HEADER DNA 10-NOV-11 2LLJ TITLE STRUCTURE OF A BIS-NAPHTHALENE BOUND TO A THYMINE-THYMINE DNA MISMATCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*TP*CP*GP*TP*AP*GP*TP*GP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*CP*AP*CP*TP*TP*CP*GP*AP*CP*G)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS DNA THYMINE MISMATCH, MACROCYLE, BISINTERCALATION, DNA EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR M.JOURDAN,A.GRANZHAN,R.GUILLOT,P.DUMY,M.TEULADE-FICHOU REVDAT 1 20-FEB-13 2LLJ 0 JRNL AUTH M.JOURDAN,A.GRANZHAN,R.GUILLOT,P.DUMY,M.P.TEULADE-FICHOU JRNL TITL DOUBLE THREADING THROUGH DNA: NMR STRUCTURAL STUDY OF A JRNL TITL 2 BIS-NAPHTHALENE MACROCYCLE BOUND TO A THYMINE-THYMINE JRNL TITL 3 MISMATCH. JRNL REF NUCLEIC ACIDS RES. V. 40 5115 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22362757 JRNL DOI 10.1093/NAR/GKS067 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 10.1 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LLJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JAN-12. REMARK 100 THE RCSB ID CODE IS RCSB102529. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 0.06 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM DNA (5'-D(*CP*GP*TP*CP* REMARK 210 GP*TP*AP*GP*TP*GP*C)-3'), 1.5 MM DNA (5'-D(*GP*CP*AP*CP*TP*TP*CP* REMARK 210 GP*AP*CP*G)-3'), 1.5 MM 2,7-BISNAPHTHALENE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D DQF-COSY; 2D REMARK 210 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER 10.1 REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 1 DC B 15 C5' DC B 15 C4' 0.045 REMARK 500 2 DC B 15 C5' DC B 15 C4' 0.044 REMARK 500 3 DC B 15 C5' DC B 15 C4' 0.043 REMARK 500 3 DA B 20 C8 DA B 20 N9 -0.048 REMARK 500 4 DC B 15 C5' DC B 15 C4' 0.045 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 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DT A 3 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC A 4 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DA A 7 C4 - C5 - C6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DA A 7 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 7 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 9 C4 - C5 - C7 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -7.8 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC B 13 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DA B 14 C4 - C5 - C6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DA B 14 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DA B 14 N1 - C6 - N6 ANGL. DEV. = -6.9 DEGREES REMARK 500 1 DC B 15 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DC B 15 N1 - C1' - C2' ANGL. DEV. = 11.0 DEGREES REMARK 500 1 DC B 15 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DT B 16 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DT B 16 C4' - C3' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DT B 16 O4' - C1' - C2' ANGL. DEV. = -7.4 DEGREES REMARK 500 1 DT B 16 O4' - C1' - N1 ANGL. DEV. = 25.4 DEGREES REMARK 500 1 DT B 16 C4 - C5 - C6 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DT B 16 C5 - C6 - N1 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT B 16 C6 - C5 - C7 ANGL. DEV. = -7.7 DEGREES REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT B 17 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC B 18 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DA B 20 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DA