HEADER DNA 30-JUN-05 2A5P TITLE MONOMERIC PARALLEL-STRANDED DNA TETRAPLEX WITH SNAP-BACK TITLE 2 3+1 3' G-TETRAD, SINGLE-RESIDUE CHAIN REVERSAL LOOPS, GAG TITLE 3 TRIAD IN THE CONTEXT OF GAAG DIAGONAL LOOP, NMR, 8 STRUCT. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*IP*GP*AP*GP*GP*GP*TP*GP*GP*GP COMPND 4 *GP*AP*AP*GP*G)-3'; COMPND 5 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 OTHER_DETAILS: C-MYC GENE KEYWDS MONOMERIC PARALLEL-STRANDED QUADRUPLEX; C-MYC PROMOTER 3+1 KEYWDS 2 G-TETRAD; SINGLE NUCLEOTIDE CHAIN REVERSAL LOOP; GAG TRIAD; KEYWDS 3 GAAG LOOP, DNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR A.T.PHAN,V.V.KURYAVYI,H.Y.GAW,D.J.PATEL REVDAT 2 24-FEB-09 2A5P 1 VERSN REVDAT 1 26-JUL-05 2A5P 0 JRNL AUTH A.T.PHAN,V.KURYAVYI,H.Y.GAW,D.J.PATEL JRNL TITL SMALL-MOLECULE INTERACTION WITH A JRNL TITL 2 FIVE-GUANINE-TRACT G-QUADRUPLEX STRUCTURE FROM THE JRNL TITL 3 HUMAN MYC PROMOTER. JRNL REF NAT.CHEM.BIOL. V. 1 167 2005 JRNL REFN ISSN 1552-4450 JRNL PMID 16408022 JRNL DOI 10.1038/NCHEMBIO723 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR 3.851 REMARK 3 AUTHORS : AT BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2A5P COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-05. REMARK 100 THE RCSB ID CODE IS RCSB033519. 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 : 90 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 70 MM KCL 20 MM POTASSIUM REMARK 210 PHOSPHATE, 90% H2O, 10% D2O; REMARK 210 70 MM KCL 20 MM POTASSIUM REMARK 210 PHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-1H NOESY, 1H-1H TOCSY, 1H- REMARK 210 31P COSY, 1H-1H COSY, 1H-15N REMARK 210 JRHMQC, 1H-15N HMBC, 1H-13C REMARK 210 JRHM 1H-13C HMBC, 1H-13C HSQC, REMARK 210 1H-13C SHMBC, 1H-31P TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : VARIAN UNITY INOVA, AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN, BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.0, FELIX 2000 REMARK 210 METHOD USED : DISTANCE GEOMETRY AND REMARK 210 SIMULATED ANNEALING, DISTANCE REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 REFINEMENT AND RELAXATION REMARK 210 MATRIX INTENSITY REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE REMARK 210 WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: A TOTAL OF 100 INITIAL DNA STRUCTURES WERE GENERATED REMARK 210 USING THE METRIC MATRIX DISTANCE GEOMETRY PROTOCOL WITH THE REMARK 210 EXPERIMENTAL DISTANCE RESTRAINTS SPECIFIED WITH THE R-6 REMARK 210 AVERAGING OPTION. EIGHT BEST STRUCTURES SELECTED ON THE BASIS REMARK 210 OF GOOD COVALENT GEOMETRY, LOW DISTANCE RESTRAINT VIOLATION REMARK 210 AND FAVOURABLE NON-BONDED ENERGY TERMS WERE FURTHER OPTIMIZED REMARK 210 WITH RESTRAINED MOLECULAR DYNAMICS, MOLECULAR MECHANICS AND REMARK 210 RELAXATION MATRIX INTENSITY REFINEMENT.THE PROTOCOLS ARE AS REMARK 210 FOLLOWS. THE DYNAMICS WAS INITIATED AT 300K AND THE REMARK 210 TEMPERATURE WAS INCREASED TO 1000K DURING 7PS. AFTER 0.5 PS REMARK 210 THE FORCE CONSTANTS WERE GRADUALLY SCALED DURING 17.5 PSEC IN REMARK 210 THE PROPORTION 1:4:8 FOR THREE CLASSES OF NOE: EXCHANGEABLE, REMARK 210 NONEXCHANGEABLE AND HYDROGEN BONDS, RESP. THE STRUCTURES WERE REMARK 210 THEN SLOWLY COOLED TO 300K IN 14 PS AND EQUILIBRATED AT 300K REMARK 210 FOR 12 PS. THE COORDINATES SAVED EVERY 0.5 PS DURING THE LAST REMARK 210 4.0 PS WERE AVERAGED AND THE AVERAGE STRUCTURE WAS SUBJECTED REMARK 210 TO MINIMIZATION UNTIL THE GRADIENT OF ENERGY WAS LESS THAN REMARK 210 0.1KCAL/MOL. SOFT PLANARITY RESTRAINTS IMPOSED ON TETRADS AND REMARK 210 TRIAD BEFORE HEATING WERE EXCLUDED AT THE EQUILIBRATION STAGE. REMARK 210 THE DIHEDRAL AND HYDROGEN-BONDING RESTRAINTS FOR TETRADS, WERE REMARK 210 MAINTAINED THROUGHOUT. ALL EIGHT STRUCTURES WERE SUBJECTED TO REMARK 210 RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSITY VOLUMES REMARK 210 OF NON-EXCHANGEABLE PROTONS WERE USED AS RESTRAINTS WITH REMARK 210 EXCHANGEABLE PROTONS REPLACED BY DEUTERONS. DYNAMICS STARTED REMARK 210 AT 5K AND THE SYSTEM WAS HEATHED UP TO 300 K IN 0.6 PSEC. THE REMARK 210 FORCE CONSTANT FOR NOE INTENSITIES WAS GRADUALLY INCREASED REMARK 210 FROM 0 TO 400 KCAL*MOL-1*A-2 WITH SIMULTANEOUS DECREASE OF THE REMARK 210 DISTANCE FORCE CONSTANTS FOR NON-EXCHANGEABLE PROTONS FROM 32 REMARK 210 TO 16. AFTER EQUILIBRATION AT 300 K FOR 3 PSEC THE RESULTING REMARK 210 STRUCTURES WERE SUBJECTED TO MINIMIZATION UNTIL THE GRADIENT REMARK 210 OF ENERGY WAS LESS THAN 0.1KCAL/MOL. THE DISTANCE RESTRAINTS REMARK 210 FOR EXCHANGEABLE PROTONS HYDROGEN BONDS AND DIHEDRAL ANGLE REMARK 210 RESTRAINTS WERE MAINTAINED. SOFT PLANARITY RESTRAINTS WEERE REMARK 210 SET FOR TETRAD (1 KCAL*MOL-1*A-2) AND TRIAD (0.5 KCAL*MOL-1*A- REMARK 210 2). 