HEADER DNA 06-MAR-97 1AFF TITLE DNA QUADRUPLEX CONTAINING GGGG TETRADS AND (T.A).A TRIADS, NMR, 8 TITLE 2 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: QUADRUPLEX DNA (5'-D(TP*AP*GP*G)-3'); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: TRUNCATED BIOLOGICAL SEQUENCE KEYWDS DNA-QUADRUPLEX, (T.A).A BASE TRIAD, BOMBYX MORI TELOMERIQUE SINGLE KEYWDS 2 REPEAT, T-A PLATFORM, DEOXYRIBONUCLEIC ACID, DNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR A.KETTANI,S.BOUAZIZ,W.WANG,R.A.JONES,D.J.PATEL REVDAT 4 22-MAY-24 1AFF 1 REMARK REVDAT 3 16-FEB-22 1AFF 1 REMARK REVDAT 2 24-FEB-09 1AFF 1 VERSN REVDAT 1 20-AUG-97 1AFF 0 JRNL AUTH A.KETTANI,S.BOUAZIZ,W.WANG,R.A.JONES,D.J.PATEL JRNL TITL BOMBYX MORI SINGLE REPEAT TELOMERIC DNA SEQUENCE FORMS A JRNL TITL 2 G-QUADRUPLEX CAPPED BY BASE TRIADS. JRNL REF NAT.STRUCT.BIOL. V. 4 382 1997 JRNL REFN ISSN 1072-8368 JRNL PMID 9145109 JRNL DOI 10.1038/NSB0597-382 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1AFF 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_1000170749. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 277 REMARK 210 PH : 6.2 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; TOCSY; 1H-31P COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 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 : LEAST ENERGY AND LEAST RESTRAINT REMARK 210 VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: STRUCTURE DETERMINED USING NMR EXPERIMENTS IN D2O: NOESY, REMARK 210 COSY, TOCSY AND 1H-31P COSY. NOESY BUILDUP AT 50, 100, 150, 200 REMARK 210 AND 300 MS. NMR EXPERIMENTS IN H2O: NOESY (60, 120 AND 200 MS) 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 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 C7 0.038 REMARK 500 1 DA A 2 N9 DA A 2 C4 -0.045 REMARK 500 1 DT B 1 C5' DT B 1 C4' 0.078 REMARK 500 1 DA B 2 C5' DA B 2 C4' 0.101 REMARK 500 1 DA B 2 C4' DA B 2 C3' 0.071 REMARK 500 1 DA B 2 C2' DA B 2 C1' -0.087 REMARK 500 1 DA B 2 C8 DA B 2 N9 -0.056 REMARK 500 1 DG B 4 C5' DG B 4 C4' 0.050 REMARK 500 1 DT C 1 C2' DT C 1 C1' 0.065 REMARK 500 1 DT C 1 C5 DT C 1 C7 0.038 REMARK 500 1 DG C 3 C6 DG C 3 N1 -0.042 REMARK 500 1 DT D 1 C5' DT D 1 C4' 0.088 REMARK 500 1 DA D 2 C5' DA D 2 C4' 0.100 REMARK 500 1 DA D 2 C4' DA D 2 C3' 0.087 REMARK 500 1 DG D 4 C5' DG D 4 C4' 0.050 REMARK 500 2 DT A 1 C2' DT A 1 C1' 0.120 REMARK 500 2 DT A 1 O4' DT A 1 C4' -0.069 REMARK 500 2 DA A 2 C5' DA A 2 C4' 0.075 REMARK 500 2 DT B 1 C5' DT B 1 C4' 0.102 REMARK 500 2 DT B 1 C5 DT B 1 C7 0.039 REMARK 500 2 DA B 2 C5' DA B 2 C4' 0.069 REMARK 500 2 DA B 2 C4' DA B 2 C3' 0.075 REMARK 500 2 DA B 2 N9 DA B 2 C4 0.040 REMARK 500 2 DG B 4 C5' DG B 4 C4' 0.070 REMARK 500 2 DT C 1 C2' DT C 1 C1' 0.060 REMARK 500 2 DT D 1 C5' DT D 1 C4' 0.096 REMARK 500 2 DT D 1 C5 DT D 1 C7 0.037 REMARK 500 2 DA D 2 C5' DA D 2 C4' 0.082 REMARK 500 2 DA D 2 C4' DA D 2 C3' 0.085 REMARK 500 2 DA D 2 C2' DA D 2 C1' -0.074 REMARK 500 2 DA D 2 C8 DA D 2 N9 -0.050 REMARK 500 2 DG D 4 C5' DG D 4 C4' 0.069 REMARK 500 3 DT A 1 C5 DT A 1 C7 0.042 REMARK 500 3 DA A 2 N9 DA A 2 C4 -0.039 REMARK 500 3 DT B 1 C5' DT B 1 C4' 0.098 REMARK 500 3 DT B 1 C5 DT B 1 C7 0.053 REMARK 500 3 DA B 2 C5' DA B 2 C4' 0.062 REMARK 500 3 DA B 2 C2' DA B 2 C1' -0.067 REMARK 500 3 DG B 4 C5' DG B 4 C4' 0.059 REMARK 500 3 DT C 1 C5 DT C 1 C7 0.039 REMARK 500 3 DT D 1 C5' DT D 1 C4' 0.105 REMARK 500 3 DT D 1 C5 DT D 1 C7 0.039 REMARK 500 3 DA D 2 C5' DA D 2 C4' 0.064 REMARK 500 3 DA D 2 N9 DA D 2 C4 0.036 REMARK 500 3 DG D 4 C5' DG D 4 C4' 0.064 REMARK 500 4 DA A 2 N9 DA A 2 C4 -0.047 REMARK 