PDB Short entry for 1WAN HEADER DNA 14-JAN-96 1WAN TITLE DNA DTA TRIPLEX, NMR, 7 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*AP*GP*AP*TP*AP*GP*AP*AP*CP*CP*CP*CP*TP*TP*CP*TP*AP*TP*CP*TP*TP*AP* COMPND 4 TP*AP*TP*CP*TP*(D3)P*TP*CP*TP*T)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: THE STANDARD DNA BASE AT POSITION 28 HAS BEEN REPLACED COMPND 8 BY THE NON-NATURAL SYNTHETIC BASE DP, 1-(2-DEOXY-BETA-D- COMPND 9 RIBOFURANOSYL)-4-(3-BENZAMIDO) PHENYLIMIDAZOLE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS TRIPLEX, INTERCALATOR, DEOXYRIBONUCLEIC ACID, DNA EXPDTA SOLUTION NMR NUMMDL 7 AUTHOR E.WANG,K.M.KOSHLAP,P.GILLESPIE,P.B.DERVAN,J.FEIGON REVDAT 3 02-MAR-22 1WAN 1 REMARK LINK REVDAT 2 24-FEB-09 1WAN 1 VERSN REVDAT 1 11-JUL-96 1WAN 0 JRNL AUTH E.WANG,K.M.KOSHLAP,P.GILLESPIE,P.B.DERVAN,J.FEIGON JRNL TITL SOLUTION STRUCTURE OF A PYRIMIDINE-PURINE-PYRIMIDINE TRIPLEX JRNL TITL 2 CONTAINING THE SEQUENCE-SPECIFIC INTERCALATING NON-NATURAL JRNL TITL 3 BASE D3. JRNL REF J.MOL.BIOL. V. 257 1052 1996 JRNL REFN ISSN 0022-2836 JRNL PMID 8632468 JRNL DOI 10.1006/JMBI.1996.0223 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.M.KOSHLAP,P.GILLESPIE,P.B.DERVAN,J.FEIGON REMARK 1 TITL NONNATURAL DEOXYRIBONUCLEOSIDE D3 INCORPORATED IN AN REMARK 1 TITL 2 INTRAMOLECULAR DNA TRIPLEX BINDS SEQUENCE-SPECIFICALLY BY REMARK 1 TITL 3 INTERCALATION REMARK 1 REF J.AM.CHEM.SOC. V. 115 7908 1993 REMARK 1 REFN ISSN 0002-7863 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 1WAN 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_1000177166. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.2 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 : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 7 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: 2MM DNA, 100MM NACL, 5MM MGCL2 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' DA A 8 OP1 DC A 9 1.48 REMARK 500 H4' DG A 6 OP1 DA A 7 1.54 REMARK 500 H4' DC A 26 OP1 DT A 27 1.56 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. = 3.7 DEGREES REMARK 500 1 DA A 1 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DA A 5 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 5 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 6 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG A 6 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DA A 7 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 8 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DA A 8 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 14 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT A 14 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC A 15 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT A 16 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 17 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DA A 17 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 19 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 20 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT A 21 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DA A 22 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA A 22 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT A 23 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DA A 24 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 24 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT A 25 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC A 26 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT A 27 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT A 29 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC A 30 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 31 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 32 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA A 1 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA A 3 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 306 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1WAN A 1 32 PDB 1WAN 1WAN 1 32 SEQRES 1 A 32 DA DG DA DT DA DG DA DA DC DC DC DC DT SEQRES 2 A 32 DT DC DT DA DT DC DT DT DA DT DA DT DC SEQRES 3 A 32 DT D3 DT DC DT DT HET D3 A 28 50 HETNAM D3 1-(2-DEOXY-BETA-D-RIBOFURANOSYL)-4-(3-BENZAMIDO) HETNAM 2 D3 PHENYLIMIDAZOLE FORMUL 1 D3 C21 H22 N3 O7 P LINK O3' DT A 27 P D3 A 28 1555 1555 1.61 LINK O3' D3 A 28 P DT A 29 1555 1555 1.62 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