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 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 DA A 3 C5' DA A 3 C4' 0.046 REMARK 500 1 DG A 20 C5' DG A 20 C4' 0.053 REMARK 500 1 DG A 23 C5' DG A 23 C4' 0.058 REMARK 500 2 DG A 2 C5' DG A 2 C4' 0.051 REMARK 500 2 DA A 3 C5' DA A 3 C4' 0.055 REMARK 500 2 DG A 20 C5' DG A 20 C4' 0.052 REMARK 500 2 DG A 23 C5' DG A 23 C4' 0.052 REMARK 500 3 DA A 3 C5' DA A 3 C4' 0.047 REMARK 500 3 DG A 20 C5' DG A 20 C4' 0.053 REMARK 500 3 DG A 23 C5' DG A 23 C4' 0.056 REMARK 500 4 DG A 2 C5' DG A 2 C4' 0.053 REMARK 500 4 DA A 3 C5' DA A 3 C4' 0.053 REMARK 500 4 DG A 20 C5' DG A 20 C4' 0.050 REMARK 500 4 DG A 23 C5' DG A 23 C4' 0.055 REMARK 500 5 DG A 2 C5' DG A 2 C4' 0.044 REMARK 500 5 DA A 3 C5' DA A 3 C4' 0.043 REMARK 500 5 DG A 20 C5' DG A 20 C4' 0.051 REMARK 500 5 DG A 23 C5' DG A 23 C4' 0.058 REMARK 500 6 DG A 2 C5' DG A 2 C4' 0.045 REMARK 500 6 DA A 3 C5' DA A 3 C4' 0.046 REMARK 500 6 DG A 20 C5' DG A 20 C4' 0.054 REMARK 500 6 DG A 23 C5' DG A 23 C4' 0.058 REMARK 500 7 DG A 2 C5' DG A 2 C4' 0.043 REMARK 500 7 DA A 3 C5' DA A 3 C4' 0.043 REMARK 500 7 DG A 20 C5' DG A 20 C4' 0.050 REMARK 500 7 DG A 23 C5' DG A 23 C4' 0.050 REMARK 500 8 DA A 3 C5' DA A 3 C4' 0.045 REMARK 500 8 DG A 20 C5' DG A 20 C4' 0.051 REMARK 500 8 DG A 23 C5' DG A 23 C4' 0.054 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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA A 12 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 23 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DG A 11 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 DA A 12 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DT A 16 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DG A 23 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DG A 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 4 DA A 12 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DG A 13 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 4 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 4 DG A 23 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 5 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 5 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 5 DG A 6 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 5 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 5 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 5 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 5 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 5 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 5 DG A 23 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 6 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 6 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 6 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 6 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 6 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 6 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 68 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EEG RELATED DB: PDB REMARK 900 A(GGGG)A HEXAD REMARK 900 RELATED ID: 1JJP RELATED DB: PDB REMARK 900 A(GGGG) PENTAD, 5' 3+1 TETRAD REMARK 900 RELATED ID: 1Y8D RELATED DB: PDB REMARK 900 A(GGGG) PENTAD, 5' 3+1 TETRAD REMARK 900 RELATED ID: 1D6D RELATED DB: PDB REMARK 900 AAT TRIAD IN DIAGONAL LOOP REMARK 900 RELATED ID: 2A5R RELATED DB: PDB DBREF 2A5P A 1 24 PDB 2A5P 2A5P 1 24 SEQRES 1 A 24 DT DG DA DG DG DG DT DG DG DI DG DA DG SEQRES 2 A 24 DG DG DT DG DG DG DG DA DA DG DG 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 220 0 0 0 0 0 0 6 0 0 0 2 END