HEADER DNA 28-SEP-93 139D TITLE SOLUTION STRUCTURE OF A PARALLEL-STRANDED G-QUADRUPLEX DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*TP*GP*GP*GP*GP*T)-3'); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, G-QUADRUPLEX, ANTI GLYCOSIDIC TORSION ANGLES EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR D.J.PATEL,Y.WANG REVDAT 5 22-MAY-24 139D 1 REMARK REVDAT 4 16-FEB-22 139D 1 REMARK REVDAT 3 07-APR-09 139D 1 REMARK REVDAT 2 24-FEB-09 139D 1 VERSN REVDAT 1 31-JAN-94 139D 0 JRNL AUTH Y.WANG,D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF A PARALLEL-STRANDED G-QUADRUPLEX DNA. JRNL REF J.MOL.BIOL. V. 234 1171 1993 JRNL REFN ISSN 0022-2836 JRNL PMID 8263919 JRNL DOI 10.1006/JMBI.1993.1668 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.WANG,D.J.PATEL REMARK 1 TITL GUANINE RESIDUES IN D(T2AG3) AND D(T2G4) FORM REMARK 1 TITL 2 PARALLEL-STRANDED POTASSIUM CATION STABILIZED G-QUADRUPLEXES REMARK 1 TITL 3 WITH ANTI GLYCOSIDIC TORSION ANGLES IN SOLUTION REMARK 1 REF BIOCHEMISTRY V. 31 8112 1992 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED MOLECULAR DYNAMICS REMARK 3 CALCULATIONS WERE DONE ON A MOLECULAR MODEL BUILT TO REMARK 3 QUALITATIVELY FIT THE NMR DATA. THE REFINEMENT WAS CONDUCTED IN REMARK 3 TWO STAGES. IN THE FIRST STAGE, SEVEN STRUCTURES WERE CALCULATED REMARK 3 USING DISTANCE RESTRAINTS (WITH DIFFERENT SEEDS FOR INITIAL REMARK 3 VELOCITY ASSIGNMENTS). IN THE SECOND STAGE, FOUR OF THE SEVEN REMARK 3 DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER BY NOE REMARK 3 INTENSITY-RESTRAINED MOLECULAR DYNAMICS CALCULATIONS. THE R(1/6) REMARK 3 VALUE WAS USED TO MONITOR THE REFINEMENT DURING THE SECOND REMARK 3 STAGE. THE FINAL R(1/6) VALUES FOR THE FOUR AVERAGED MINIMIZED REMARK 3 STRUCTURES WERE BETWEEN 0.025 AND 0.033. RMS DEVIATIONS FROM REMARK 3 IDEALIZED GEOMETRY FOR THE TWO AVERAGED MINIMIZED STRUCTURES ARE REMARK 3 AS FOLLOWS: MODEL1 MODEL2 MODEL3 MODEL4 BOND (ANGSTROMS) 0.013 REMARK 3 0.013 0.012 0.011 ANGLES (DEGREES) 2.713 2.634 2.731 2.728 REMARK 3 IMPROPERS (DEGREES) 0.476 0.560 0.242 0.280. THE STRUCTURE HAS REMARK 3 AN APPROXIMATE FOUR-FOLD SYMMETRY RELATING THE FOUR STRANDS WITH REMARK 3 THE SYMMETRY AXIS COINCIDENT WITH THE HELICAL AXIS. THE REMARK 3 TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD REMARK 3 APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. REMARK 3 IT WILL ALSO YIELD APPROXIMATE COORDINATES FOR CHAIN *C* WHEN REMARK 3 APPLIED TO CHAIN *B* AND WILL YIELD APPROXIMATE COORDINATES FOR REMARK 3 CHAIN *D* WHEN APPLIED TO CHAIN *C*. REMARK 4 REMARK 4 139D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170090. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE GEOMETRY, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 7 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 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 O4 DT A 7 HO3' DT B 7 1.58 REMARK 500 O4 DT B 7 HO3' DT C 7 1.59 REMARK 500 O4 DT C 7 HO3' DT D 7 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 DT A 1 C5' DT A 1 C4' 0.064 REMARK 500 1 DT A 7 C4' DT A 7 C3' 0.067 REMARK 500 1 DT B 1 C5' DT B 1 C4' 0.059 REMARK 500 1 DT B 7 C5' DT B 7 C4' 0.043 REMARK 500 1 DT B 7 C4' DT B 7 C3' 0.061 REMARK 500 1 DT C 1 C5' DT C 1 C4' 0.063 REMARK 500 1 DT C 1 C5 DT C 1 C7 0.037 REMARK 500 1 DT C 2 C5' DT C 2 C4' 0.048 REMARK 500 1 DT C 7 C5' DT C 7 C4' 0.057 REMARK 500 1 DT C 7 C4' DT C 7 C3' 0.080 REMARK 500 1 DT C 7 C5 DT C 7 C7 0.041 REMARK 500 1 DT D 1 C5' DT D 1 C4' 0.075 REMARK 500 1 DT D 1 C4' DT D 1 C3' 0.065 REMARK 500 1 DT D 7 C5' DT D 7 C4' 0.057 REMARK 500 1 DT D 7 C4' DT D 7 C3' 0.073 REMARK 500 2 DT A 2 C5 DT A 2 C7 0.048 REMARK 500 2 DG A 6 C6 DG A 6 N1 -0.044 REMARK 500 2 DT B 7 C5' DT B 7 C4' 0.048 REMARK 500 2 DT B 7 C5 DT B 7 C7 0.050 REMARK 500 2 DT C 1 C5' DT C 1 C4' 0.067 REMARK 500 2 DT C 1 C5 DT C 1 C7 0.048 REMARK 500 2 DT D 1 C5 DT D 1 C7 0.040 REMARK 500 2 DT D 7 C5' DT D 7 C4' 0.053 REMARK 500 3 DT A 1 C5' DT A 1 C4' 0.083 REMARK 500 3 DT A 1 C5 DT