HEADER DNA 30-DEC-98 1B4Y TITLE STRUCTURE AND MECHANISM OF FORMATION OF THE H-Y5 ISOMER OF AN TITLE 2 INTRAMOLECULAR DNA TRIPLE HELIX. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (H-Y5 TRIPLE HELIX); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: H-DNA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE DESIGNED DNA SEQUENCE WAS CHEMICALLY SYNTHESIZED. KEYWDS H-DNA, TRIPLE HELIX, DNA EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR M.J.P.VAN DONGEN,J.F.DORELEIJERS,G.A.VAN DER MAREL,J.H.VAN BOOM, AUTHOR 2 C.W.HILBERS,S.S.WIJMENGA REVDAT 5 27-DEC-23 1B4Y 1 REMARK REVDAT 4 23-MAR-22 1B4Y 1 REMARK REVDAT 3 24-FEB-09 1B4Y 1 VERSN REVDAT 2 01-APR-03 1B4Y 1 JRNL REVDAT 1 13-SEP-99 1B4Y 0 JRNL AUTH M.J.VAN DONGEN,J.F.DORELEIJERS,G.A.VAN DER MAREL, JRNL AUTH 2 J.H.VAN BOOM,C.W.HILBERS,S.S.WIJMENGA JRNL TITL STRUCTURE AND MECHANISM OF FORMATION OF THE H-Y5 ISOMER OF JRNL TITL 2 AN INTRAMOLECULAR DNA TRIPLE HELIX. JRNL REF NAT.STRUCT.BIOL. V. 6 854 1999 JRNL REFN ISSN 1072-8368 JRNL PMID 10467098 JRNL DOI 10.1038/12313 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.815 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURES WERE OBTAINED BY TORSION ANGLE DYNAMICS, AND REMARK 3 SUBSEQUENTLY REFINED REMARK 3 BY MEANS OF SIMULATED ANNEALING. REMARK 4 REMARK 4 1B4Y COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000007017. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 100 MM REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : H2O/D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; PE-COSY; TOCSY; 31P-1H; REMARK 210 TOCSY-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : AMX 600; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOW ENERGIES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 10 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 H4' DT A 24 O5' DT A 25 1.55 REMARK 500 O2 DC A 1 H21 DG A 16 1.57 REMARK 500 H3 DT A 17 N7 DA A 11 1.58 REMARK 500 H3 DT A 6 N1 DA A 11 1.59 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 17 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC A 18 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DT A 19 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT A 20 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC A 21 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC A 22 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT A 23 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT A 24 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 24 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 25 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT A 26 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 10 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 10 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DA A 11 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DA A 11 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 12 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 12 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DA A 13 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 13 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 14 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 14 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 15 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 16 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 16 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 DT A 27 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT A 28 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT A 29 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 29 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT A 30 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DT A 17 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 18 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DT A 19 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DT A 20 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DC A 21 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DC A 22 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DT A 23 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 509 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 3 DG A 16 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1B4Y A 17 30 PDB 1B4Y 1B4Y 17 30 SEQRES 1 A 30 DT DC DT DT DC DC DT DT DT DT DC DC DT SEQRES 2 A 30 DT DC DT DC DC DC DG DA DG DA DA DG DG SEQRES 3 A 30 DT DT DT 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