HEADER DNA 19-JAN-21 7BMA TITLE AG REPETITION ATTACHED TO AN EXTENDED I-MOTIF CLIP AT 3'-END COMPND MOL_ID: 1; COMPND 2 MOLECULE: AGAG(CH+)C(5MECH+); COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: AGAGC(CH+)(5MEC); COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS AG REPETITION, PARALLEL DUPLEX, TETRAMOLECULAR I-MOTIF, EXTENDED KEYWDS 2 TOPOLOGY, DNA EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR A.NOVOTNY,J.NOVOTNY REVDAT 2 01-DEC-21 7BMA 1 JRNL REVDAT 1 10-NOV-21 7BMA 0 JRNL AUTH A.NOVOTNY,J.NOVOTNY,I.KEJNOVSKA,M.VORLICKOVA,R.FIALA,R.MAREK JRNL TITL REVEALING STRUCTURAL PECULIARITIES OF HOMOPURINE GA JRNL TITL 2 REPETITION STUCK BY I-MOTIF CLIP. JRNL REF NUCLEIC ACIDS RES. V. 49 11425 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 34718718 JRNL DOI 10.1093/NAR/GKAB915 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 16 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1 MICROSECOND OF UNRESTRAINED MOLECULAR REMARK 3 DYNAMICS IN EXPLICIT SOLVENT REMARK 4 REMARK 4 7BMA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1292113588. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 5 REMARK 210 IONIC STRENGTH : 60 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM AGAGCCMC, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER 16, NMRFAM-SPARKY 1.413, REMARK 210 TOPSPIN 4 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : SNAPSHOT EVERY 100 NS TAKEN FROM REMARK 210 1 MICROSECOND OF UNRESTRAINED MD 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 DC A 6 N1 DC A 6 C6 0.040 REMARK 500 1 DC A 6 C2 DC A 6 N3 0.059 REMARK 500 1 DC A 6 C5 DC A 6 C6 0.096 REMARK 500 1 DC B 12 N1 DC B 12 C6 0.040 REMARK 500 1 DC B 12 C2 DC B 12 N3 0.060 REMARK 500 1 DC B 12 C5 DC B 12 C6 0.096 REMARK 500 1 DC C 20 N1 DC C 20 C6 0.042 REMARK 500 1 DC C 20 C2 DC C 20 N3 0.057 REMARK 500 1 DC C 20 C5 DC C 20 C6 0.096 REMARK 500 1 DC D 26 N1 DC D 26 C6 0.042 REMARK 500 1 DC D 26 C2 DC D 26 N3 0.062 REMARK 500 1 DC D 26 C5 DC D 26 C6 0.096 REMARK 500 2 DC A 6 N1 DC A 6 C6 0.042 REMARK 500 2 DC A 6 C2 DC A 6 N3 0.059 REMARK 500 2 DC A 6 C5 DC A 6 C6 0.097 REMARK 500 2 DC B 12 N1 DC B 12 C6 0.039 REMARK 500 2 DC B 12 C2 DC B 12 N3 0.061 REMARK 500 2 DC B 12 C5 DC B 12 C6 0.098 REMARK 500 2 DC C 20 N1 DC C 20 C6 0.042 REMARK 500 2 DC C 20 C2 DC C 20 N3 0.063 REMARK 500 2 DC C 20 C5 DC C 20 C6 0.097 REMARK 500 2 DC D 26 N1 DC D 26 C6 0.041 REMARK 500 2 DC D 26 C2 DC D 26 N3 0.061 REMARK 500 2 DC D 26 C5 DC D 26 C6 0.096 REMARK 500 3 DC A 6 N1 DC A 6 C6 0.042 REMARK 500 3 DC A 6 C2 DC A 6 N3 0.059 REMARK 500 3 DC A 6 C5 DC A 6 C6 0.096 REMARK 500 3 DC B 12 N1 DC B 12 C6 0.045 REMARK 500 3 DC B 12 C2 DC B 12 N3 0.062 REMARK 500 3 DC B 12 C5 DC B 12 C6 0.095 REMARK 500 3 DC C 20 N1 DC C 20 C6 0.041 REMARK 500 3 DC C 20 C2 DC C 20 N3 0.063 REMARK 500 3 DC C 20 C5 DC C 20 C6 0.097 REMARK 500 3 DC D 26 N1 DC D 26 C6 0.043 REMARK 500 3 DC D 26 C2 DC D 26 N3 0.062 REMARK 500 3 DC D 26 C5 DC D 26 C6 0.096 REMARK 500 4 DC A 6 N1 DC A 6 C6 0.041 REMARK 500 4 DC A 6 C2 DC A 6 N3 0.061 REMARK 500 4 DC A 6 C5 DC A 6 C6 0.098 REMARK 500 4 DC B 12 N1 DC B 12 C6 0.042 REMARK 500 4 DC B 12 C2 DC B 12 N3 0.062 REMARK 500 4 DC B 12 C5 DC B 12 C6 0.095 REMARK 500 4 DC C 20 N1 DC C 20 C6 0.042 REMARK 500 4 DC C 20 C2 DC C 20 N3 0.060 REMARK 500 4 DC C 20 C5 DC C 20 C6 0.097 REMARK 500 4 DC D 26 N1 DC D 26 C6 0.041 REMARK 500 4 DC D 26 C2 DC D 26 N3 0.064 REMARK 500 4 DC D 26 C5 DC D 26 C6 0.096 REMARK 500 5 DC A 6 N1 DC A 6 C6 0.042 REMARK 500 5 DC A 6 C2 DC A 6 N3 0.060 REMARK 500 REMARK 500 THIS ENTRY HAS 132 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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 DA A 1 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 1 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DG A 2 OP1 - P - OP2 ANGL. DEV. = -12.1 DEGREES REMARK 500 1 DA A 3 OP1 - P - OP2 ANGL. DEV. = -10.5 DEGREES REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DG A 4 OP1 - P - OP2 ANGL. DEV. = -12.2 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC A 6 OP1 - P - OP2 ANGL. DEV. = -10.9 DEGREES REMARK 500 1 DC A 6 N3 - C4 - C5 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 6 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC A 6 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DA B 8 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA