HEADER DNA 17-JAN-03 1NP9 TITLE STRUCTURE OF THE PARALLEL-STRANDED DNA QUADRUPLEX D(TTAGGGA)4 TITLE 2 CONTAINING THE HUMAN TELOMERIC REPEAT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*TP*AP*GP*GP*GP*T)-3'; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS PARALLEL-STRANDED QUADRUPLEX DNA, TTAGGGT REPEAT, A-TETRAD, DNA EXPDTA SOLUTION NMR NUMMDL 11 MDLTYP MINIMIZED AVERAGE AUTHOR E.GAVATHIOTIS,M.S.SEARLE REVDAT 4 23-FEB-22 1NP9 1 REMARK REVDAT 3 24-FEB-09 1NP9 1 VERSN REVDAT 2 30-SEP-03 1NP9 3 ATOM REVDAT 1 16-SEP-03 1NP9 0 JRNL AUTH E.GAVATHIOTIS,M.S.SEARLE JRNL TITL STRUCTURE OF THE PARALLEL-STRANDED DNA QUADRUPLEX JRNL TITL 2 D(TTAGGGT)4 CONTAINING THE HUMAN TELOMERIC REPEAT: EVIDENCE JRNL TITL 3 FOR A-TETRAD FORMATION FROM NMR AND MOLECULAR DYNAMICS JRNL TITL 4 SIMULATIONS. JRNL REF ORG.BIOMOL.CHEM. V. 1 1650 2003 JRNL REFN ISSN 1477-0520 JRNL PMID 12926351 JRNL DOI 10.1039/B300845M REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, AMBER 6 REMARK 3 AUTHORS : REMARK 3 PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH, REMARK 3 WEINER,KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURES CALCULATED USING RESTRAINED MOLECULAR DYNAMICS.TOTAL REMARK 3 NUMBER OF NOE RESTRAINTS 728 OF WHICH 24 HYDROGEN-BOND RESTRAINTS REMARK 3 INCLUDED FOR THE HYDROGEN-BONDING GEOMETRY OF THE G-TETRADS. REMARK 3 ENERGY MINIMISATIONS AND RESTRAINED MOLECULAR DYNAMICS WERE REMARK 3 CARRIED OUT USING THE SANDER MODULE OF AMBER 6. CALCULATIONS WITH REMARK 3 SANDER WERE PERFORMED WITH A 2 FS TIME STEP, WITH THE SHAKE REMARK 3 ALGORITHM (TOLERANCE 0.00005 A) APPLIED TO ALL BONDS TO REMOVE REMARK 3 BOND STRETCHING, AND A 9 A CUT OFF TO THE LENNARD JONES REMARK 3 INTERACTIONS. THE RESTRAINED MOLECULAR DYNAMICS WERE PERFORMED AT REMARK 3 300K AND A CONSTANT PRESSURE OF 1.0 ATM WITH ISOTROPIC POSITION REMARK 3 SCALING UTILISING THE BERENDSEN ALGORITHM FOR TEMPERATURE REMARK 3 COUPLING. TRANSLATIONAL AND ROTATIONAL MOTIONS WERE REMOVED EVERY REMARK 3 100 FS. ALL CALCULATIONS WERE CARRIED OUT WITH THE PME METHOD REMARK 3 USING A 9 A CUT-OFF FOR DIRECT SPACE NON-BONDED CALCULATIONS AND A REMARK 3 0.00001 EWALD CONVERGENCE TOLERANCE FOR THE INCLUSION OF LONG- REMARK 3 RANGE ELECTROSTATICS IN OUR CALCULATIONS. REMARK 3 THE QUADRUPLEX SYSTEM WAS ALLOWED TO EQUILIBRATE FULLY BEFORE THE REMARK 3 MOLECULAR DYNAMICS CALCULATIONS. MINIMISATION WAS PERFORMED WITH REMARK 3 50 STEPS OF STEEPEST DESCENT AND 5000 STEPS OF CONJUGATE GRADIENT REMARK 3 TO FIRST THE WATER AND COUNTERIONS, WITH THE DNA COORDINATES REMARK 3 FROZEN, FOLLOWED BY A FURTHER 5000 STEPS ON ALL THE COMPONENTS OF REMARK 3 THE SYSTEM. NEXT, 10 PS UNRESTRAINED MOLECULAR DYNAMICS WERE RUN REMARK 3 AT 100K ON THE WATER ALONE WITH THE DNA AND POTASSIUM IONS REMARK 3 CONSTRAINED, FOLLOWED FOR ANOTHER 10 PS TO ALLOW THE POTASSIUM REMARK 3 IONS TO MOVE. IN THE FOLLOWING 5 PS OF DYNAMICS THE TEMPERATURE REMARK 3 OF THE SYSTEM WAS INCREASED FROM 100K TO 300K. THE NEXT RUNS, REMARK 3 EACH OF THEM OF 10 PS DYNAMICS, THE DNA FORCE CONSTANT IS REMARK 3 GRADUALLY REDUCED FROM 100 TO 50, 25, 10, 5 AND 2.5 REMARK 3 KCAL MOL-1 A-2. THE EQUILIBRATION STEP ENDS WITH 100 PS OF REMARK 3 DYNAMICS ON THE WHOLE FULLY UNRESTRAINED SYSTEM. THE SYSTEM NOW REMARK 3 IS FULLY EQUILIBRATED AND NOE RESTRAINTS CAN BE APPLIED TO THE REMARK 3 QUADRUPLEX