A 1 C7 0.039 REMARK 500 3 DT A 2 C5 DT A 2 C7 0.038 REMARK 500 3 DT A 7 C5' DT A 7 C4' 0.048 REMARK 500 3 DT A 7 C4' DT A 7 C3' 0.064 REMARK 500 3 DT B 1 C5' DT B 1 C4' 0.083 REMARK 500 3 DT B 1 C5 DT B 1 C7 0.041 REMARK 500 3 DT B 2 C5 DT B 2 C7 0.039 REMARK 500 3 DT B 7 C5' DT B 7 C4' 0.048 REMARK 500 3 DT B 7 C4' DT B 7 C3' 0.064 REMARK 500 3 DT C 1 C5' DT C 1 C4' 0.083 REMARK 500 3 DT C 1 C5 DT C 1 C7 0.041 REMARK 500 3 DT C 2 C5 DT C 2 C7 0.038 REMARK 500 3 DT C 7 C5' DT C 7 C4' 0.047 REMARK 500 3 DT C 7 C4' DT C 7 C3' 0.066 REMARK 500 3 DT D 1 C5' DT D 1 C4' 0.083 REMARK 500 3 DT D 1 C5 DT D 1 C7 0.039 REMARK 500 3 DT D 2 C5 DT D 2 C7 0.038 REMARK 500 3 DT D 7 C5' DT D 7 C4' 0.046 REMARK 500 3 DT D 7 C4' DT D 7 C3' 0.065 REMARK 500 4 DT A 1 C5' DT A 1 C4' 0.078 REMARK 500 4 DT A 1 C5 DT A 1 C7 0.036 REMARK 500 4 DT A 2 C5 DT A 2 C7 0.038 REMARK 500 4 DT A 7 C5 DT A 7 C7 0.040 REMARK 500 4 DT B 1 C5' DT B 1 C4' 0.079 REMARK 500 4 DT B 2 C5 DT B 2 C7 0.036 REMARK 500 4 DT B 7 C5 DT B 7 C7 0.040 REMARK 500 REMARK 500 THIS ENTRY HAS 58 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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 6 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 10.3 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT B 1 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DT B 1 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DT B 1 O4' - C1' - N1 ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DT B 2 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 4 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 6 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG B 6 O4' - C1' - N9 ANGL. DEV. = 9.4 DEGREES REMARK 500 1 DT B 7 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DT B 7 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT B 7 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT C 1 O4' - C1' - N1 ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DT C 2 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG C 3 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG C 4 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG C 6 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DG C 6 O4' - C1' - N9 ANGL. DEV. = 9.9 DEGREES REMARK 500 1 DT C 7 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DT C 7 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT C 7 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT D 1 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DT D 2 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG D 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG D 4 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG D 6 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG D 6 O4' - C1' - N9 ANGL. DEV. = 9.3 DEGREES REMARK 500 1 DT D 7 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT D 7 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DT A 1 C4 - C5 - C6 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DT A 7 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 8.0 DEGREES REMARK 500 2 DT B 1 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DT B 2 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DG B 6 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG B 6 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DT B 7 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 2 DT B 7 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DT B 7 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 2 DT B 7 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DT C 1 C4 - C5 - C6 ANGL. DEV. = 4.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 112 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 139D A 1 7 PDB 139D 139D 1 7 DBREF 139D B 1 7 PDB 139D 139D 1 7 DBREF 139D C 1 7 PDB 139D 139D 1 7 DBREF 139D D 1 7 PDB 139D 139D 1 7 SEQRES 1 A 7 DT DT DG DG DG DG DT SEQRES 1 B 7 DT DT DG DG DG DG DT SEQRES 1 C 7 DT DT DG DG DG DG DT SEQRES 1 D 7 DT DT DG 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