B 8 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA B 8 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DG B 9 OP1 - P - OP2 ANGL. DEV. = -11.9 DEGREES REMARK 500 1 DA B 10 OP1 - P - OP2 ANGL. DEV. = -10.5 DEGREES REMARK 500 1 DA B 10 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA B 10 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA B 10 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DG B 11 OP1 - P - OP2 ANGL. DEV. = -12.3 DEGREES REMARK 500 1 DC B 12 OP1 - P - OP2 ANGL. DEV. = -12.2 DEGREES REMARK 500 1 DC B 12 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC B 12 N3 - C4 - C5 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DC B 12 N1 - C2 - O2 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DC B 12 N3 - C2 - O2 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DA C 15 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA C 15 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA C 15 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DG C 16 OP1 - P - OP2 ANGL. DEV. = -11.9 DEGREES REMARK 500 1 DG C 16 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA C 17 OP1 - P - OP2 ANGL. DEV. = -9.8 DEGREES REMARK 500 1 DA C 17 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA C 17 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA C 17 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DG C 18 OP1 - P - OP2 ANGL. DEV. = -12.4 DEGREES REMARK 500 1 DG C 18 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC C 20 OP1 - P - OP2 ANGL. DEV. = -12.3 DEGREES REMARK 500 1 DC C 20 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DC C 20 N3 - C4 - C5 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC C 20 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DC C 20 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DA D 22 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA D 22 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DG D 23 OP1 - P - OP2 ANGL. DEV. = -11.9 DEGREES REMARK 500 1 DG D 23 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA D 24 OP1 - P - OP2 ANGL. DEV. = -10.8 DEGREES REMARK 500 1 DA D 24 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 670 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 5 DG D 23 0.06 SIDE CHAIN REMARK 500 6 DA C 15 0.08 SIDE CHAIN REMARK 500 6 DC C 20 0.06 SIDE CHAIN REMARK 500 8 DC A 6 0.06 SIDE CHAIN REMARK 500 8 DA C 17 0.06 SIDE CHAIN REMARK 500 8 DG C 18 0.06 SIDE CHAIN REMARK 500 9 DC C 20 0.13 SIDE CHAIN REMARK 500 10 DG B 11 0.07 SIDE CHAIN REMARK 500 10 DC B 12 0.07 SIDE CHAIN REMARK 500 10 DC C 20 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7BI0 RELATED DB: PDB REMARK 900 RELATED SEQUENCE REMARK 900 RELATED ID: 7BLM RELATED DB: PDB REMARK 900 RELATED SEQUENCE REMARK 900 RELATED ID: 7BL0 RELATED DB: PDB REMARK 900 RELATED SEQUENCE REMARK 900 RELATED ID: 34593 RELATED DB: BMRB REMARK 900 AG REPETITION ATTACHED TO AN EXTENDED I-MOTIF CLIP AT 3'-END DBREF 7BMA A 1 7 PDB 7BMA 7BMA 1 7 DBREF 7BMA B 8 14 PDB 7BMA 7BMA 8 14 DBREF 7BMA C 15 21 PDB 7BMA 7BMA 15 21 DBREF 7BMA D 22 28 PDB 7BMA 7BMA 22 28 SEQRES 1 A 7 DA DG DA DG DNR DC U48 SEQRES 1 B 7 DA DG DA DG DC DNR 5CM SEQRES 1 C 7 DA DG DA DG DNR DC U48 SEQRES 1 D 7 DA DG DA DG DC DNR 5CM HET DNR A 5 31 HET U48 A 7 35 HET DNR B 13 31 HET 5CM B 14 34 HET DNR C 19 31 HET U48 C 21 35 HET DNR D 27 31 HET 5CM D 28 34 HETNAM DNR 2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE HETNAM U48 5-METHYL-2'-DEOXY-N3-PROTONATED CYTIDINE-5'- HETNAM 2 U48 MONOPHOSPHATE HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETSYN U48 [(2~{R},3~{S},5~{R})-5-(4-AZANYL-5-METHYL-2- HETSYN 2 U48 OXIDANYLIDENE-PYRIMIDIN-3-IUM-1-YL)-3-OXIDANYL-OXOLAN- HETSYN 3 U48 2-YL]METHYL DIHYDROGEN PHOSPHATE FORMUL 1 DNR 4(C9 H15 N3 O7 P 1+) FORMUL 1 U48 2(C10 H17 N3 O7 P 1+) FORMUL 2 5CM 2(C10 H16 N3 O7 P) LINK O3' DG A 4 P DNR A 5 1555 1555 1.64 LINK O3' DNR A 5 P DC A 6 1555 1555 1.63 LINK O3' DC A 6 P U48 A 7 1555 1555 1.64 LINK O3' DC B 12 P DNR B 13 1555 1555 1.64 LINK O3' DNR B 13 P 5CM B 14 1555 1555 1.63 LINK O3' DG C 18 P DNR C 19 1555 1555 1.64 LINK O3' DNR C 19 P DC C 20 1555 1555 1.63 LINK O3' DC C 20 P U48 C 21 1555 1555 1.63 LINK O3' DC D 26 P DNR D 27 1555 1555 1.64 LINK O3' DNR D 27 P 5CM D 28 1555 1555 1.63 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