500 4 DG A 4 O3' DG A 4 C3' -0.075 REMARK 500 4 DT B 1 C5' DT B 1 C4' 0.056 REMARK 500 4 DT B 1 C5 DT B 1 C7 -0.346 REMARK 500 4 DA B 2 C5' DA B 2 C4' 0.111 REMARK 500 REMARK 500 THIS ENTRY HAS 121 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 N1 - C1' - C2' ANGL. DEV. = 10.8 DEGREES REMARK 500 1 DT A 1 O4' - C1' - N1 ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DT A 1 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG A 3 C4' - C3' - C2' ANGL. DEV. = -7.8 DEGREES REMARK 500 1 DG A 3 O4' - C1' - C2' ANGL. DEV. = -7.5 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG A 4 C4' - C3' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG A 4 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DT B 1 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DA B 2 O4' - C4' - C3' ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DA B 2 O4' - C1' - C2' ANGL. DEV. = -10.3 DEGREES REMARK 500 1 DA B 2 O4' - C1' - N9 ANGL. DEV. = 8.2 DEGREES REMARK 500 1 DA B 2 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 1 DG B 3 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 1 DG B 4 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG B 4 O4' - C1' - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DT C 1 O4' - C1' - N1 ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DT C 1 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA C 2 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES REMARK 500 1 DG C 3 C5' - C4' - O4' ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DG C 3 C4' - C3' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG C 3 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG C 4 C4' - C3' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DG C 4 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG C 4 O4' - C1' - N9 ANGL. DEV. = 8.2 DEGREES REMARK 500 1 DT D 1 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DT D 1 O4' - C1' - C2' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 DT D 1 O4' - C1' - N1 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DA D 2 O4' - C4' - C3' ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA D 2 O4' - C1' - C2' ANGL. DEV. = -8.1 DEGREES REMARK 500 1 DA D 2 O4' - C1' - N9 ANGL. DEV. = 13.1 DEGREES REMARK 500 1 DA D 2 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA D 2 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DG D 3 C3' - O3' - P ANGL. DEV. = 10.2 DEGREES REMARK 500 1 DG D 4 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 DT A 1 N1 - C1' - C2' ANGL. DEV. = 10.4 DEGREES REMARK 500 2 DT A 1 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DT A 1 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DA A 2 C5' - C4' - C3' ANGL. DEV. = 9.8 DEGREES REMARK 500 2 DA A 2 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DG A 3 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 2 DG A 4 C4' - C3' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG A 4 C5 - N7 - C8 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DG A 4 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DT B 1 O4' - C4' - C3' ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DT B 1 C5' - C4' - C3' ANGL. DEV. = 12.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 295 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1AFF A 1 4 PDB 1AFF 1AFF 1 4 DBREF 1AFF B 1 4 PDB 1AFF 1AFF 1 4 DBREF 1AFF C 1 4 PDB 1AFF 1AFF 1 4 DBREF 1AFF D 1 4 PDB 1AFF 1AFF 1 4 SEQRES 1 A 4 DT DA DG DG SEQRES 1 B 4 DT DA DG DG SEQRES 1 C 4 DT DA DG DG SEQRES 1 D 4 DT 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