HEADER DNA 18-JUN-03 1PQQ TITLE NMR STRUCTURE OF A CYCLIC POLYAMIDE-DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*TP*AP*AP*CP*AP*GP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*CP*CP*TP*GP*TP*TP*AP*GP*CP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DNA EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR Q.ZHANG,T.J.DWYER,V.TSUI,D.A.CASE,J.CHO,P.B.DERVAN,D.E.WEMMER REVDAT 4 22-MAY-24 1PQQ 1 REMARK REVDAT 3 02-MAR-22 1PQQ 1 REMARK REVDAT 2 24-FEB-09 1PQQ 1 VERSN REVDAT 1 29-JUN-04 1PQQ 0 JRNL AUTH Q.ZHANG,T.J.DWYER,V.TSUI,D.A.CASE,J.CHO,P.B.DERVAN, JRNL AUTH 2 D.E.WEMMER JRNL TITL NMR STRUCTURE OF A CYCLIC POLYAMIDE-DNA COMPLEX. JRNL REF J.AM.CHEM.SOC. V. 126 7958 2004 JRNL REFN ISSN 0002-7863 JRNL PMID 15212545 JRNL DOI 10.1021/JA0373622 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PQQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000019511. 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 : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 21 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 21 DC A 1 O5' DC A 1 C5' -0.505 REMARK 500 21 DC A 1 C5' DC A 1 C4' -0.288 REMARK 500 21 DC A 1 C4' DC A 1 C3' -0.216 REMARK 500 21 DC A 1 C3' DC A 1 C2' -0.158 REMARK 500 21 DC A 1 C2' DC A 1 C1' -0.138 REMARK 500 21 DC A 1 O4' DC A 1 C1' -0.187 REMARK 500 21 DC A 1 O4' DC A 1 C4' -0.148 REMARK 500 21 DC A 1 O3' DC A 1 C3' -0.271 REMARK 500 21 DC A 1 C1' DC A 1 N1 -0.116 REMARK 500 21 DC A 1 C2 DC A 1 O2 -0.111 REMARK 500 21 DC A 1 C4 DC A 1 N4 -0.152 REMARK 500 21 DC A 1 N1 DC A 1 C2 -0.140 REMARK 500 21 DC A 1 N1 DC A 1 C6 -0.110 REMARK 500 21 DC A 1 C2 DC A 1 N3 -0.122 REMARK 500 21 DC A 1 N3 DC A 1 C4 -0.130 REMARK 500 21 DC A 1 C4 DC A 1 C5 -0.153 REMARK 500 21 DC A 1 C5 DC A 1 C6 -0.106 REMARK 500 21 DC A 1 O3' DG A 2 P -0.316 REMARK 500 21 DG A 2 P DG A 2 OP1 -0.245 REMARK 500 21 DG A 2 P DG A 2 OP2 -0.168 REMARK 500 21 DG A 2 P DG A 2 O5' -0.238 REMARK 500 21 DG A 2 O5' DG A 2 C5' -0.389 REMARK 500 21 DG A 2 C5' DG A 2 C4' -0.199 REMARK 500 21 DG A 2 C3' DG A 2 C2' -0.122 REMARK 500 21 DG A 2 C2' DG A 2 C1' -0.076 REMARK 500 21 DG A 2 O4' DG A 2 C1' -0.075 REMARK 500 21 DG A 2 O4' DG A 2 C4' -0.176 REMARK 500 21 DG A 2 O3' DG A 2 C3' -0.158 REMARK 500 21 DG A 2 C1' DG A 2 N9 -0.112 REMARK 500 21 DG A 2 N1 DG A 2 C2 -0.127 REMARK 500 21 DG A 2 C2 DG A 2 N3 -0.128 REMARK 500 21 DG A 2 N3 DG A 2 C4 -0.102 REMARK 500 21 DG A 2 C4 DG A 2 C5 -0.108 REMARK 500 21 DG A 2 C5 DG A 2 C6 -0.119 REMARK 500 21 DG A 2 C6 DG A 2 N1 -0.131 REMARK 500 21 DG A 2 C5 DG A 2 N7 -0.113 REMARK 500 21 DG A 2 N7 DG A 2 C8 -0.112 REMARK 500 21 DG A 2 C8 DG A 2 N9 -0.109 REMARK 500 21 DG A 2 N9 DG A 2 C4 -0.134 REMARK 500 21 DG A 2 C2 DG A 2 N2 -0.160 REMARK 500 21 DG A 2 C6 DG A 2 O6 -0.104 REMARK 500 21 DG A 2 O3' DC A 3 P -0.174 REMARK 500 21 DC A 3 P DC A 3 OP1 -0.269 REMARK 500 21 DC A 3 P DC A 3 OP2 -0.186 REMARK 500 21 DC A 3 P DC A 3 O5' -0.221 REMARK 500 21 DC A 3 O5' DC A 3 C5' -0.467 REMARK 500 21 DC A 3 C5' DC A 3 C4' -0.232 REMARK 500 21 DC A 3 C4' DC A 3 C3' -0.126 REMARK 500 21 DC A 3 C3' DC A 3 C2' -0.127 REMARK 500 21 DC A 3 C2' DC A 3 C1' -0.106 REMARK 500 REMARK 500 THIS ENTRY HAS 456 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DC A 3 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DT A 4 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DA A 6 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 6 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 6 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DC A 7 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DA A 8 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA A 8 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 8 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 