SYSTEM. DISTANCE RESTRAINTS WERE INTRODUCED GRADUALLY REMARK 3 ON THE SYSTEM OVER THE FIRST 10 PS OF 100 PS MD RUN WITH THE REMARK 3 TEMPERATURE STABLE AT 300K AND PME ON. ALL NOE RESTRAINTS WERE REMARK 3 INTRODUCED IN THE FORM OF SQUARE WELL POTENTIALS WITH A FORCE REMARK 3 CONSTANT OF 50 KCAL MOL-1 A-1 FOR THE HYDROGEN-BOND RESTRAINTS AND REMARK 3 30 KCAL MOL-1 A-1 FOR ALL THE OTHER NOE DISTANCE RESTRAINTS. A REMARK 3 TOTAL OF 1000 PS SIMULATION WAS PERFORMED UNDER THE SAME REMARK 3 CONDITIONS.CALCULATED STRUCTURES SATISFIED THE VAST MAJORITY OF REMARK 3 THE NOE RESTRAINTS FROM THE SET OF 728 RESTRAINTS. THE AVERAGE REMARK 3 MINIMISED STRUCTURE HAD NO RESTRAINT VIOLATION > 0.3 A THAT REMARK 3 CONTRIBUTED TO A 48.22 KCAL MOL-1 ENERGY PENALTY. SNAPSHOTS OF REMARK 3 EACH PICOSECOND WERE EXTRACTED FROM THE WHOLE SIMULATION AND THE REMARK 3 STRUCTURES WERE DETERMINED TO BE EQUILIBRATED ON THE BASIS OF RMSD REMARK 3 ANALYSIS. REMARK 4 REMARK 4 1NP9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018075. 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 : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 6.4MM TTAGGGT, 100MM KCL, 10MM REMARK 210 K2HPO4, 0.1 MM EDTA, 0.1 MM NAN3, REMARK 210 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, ANSIG V3.3 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 11 REMARK 210 REMARK 210 REMARK: STANDARD PHASE SENSITIVE 2D NMR PULSE SEQUENCES WERE USED. 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 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 C4 - C5 - C6 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DT A 1 C5 - C6 - N1 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DT A 1 C5 - C4 - O4 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT A 1 C6 - C5 - C7 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DT A 2 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DT A 2 O4' - C1' - N1 ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DT A 2 C4 - C5 - C6 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DT A 2 C4 - C5 - C7 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DT A 2 C6 - C5 - C7 ANGL. DEV. = -9.1 DEGREES REMARK 500 1 DT A 2 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 3 C2 - N3 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA A 3 N3 - C4 - C5 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DA A 3 C4 - C5 - N7 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA A 3 C5 - N7 - C8 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA A 3 N9 - C4 - C5 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -7.3 DEGREES REMARK 500 1 DG A 4 O4' - C4' - C3' ANGL. DEV. = 10.1 DEGREES REMARK 500 1 DG A 4 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 1 DG A 4 C4' - C3' - C2' ANGL. DEV. = -8.8 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 DG A 4 C6 - N1 - C2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DG A 4 N3 - C4 - C5 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG A 4 C5 - N7 - C8 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG A 4 N9 - C4 - C5 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 4 N1 - C6 - O6 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG A 4 C5 - C6 - O6 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG A 5 C5' - C4' - O4' ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 