B 20 O4' - C1' - N9 ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DA B 20 C4 - C5 - C6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DA B 20 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA B 20 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG B 19 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DC B 21 O4' - C1' - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DC B 21 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 2 DT A 3 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 226 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 DG A 5 0.12 SIDE CHAIN REMARK 500 1 DT A 6 0.11 SIDE CHAIN REMARK 500 1 DA A 7 0.07 SIDE CHAIN REMARK 500 1 DG A 8 0.10 SIDE CHAIN REMARK 500 1 DT A 9 0.10 SIDE CHAIN REMARK 500 1 DG A 10 0.09 SIDE CHAIN REMARK 500 1 DC A 11 0.11 SIDE CHAIN REMARK 500 1 DG B 12 0.12 SIDE CHAIN REMARK 500 1 DC B 13 0.07 SIDE CHAIN REMARK 500 1 DC B 15 0.12 SIDE CHAIN REMARK 500 1 DT B 16 0.12 SIDE CHAIN REMARK 500 1 DC B 18 0.09 SIDE CHAIN REMARK 500 1 DG B 22 0.10 SIDE CHAIN REMARK 500 2 DG A 5 0.12 SIDE CHAIN REMARK 500 2 DT A 6 0.11 SIDE CHAIN REMARK 500 2 DA A 7 0.07 SIDE CHAIN REMARK 500 2 DG A 8 0.10 SIDE CHAIN REMARK 500 2 DT A 9 0.09 SIDE CHAIN REMARK 500 2 DG A 10 0.09 SIDE CHAIN REMARK 500 2 DC A 11 0.10 SIDE CHAIN REMARK 500 2 DG B 12 0.12 SIDE CHAIN REMARK 500 2 DC B 13 0.07 SIDE CHAIN REMARK 500 2 DC B 15 0.12 SIDE CHAIN REMARK 500 2 DT B 16 0.13 SIDE CHAIN REMARK 500 2 DC B 18 0.09 SIDE CHAIN REMARK 500 2 DG B 22 0.11 SIDE CHAIN REMARK 500 3 DG A 5 0.12 SIDE CHAIN REMARK 500 3 DT A 6 0.10 SIDE CHAIN REMARK 500 3 DA A 7 0.08 SIDE CHAIN REMARK 500 3 DG A 8 0.10 SIDE CHAIN REMARK 500 3 DT A 9 0.10 SIDE CHAIN REMARK 500 3 DG A 10 0.09 SIDE CHAIN REMARK 500 3 DC A 11 0.11 SIDE CHAIN REMARK 500 3 DG B 12 0.13 SIDE CHAIN REMARK 500 3 DC B 13 0.07 SIDE CHAIN REMARK 500 3 DA B 14 0.06 SIDE CHAIN REMARK 500 3 DC B 15 0.11 SIDE CHAIN REMARK 500 3 DT B 16 0.12 SIDE CHAIN REMARK 500 3 DC B 18 0.09 SIDE CHAIN REMARK 500 3 DG B 22 0.10 SIDE CHAIN REMARK 500 4 DG A 5 0.12 SIDE CHAIN REMARK 500 4 DT A 6 0.10 SIDE CHAIN REMARK 500 4 DA A 7 0.07 SIDE CHAIN REMARK 500 4 DG A 8 0.10 SIDE CHAIN REMARK 500 4 DT A 9 0.10 SIDE CHAIN REMARK 500 4 DG A 10 0.09 SIDE CHAIN REMARK 500 4 DC A 11 0.10 SIDE CHAIN REMARK 500 4 DG B 12 0.11 SIDE CHAIN REMARK 500 4 DC B 13 0.07 SIDE CHAIN REMARK 500 4 DA B 14 0.05 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 68 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 LLJ B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18050 RELATED DB: BMRB DBREF 2LLJ A 1 11 PDB 2LLJ 2LLJ 1 11 DBREF 2LLJ B 12 22 PDB 2LLJ 2LLJ 12 22 SEQRES 1 A 11 DC DG DT DC DG DT DA DG DT DG DC SEQRES 1 B 11 DG DC DA DC DT DT DC DG DA DC DG HET LLJ B 101 82 HETNAM LLJ 6,22-DIOXA-3,9,19,25-TETRAAZONIAPENTACYCLO[25.5.3.3~11, HETNAM 2 LLJ 17~.0~14,37~.0~30,34~]OCTATRIACONTA-1(33),11(38),12, HETNAM 3 LLJ 14(37),15,17(36),27,29,31,34-DECAENE HETSYN LLJ 2,8,19,25-TETRAAZA-5,22-DIOXA-[9,9](2,7) HETSYN 2 LLJ NAPHTHALENOPHANE FORMUL 3 LLJ C32 H44 N4 O2 4+ FORMUL 4 HOH *51(H2 O) SITE 1 AC1 19 DG A 5 DT A 6 DA A 7 DG A 8 SITE 2 AC1 19 HOH A 108 HOH A 109 HOH A 112 HOH A 114 SITE 3 AC1 19 DC B 15 DT B 16 DT B 17 DC B 18 SITE 4 AC1 19 HOH B 206 HOH B 215 HOH B 216 HOH B 217 SITE 5 AC1 19 HOH B 223 HOH B 225 HOH B 228 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 236 0 1 0 0 0 5 6 0 0 0 2 END