8 N1 - C6 - N6 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC B 13 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DC B 14 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DC B 14 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DT B 15 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT B 15 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT B 15 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT B 18 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA B 19 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA B 19 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA B 19 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 19 N1 - C6 - N6 ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DC B 21 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC B 21 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC A 1 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DC A 3 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 945 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 1 DA A 6 0.07 SIDE CHAIN REMARK 500 1 DC B 13 0.08 SIDE CHAIN REMARK 500 1 DT B 17 0.11 SIDE CHAIN REMARK 500 2 DA A 6 0.11 SIDE CHAIN REMARK 500 2 DA A 8 0.06 SIDE CHAIN REMARK 500 2 DT B 17 0.12 SIDE CHAIN REMARK 500 2 DA B 19 0.06 SIDE CHAIN REMARK 500 3 DA A 6 0.07 SIDE CHAIN REMARK 500 3 DG A 9 0.06 SIDE CHAIN REMARK 500 3 DT B 17 0.10 SIDE CHAIN REMARK 500 4 DA A 6 0.07 SIDE CHAIN REMARK 500 4 DG A 9 0.05 SIDE CHAIN REMARK 500 4 DC B 14 0.06 SIDE CHAIN REMARK 500 4 DT B 17 0.12 SIDE CHAIN REMARK 500 4 DC B 21 0.07 SIDE CHAIN REMARK 500 5 DT A 4 0.08 SIDE CHAIN REMARK 500 5 DA A 6 0.12 SIDE CHAIN REMARK 500 5 DA A 8 0.07 SIDE CHAIN REMARK 500 5 DG A 9 0.06 SIDE CHAIN REMARK 500 5 DC B 13 0.06 SIDE CHAIN REMARK 500 5 DT B 17 0.12 SIDE CHAIN REMARK 500 5 DA B 19 0.08 SIDE CHAIN REMARK 500 6 DA A 6 0.07 SIDE CHAIN REMARK 500 6 DA A 8 0.06 SIDE CHAIN REMARK 500 6 DC B 13 0.07 SIDE CHAIN REMARK 500 6 DT B 15 0.07 SIDE CHAIN REMARK 500 6 DT B 17 0.10 SIDE CHAIN REMARK 500 7 DA A 5 0.07 SIDE CHAIN REMARK 500 7 DA A 6 0.09 SIDE CHAIN REMARK 500 7 DG A 9 0.05 SIDE CHAIN REMARK 500 7 DT B 17 0.11 SIDE CHAIN REMARK 500 7 DG B 22 0.05 SIDE CHAIN REMARK 500 8 DA A 6 0.13 SIDE CHAIN REMARK 500 8 DG A 9 0.06 SIDE CHAIN REMARK 500 8 DC A 11 0.06 SIDE CHAIN REMARK 500 8 DT B 17 0.12 SIDE CHAIN REMARK 500 9 DA A 6 0.13 SIDE CHAIN REMARK 500 9 DG A 9 0.07 SIDE CHAIN REMARK 500 9 DT B 17 0.12 SIDE CHAIN REMARK 500 10 DA A 5 0.07 SIDE CHAIN REMARK 500 10 DA A 6 0.11 SIDE CHAIN REMARK 500 10 DT B 17 0.12 SIDE CHAIN REMARK 500 11 DA A 6 0.10 SIDE CHAIN REMARK 500 11 DA A 8 0.07 SIDE CHAIN REMARK 500 11 DG A 9 0.09 SIDE CHAIN REMARK 500 11 DC B 14 0.08 SIDE CHAIN REMARK 500 11 DT B 17 0.12 SIDE CHAIN REMARK 500 11 DA B 19 0.06 SIDE CHAIN REMARK 500 11 DG B 22 0.06 SIDE CHAIN REMARK 500 12 DA A 6 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 102 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CYE B 23 DBREF 1PQQ A 1 11 PDB 1PQQ 1PQQ 1 11 DBREF 1PQQ B 12 22 PDB 1PQQ 1PQQ 12 22 SEQRES 1 A 11 DC DG DC DT DA DA DC DA DG DG DC SEQRES 1 B 11 DG DC DC DT DG DT DT DA DG DC DG HET CYE B 23 124 HETNAM CYE 45-(3-AMINOPROPYL)-5,11,22,28,34-PENTAMETHYL-3,9,15,20, HETNAM 2 CYE 26,32,38,43-OCTAOXO-2,5,8,14,19,22,25,28,31,34,37,42, HETNAM 3 CYE 45,48-TETRADECAAZA-11-AZONIAHEPTACYCLO[42.2.1.1~4, HETNAM 4 CYE 7~.1~10,13~.1~21,24~.1~27,30~.1~33,36~]DOPENTACONTA- HETNAM 5 CYE 1(46),4(52),6,10(51),12,21(50),23,27(49),29,33(48),35, HETNAM 6 CYE 44(47)-DODECAENE FORMUL 3 CYE C45 H55 N16 O8 1+ SITE 1 AC1 12 DT A 4 DA A 5 DA A 6 DC A 7 SITE 2 AC1 12 DA A 8 DG A 9 DT B 15 DG B 16 SITE 3 AC1 12 DT B 17 DT B 18 DA B 19 DG B 20 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