8.8 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DG A 5 N1 - C2 - N2 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DG A 5 N3 - C2 - N2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C1' ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 9.4 DEGREES REMARK 500 1 DG A 6 C8 - N9 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 6 N9 - C4 - C5 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT A 7 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DT A 7 C4' - C3' - C2' ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT A 7 N1 - C2 - N3 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT A 7 C2 - N3 - C4 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DT A 7 N3 - C4 - C5 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT A 7 N3 - C2 - O2 ANGL. DEV. = -7.8 DEGREES REMARK 500 1 DT A 7 C4 - C5 - C7 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DT B 8 O4' - C1' - C2' ANGL. DEV. = -8.8 DEGREES REMARK 500 1 DT B 8 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1679 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 0.09 SIDE CHAIN REMARK 500 1 DA A 3 0.09 SIDE CHAIN REMARK 500 1 DG A 4 0.08 SIDE CHAIN REMARK 500 1 DG A 5 0.19 SIDE CHAIN REMARK 500 1 DG A 6 0.09 SIDE CHAIN REMARK 500 1 DT B 9 0.22 SIDE CHAIN REMARK 500 1 DA B 10 0.08 SIDE CHAIN REMARK 500 1 DG B 13 0.07 SIDE CHAIN REMARK 500 1 DT C 15 0.10 SIDE CHAIN REMARK 500 1 DG C 18 0.12 SIDE CHAIN REMARK 500 1 DG C 19 0.13 SIDE CHAIN REMARK 500 1 DG C 20 0.06 SIDE CHAIN REMARK 500 1 DT D 22 0.08 SIDE CHAIN REMARK 500 1 DT D 23 0.11 SIDE CHAIN REMARK 500 1 DA D 24 0.14 SIDE CHAIN REMARK 500 1 DG D 25 0.11 SIDE CHAIN REMARK 500 1 DG D 26 0.08 SIDE CHAIN REMARK 500 2 DT A 1 0.08 SIDE CHAIN REMARK 500 2 DA A 3 0.13 SIDE CHAIN REMARK 500 2 DG A 5 0.09 SIDE CHAIN REMARK 500 2 DT A 7 0.12 SIDE CHAIN REMARK 500 2 DT B 9 0.20 SIDE CHAIN REMARK 500 2 DG B 11 0.12 SIDE CHAIN REMARK 500 2 DG B 12 0.11 SIDE CHAIN REMARK 500 2 DT C 15 0.10 SIDE CHAIN REMARK 500 2 DT C 16 0.12 SIDE CHAIN REMARK 500 2 DG C 19 0.08 SIDE CHAIN REMARK 500 2 DT D 23 0.15 SIDE CHAIN REMARK 500 2 DG D 25 0.10 SIDE CHAIN REMARK 500 2 DG D 26 0.08 SIDE CHAIN REMARK 500 2 DG D 27 0.08 SIDE CHAIN REMARK 500 3 DT A 1 0.12 SIDE CHAIN REMARK 500 3 DT A 2 0.07 SIDE CHAIN REMARK 500 3 DG A 4 0.10 SIDE CHAIN REMARK 500 3 DG A 5 0.13 SIDE CHAIN REMARK 500 3 DT A 7 0.07 SIDE CHAIN REMARK 500 3 DT B 8 0.13 SIDE CHAIN REMARK 500 3 DT B 9 0.21 SIDE CHAIN REMARK 500 3 DG B 11 0.07 SIDE CHAIN REMARK 500 3 DG B 12 0.06 SIDE CHAIN REMARK 500 3 DG B 13 0.08 SIDE CHAIN REMARK 500 3 DT B 14 0.12 SIDE CHAIN REMARK 500 3 DT C 16 0.15 SIDE CHAIN REMARK 500 3 DA C 17 0.08 SIDE CHAIN REMARK 500 3 DG C 18 0.09 SIDE CHAIN REMARK 500 3 DG C 19 0.14 SIDE CHAIN REMARK 500 3 DG C 20 0.07 SIDE CHAIN REMARK 500 3 DT D 22 0.17 SIDE CHAIN REMARK 500 3 DA D 24 0.08 SIDE CHAIN REMARK 500 3 DG D 25 0.05 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 190 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1NP9 A 1 7 PDB 1NP9 1NP9 1 7 DBREF 1NP9 B 8 14 PDB 1NP9 1NP9 8 14 DBREF 1NP9 C 15 21 PDB 1NP9 1NP9 15 21 DBREF 1NP9 D 22 28 PDB 1NP9 1NP9 22 28 SEQRES 1 A 7 DT DT DA DG DG DG DT SEQRES 1 B 7 DT DT DA DG DG DG DT SEQRES 1 C 7 DT DT DA DG DG DG DT SEQRES 1 D 7 DT DT DA DG DG DG DT 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