HEADER DNA 30-JUN-05 2A5P TITLE MONOMERIC PARALLEL-STRANDED DNA TETRAPLEX WITH SNAP-BACK 3+1 3' G- TITLE 2 TETRAD, SINGLE-RESIDUE CHAIN REVERSAL LOOPS, GAG TRIAD IN THE CONTEXT TITLE 3 OF GAAG DIAGONAL LOOP, NMR, 8 STRUCT. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*IP*GP*AP*GP*GP*GP*TP*GP*GP COMPND 3 *GP*GP*AP*AP*GP*G)-3'; COMPND 4 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 G-TETRAD; KEYWDS 2 SINGLE NUCLEOTIDE CHAIN REVERSAL LOOP; GAG TRIAD; GAAG LOOP, DNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR A.T.PHAN,V.V.KURYAVYI,H.Y.GAW,D.J.PATEL REVDAT 3 09-MAR-22 2A5P 1 REMARK 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 FIVE-GUANINE-TRACT JRNL TITL 2 G-QUADRUPLEX STRUCTURE FROM THE 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 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 DEPOSITION ID IS D_1000033519. 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; 70 REMARK 210 MM KCL 20 MM POTASSIUM PHOSPHATE, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-1H NOESY; 1H-1H TOCSY; 1H-31P REMARK 210 COSY; 1H-1H COSY; 1H-15N JRHMQC; REMARK 210 1H-15N HMBC; 1H-13C JRHM 1H-13C REMARK 210 HMBC; 1H-13C HSQC; 1H-13C SHMBC; REMARK 210 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 SIMULATED REMARK 210 ANNEALING, DISTANCE RESTRAINED REMARK 210 MOLECULAR DYNAMICS REFINEMENT REMARK 210 AND RELAXATION MATRIX INTENSITY REMARK 210 REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY 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 USING REMARK 210 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 OF REMARK 210 GOOD COVALENT GEOMETRY, LOW DISTANCE RESTRAINT VIOLATION AND REMARK 210 FAVOURABLE NON-BONDED ENERGY TERMS WERE FURTHER OPTIMIZED WITH REMARK 210 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 TEMPERATURE REMARK 210 WAS INCREASED TO 1000K DURING 7PS. AFTER 0.5 PS THE FORCE REMARK 210 CONSTANTS WERE GRADUALLY SCALED DURING 17.5 PSEC IN THE REMARK 210 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 FOR REMARK 210 12 PS. THE COORDINATES SAVED EVERY 0.5 PS DURING THE LAST 4.0 PS REMARK 210 WERE AVERAGED AND THE AVERAGE STRUCTURE WAS SUBJECTED TO REMARK 210 MINIMIZATION UNTIL THE GRADIENT OF ENERGY WAS LESS THAN 0.1KCAL/ REMARK 210 MOL. SOFT PLANARITY RESTRAINTS IMPOSED ON TETRADS AND TRIAD REMARK 210 BEFORE HEATING WERE EXCLUDED AT THE EQUILIBRATION STAGE. THE REMARK 210 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 OF REMARK 210 NON-EXCHANGEABLE PROTONS WERE USED AS RESTRAINTS WITH REMARK 210 EXCHANGEABLE PROTONS REPLACED BY DEUTERONS. DYNAMICS STARTED AT REMARK 210 5K AND THE SYSTEM WAS HEATHED UP TO 300 K IN 0.6 PSEC. THE FORCE REMARK 210 CONSTANT FOR NOE INTENSITIES WAS GRADUALLY INCREASED FROM 0 TO REMARK 210 400 KCAL*MOL-1*A-2 WITH SIMULTANEOUS DECREASE OF THE DISTANCE REMARK 210 FORCE CONSTANTS FOR NON-EXCHANGEABLE PROTONS FROM 32 TO 16. REMARK 210 AFTER EQUILIBRATION AT 300 K FOR 3 PSEC THE RESULTING STRUCTURES REMARK 210 WERE SUBJECTED TO MINIMIZATION UNTIL THE GRADIENT OF ENERGY WAS REMARK 210 LESS THAN 0.1KCAL/MOL. THE DISTANCE RESTRAINTS FOR EXCHANGEABLE REMARK 210 PROTONS HYDROGEN BONDS AND DIHEDRAL ANGLE RESTRAINTS WERE REMARK 210 MAINTAINED. SOFT PLANARITY RESTRAINTS WEERE SET FOR TETRAD (1 REMARK 210 KCAL*MOL-1*A-2) AND TRIAD (0.5 KCAL*MOL-1*A-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 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 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. = 2.8 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. = 2.6 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. = 1.9 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 MODEL 1