HEADER DNA 08-OCT-93 143D TITLE SOLUTION STRUCTURE OF THE HUMAN TELOMERIC REPEAT D(AG3[T2AG3]3) OF THE TITLE 2 G-QUADRUPLEX CAVEAT 143D DG A 3 HAS WRONG CHIRALITY AT ATOM C4' DG A 3 HAS WRONG CAVEAT 2 143D CHIRALITY AT ATOM C3' DG A 10 HAS WRONG CHIRALITY AT ATOM CAVEAT 3 143D C3' DT A 11 HAS WRONG CHIRALITY AT ATOM C3' DT A 11 HAS CAVEAT 4 143D WRONG CHIRALITY AT ATOM C1' DA A 13 HAS WRONG CHIRALITY AT CAVEAT 5 143D ATOM C3' DG A 2 HAS WRONG CHIRALITY AT ATOM C4' DG A 4 HAS CAVEAT 6 143D WRONG CHIRALITY AT ATOM C4' DG A 10 HAS WRONG CHIRALITY AT CAVEAT 7 143D ATOM C4' DA A 1 HAS WRONG CHIRALITY AT ATOM C4' DG A 21 HAS CAVEAT 8 143D WRONG CHIRALITY AT ATOM C4' DT A 5 HAS WRONG CHIRALITY AT CAVEAT 9 143D ATOM C1' DT A 6 HAS WRONG CHIRALITY AT ATOM C3' DA A 13 HAS CAVEAT 10 143D WRONG CHIRALITY AT ATOM C1' DT A 17 HAS WRONG CHIRALITY AT CAVEAT 11 143D ATOM C1' COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, HUMAN TELOMERIC SEQUENCE, AG3 REPEAT EXPDTA SOLUTION NMR NUMMDL 6 AUTHOR Y.WANG,D.J.PATEL REVDAT 5 29-MAR-23 143D 1 CAVEAT SOURCE REVDAT 4 16-FEB-22 143D 1 REMARK REVDAT 3 24-FEB-09 143D 1 VERSN REVDAT 2 01-APR-03 143D 1 JRNL REVDAT 1 30-APR-94 143D 0 JRNL AUTH Y.WANG,D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF THE HUMAN TELOMERIC REPEAT JRNL TITL 2 D[AG3(T2AG3)3] G-TETRAPLEX. JRNL REF STRUCTURE V. 1 263 1993 JRNL REFN ISSN 0969-2126 JRNL PMID 8081740 JRNL DOI 10.1016/0969-2126(93)90015-9 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: A SET OF SIX STRUCTURES WERE OBTAINED REMARK 3 USING METRIC MATRIX DISTANCE GEOMETRY, AND SUBSEQUENTLY REFINED REMARK 3 BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER- REMARK 3 PROTON DISTANCES AND DIHEDRAL ANGLE RESTRAINTS DERIVED FROM THE REMARK 3 NMR DATA. THE SIX DISTANCE-REFINED STRUCTURES WERE REFINED REMARK 3 FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED REMARK 3 MOLECULAR DYNAMICS. THE FINAL SIX STRUCTURES WERE OBTAINED BY REMARK 3 TAKING THE AVERAGE COORDINATES OF THE LAST 2 PS OF THE DYNAMICS REMARK 3 DURING RELAXATION MATRIX REFINEMENT AND MINIMIZED. THE R(1/6) REMARK 3 VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REMARK 3 REFINEMENT. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL REMARK 3 GEOMETRY FOR THE SIX FINAL STRUCTURES ARE: MODEL1 MODEL2 MODEL3 REMARK 3 MODEL4 MODEL5 MODEL6 R(1/6) FACTOR 0.021 0.016 0.022 0.026 0.024 REMARK 3 0.027 BOND (ANG) 0.009 0.008 0.009 0.011 0.009 0.011 ANGLES (DEG) REMARK 3 2.949 3.085 3.286 3.853 3.038 3.157 IMPROPERS (DEG) 0.285 0.221 REMARK 3 0.267 0.235 0.243 0.248 REMARK 4 REMARK 4 143D 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_1000170100. 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 : 6 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 6 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: 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: 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 H62 DA A 7 O2 DT A 18 1.43 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 5 C3' DT A 5 C2' -0.049 REMARK 500 1 DT A 6 C3' DT A 6 C2' 0.086 REMARK 500 1 DT A 6 C5 DT A 6 C7 0.050 REMARK 500 1 DT A 11 C5' DT A 11 C4' 0.042 REMARK 500 1 DT A 12 C5 DT A 12 C7 0.038 REMARK 500 1 DA A 19 C5' DA A 19 C4' 0.048 REMARK 500 2 DT A 5 C6 DT A 5 N1 -0.052 REMARK 500 2 DT A 5 C5 DT A 5 C7 0.038 REMARK 500 2 DT A 6 C5 DT A 6 C7 0.037 REMARK 500 2 DA A 13 C5' DA A 13 C4' 0.048 REMARK 500 2 DT A 17 C5 DT A 17 C7 0.037 REMARK 500 2 DT A 18 C5 DT A 18 C7 0.039 REMARK 500 2 DA A 19 C5' DA A 19 C4' 0.042 REMARK 500 3 DA A 1 C5' DA A 1 C4' 0.046 REMARK 500 3 DT A 5 C6 DT A 5 N1 -0.053 REMARK 500 3 DT A 5 C5 DT A 5 C7 0.041 REMARK 500 3 DT A 6 C3' DT A 6 C2' 0.086 REMARK 500 3 DT A 6 C5 DT A 6 C7 0.036 REMARK 500 3 DT