIDE CHAIN REMARK 500 2 DG A 4 0.20 SIDE CHAIN REMARK 500 3 DC A 1 0.11 SIDE CHAIN REMARK 500 3 DT A 2 0.06 SIDE CHAIN REMARK 500 3 DG A 4 0.21 SIDE CHAIN REMARK 500 4 DC A 1 0.09 SIDE CHAIN REMARK 500 4 DT A 2 0.07 SIDE CHAIN REMARK 500 4 DG A 4 0.21 SIDE CHAIN REMARK 500 4 DT A 7 0.06 SIDE CHAIN REMARK 500 5 DC A 1 0.06 SIDE CHAIN REMARK 500 5 DT A 2 0.07 SIDE CHAIN REMARK 500 5 DG A 4 0.20 SIDE CHAIN REMARK 500 5 DT A 7 0.08 SIDE CHAIN REMARK 500 6 DC A 1 0.08 SIDE CHAIN REMARK 500 6 DT A 2 0.07 SIDE CHAIN REMARK 500 6 DG A 4 0.21 SIDE CHAIN REMARK 500 7 DC A 1 0.12 SIDE CHAIN REMARK 500 7 DG A 4 0.21 SIDE CHAIN REMARK 500 7 DG A 8 0.06 SIDE CHAIN REMARK 500 8 DC A 1 0.07 SIDE CHAIN REMARK 500 8 DT A 2 0.07 SIDE CHAIN REMARK 500 8 DG A 4 0.21 SIDE CHAIN REMARK 500 8 DT A 7 0.06 SIDE CHAIN REMARK 500 9 DC A 1 0.13 SIDE CHAIN REMARK 500 9 DT A 3 0.06 SIDE CHAIN REMARK 500 9 DG A 4 0.21 SIDE CHAIN REMARK 500 9 DG A 8 0.07 SIDE CHAIN REMARK 500 10 DC A 1 0.07 SIDE CHAIN REMARK 500 10 DG A 4 0.22 SIDE CHAIN REMARK 500 11 DC A 1 0.07 SIDE CHAIN REMARK 500 11 DT A 2 0.06 SIDE CHAIN REMARK 500 11 DG A 4 0.21 SIDE CHAIN REMARK 500 11 DT A 7 0.06 SIDE CHAIN REMARK 500 12 DC A 1 0.06 SIDE CHAIN REMARK 500 12 DG A 4 0.21 SIDE CHAIN REMARK 500 12 DT A 6 0.07 SIDE CHAIN REMARK 500 13 DC A 1 0.12 SIDE CHAIN REMARK 500 13 DG A 4 0.21 SIDE CHAIN REMARK 500 13 DG A 8 0.06 SIDE CHAIN REMARK 500 14 DC A 1 0.10 SIDE CHAIN REMARK 500 14 DG A 4 0.21 SIDE CHAIN REMARK 500 14 DT A 7 0.06 SIDE CHAIN REMARK 500 15 DC A 1 0.07 SIDE CHAIN REMARK 500 15 DT A 2 0.06 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 68 PLANE DEVIATIONS. 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 107 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 2 OP1 REMARK 620 2 DT A 2 OP2 58.7 REMARK 620 N 1 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 DC A 5 OP1 REMARK 620 2 DC A 5 O3' 122.1 REMARK 620 N 1 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 DT A 7 OP1 REMARK 620 2 DG A 8 OP1 97.2 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 O5' REMARK 620 2 DG A 8 OP1 73.6 REMARK 620 3 DG A 8 O5' 95.6 56.1 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 7 O2 REMARK 620 2 DG A 8 O6 77.7 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: 36232 RELATED DB: BMRB REMARK 900 DNA MINIDUMBBELL STRUCTURE OF TWO CTTG REPEATS DBREF 6J37 A 1 8 PDB 6J37 6J37 1 8 SEQRES 1 A 8 DC DT DT DG DC DT 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 107 1555 1555 2.58 LINK OP2 DT A 2 NA NA A 107 1555 1555 2.59 LINK OP1 DG A 4 NA NA A 103 1555 1555 2.50 LINK OP1 DC A 5 NA NA A 101 1555 1555 2.61 LINK OP2 DC A 5 NA NA A 104 1555 1555 2.49 LINK O3' DC A 5 NA NA A 101 1555 1555 2.93 LINK OP1 DT A 7 NA NA A 105 1555 1555 2.49 LINK O5' DT A 7 NA NA A 102 1555 1555 2.66 LINK O2 DT A 7 NA NA A 106 1555 1555 2.61 LINK OP1 DG A 8 NA NA A 102 1555 1555 2.52 LINK OP1 DG A 8 NA NA A 105 1555 1555 2.50 LINK O5' DG A 8 NA NA A 102 1555 1555 2.78 LINK O6 DG A 8 NA NA A 106 1555 1555 2.57 SITE 1 AC1 2 DG A 4 DC A 5 SITE 1 AC2 2 DT A 7 DG A 8 SITE 1 AC3 2 DT A 3 DG A 4 SITE 1 AC4 2 DG A 4 DC A 5 SITE 1 AC5 2 DT A 7 DG A 8 SITE 1 AC6 2 DT A 7 DG A 8 SITE 1 AC7 1 DT A 2 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