A 12 C5 DT A 12 C7 0.042 REMARK 500 3 DT A 17 C5 DT A 17 C7 0.036 REMARK 500 4 DT A 5 C5 DT A 5 C7 0.036 REMARK 500 4 DT A 6 C3' DT A 6 C2' 0.093 REMARK 500 4 DG A 9 C2' DG A 9 C1' 0.064 REMARK 500 4 DT A 12 C2' DT A 12 C1' 0.088 REMARK 500 4 DA A 13 C5' DA A 13 C4' 0.051 REMARK 500 4 DT A 18 C5 DT A 18 C7 0.037 REMARK 500 4 DA A 19 C5' DA A 19 C4' 0.048 REMARK 500 5 DT A 5 C5 DT A 5 C7 0.037 REMARK 500 5 DT A 6 C5 DT A 6 C7 0.048 REMARK 500 5 DT A 11 C5 DT A 11 C7 0.038 REMARK 500 5 DT A 12 C5 DT A 12 C7 0.037 REMARK 500 5 DA A 19 C5' DA A 19 C4' 0.043 REMARK 500 6 DA A 1 C5' DA A 1 C4' 0.043 REMARK 500 6 DT A 5 C6 DT A 5 N1 -0.048 REMARK 500 6 DT A 6 C3' DT A 6 C2' 0.092 REMARK 500 6 DT A 6 C5 DT A 6 C7 0.036 REMARK 500 6 DG A 9 C2' DG A 9 C1' 0.060 REMARK 500 6 DT A 11 C2' DT A 11 C1' 0.067 REMARK 500 6 DT A 12 C5 DT A 12 C7 0.041 REMARK 500 6 DA A 13 C5' DA A 13 C4' 0.050 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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 3 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 3 C5' - C4' - O4' ANGL. DEV. = -21.1 DEGREES REMARK 500 1 DG A 3 C2' - C3' - O3' ANGL. DEV. = -24.0 DEGREES REMARK 500 1 DG A 3 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 3 N9 - C1' - C2' ANGL. DEV. = 9.5 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DT A 6 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DT A 6 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DA A 7 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DG A 8 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DG A 9 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DG A 9 O4' - C1' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 16 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DT A 17 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DT A 17 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 20 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DG A 20 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 1 DG A 21 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DG A 21 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DA A 1 C3' - O3' - P ANGL. DEV. = 9.9 DEGREES REMARK 500 2 DG A 2 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG A 3 O4' - C4' - C3' ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DG A 3 C4' - C3' - O3' ANGL. DEV. = 18.6 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DT A 6 C4' - C3' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 2 DT A 6 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DT A 6 O4' - C1' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA A 7 C5' - C4' - O4' ANGL. DEV. = 8.0 DEGREES REMARK 500 2 DA A 7 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 2 DA A 7 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DA A 7 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 2 DA A 7 O4' - C1' - N9 ANGL. DEV. = 8.5 DEGREES REMARK 500 2 DG A 9 C3' - O3' - P ANGL. DEV. = 11.5 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 10.7 DEGREES REMARK 500 2 DT A 11 C4' - C3' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 2 DT A 11 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES REMARK 500 2 DT A 11 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 12 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 DT A 12 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 216 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 201D RELATED DB: PDB REMARK 900 ENSEMBLE OF 6 STRUCTURES REMARK 900 RELATED ID: 179D RELATED DB: PDB REMARK 900 RELATED ID: 186D RELATED DB: PDB DBREF 143D A 1 22 PDB 143D 143D 1 22 SEQRES 1 A 22 DA DG DG DG DT DT DA DG DG DG DT DT DA SEQRES 2 A 22 DG DG DG DT DT DA DG 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