HEADER DNA 11-DEC-02 1NEV TITLE A-TRACT DECAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*CP*AP*AP*AP*AP*CP*GP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: A4; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*CP*GP*TP*TP*TP*TP*GP*CP*C)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: PHOSPHORAMIDITE SYNTHESIS, AND ZIMMER AND SOURCE 4 CROTHERS PNAS 92, 3091-5 (1995); SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: PHOSPHORAMIDITE SYNTHESIS, AND ZIMMER AND SOURCE 8 CROTHERS PNAS 92, 3091-5 (1995) KEYWDS A-TRACT, DNA BENDING, DNA DECAMER EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.BARBIC,D.P.ZIMMER,D.M.CROTHERS REVDAT 2 24-FEB-09 1NEV 1 VERSN REVDAT 1 11-MAR-03 1NEV 0 JRNL AUTH A.BARBIC,D.P.ZIMMER,D.M.CROTHERS JRNL TITL STRUCTURAL ORIGINS OF ADENINE-TRACT BENDING JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 2369 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 12586860 JRNL DOI 10.1073/PNAS.0437877100 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NEV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-03. REMARK 100 THE RCSB ID CODE IS RCSB017810. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 200 MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 200 MM NACL, 20 MM SODIUM REMARK 210 PHOSPHATE (PH=7.0), 0.5 MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY, HCCH- REMARK 210 E.COSY, HCCH-COSY, HSQC, HCCH- REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ, 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA, UNITYPLUS, OMEGA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN, GE REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 95, CNS 1.0, YARM REMARK 210 METHOD USED : TORSION ANGLE + CARTESIAN REMARK 210 SIMULATED ANNEALING. THEN REMARK 210 CARTESIAN REFINEMENT WITH REMARK 210 DIPOLAR COUPLINGS. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: DIPOLAR COUPLINGS MEASURED IN 22 MG/ML BACTERIOPHAGE REMARK 210 PF1. STRUCTURES SUPERIMPOSED OVER INNER 8 BP. 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 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 DG A 1 N1 DG A 1 C2 -0.062 REMARK 500 1 DG A 2 N1 DG A 2 C2 -0.050 REMARK 500 1 DC A 8 C4 DC A 8 N4 -0.059 REMARK 500 1 DG A 10 N1 DG A 10 C2 -0.048 REMARK 500 1 DC B 11 C4 DC B 11 N4 -0.055 REMARK 500 1 DC B 12 C4 DC B 12 N4 -0.059 REMARK 500 1 DC B 19 C4 DC B 19 N4 -0.056 REMARK 500 1 DC B 20 C4 DC B 20 N4 -0.056 REMARK 500 2 DG A 2 N1 DG A 2 C2 -0.066 REMARK 500 2 DC A 3 C4 DC A 3 N4 -0.056 REMARK 500 2 DG A 10 N1 DG A 10 C2 -0.062 REMARK 500 2 DC B 12 C4 DC B 12 N4 -0.058 REMARK 500 2 DG B 13 N1 DG B 13 C2 -0.049 REMARK 500 2 DC B 20 C4 DC B 20 N4 -0.056 REMARK 500 3 DG A 1 N1 DG A 1 C2 -0.061 REMARK 500 3 DG A 2 N1 DG A 2 C2 -0.050 REMARK 500 3 DC A 3 C4 DC A 3 N4 -0.056 REMARK 500 3 DC A 8 C4 DC A 8 N4 -0.058 REMARK 500 3 DG A 10 N1 DG A 10 C2 -0.048 REMARK 500 3 DC B 11 C4 DC B 11 N4 -0.057 REMARK 500 3 DC B 12 C4 DC B 12 N4 -0.058 REMARK 500 3 DG B 18 N1 DG B 18 C2 -0.051 REMARK 500 3 DC B 19 C4 DC B 19 N4 -0.057 REMARK 500 4 DG A 1 N1 DG A 1 C2 -0.061 REMARK 500 4 DG A 2 N1 DG A 2 C2 -0.052 REMARK 500 4 DC A 3 C4 DC A 3 N4 -0.056 REMARK 500 4 DC A 8 C4 DC A 8 N4 -0.060 REMARK 500 4 DG A 9 N1 DG A 9 C2 -0.052 REMARK 500 4 DG A 10 N1 DG A 10 C2 -0.051 REMARK 500 4 DC B 11 C4 DC B 11 N4 -0.055 REMARK 500 4 DC B 12 C4 DC B 12 N4 -0.058 REMARK 500 4 DC B 19 C4 DC B 19 N4 -0.055 REMARK 500 5 DG A 1 N1 DG A 1 C2 -0.062 REMARK 500 5 DG A 2 N1 DG A 2 C2 -0.050 REMARK 500 5 DC A 3 C4 DC A 3 N4 -0.056 REMARK 500 5 DC B 11 C4 DC B 11 N4 -0.057 REMARK 500 5 DC B 12 C4 DC B 12 N4 -0.057 REMARK 500 5 DG B 13 N1 DG B 13 C2 -0.065 REMARK 500 5 DG B 13 C2 DG B 13 N2 -0.065 REMARK 500 5 DC B 19 C4 DC B 19 N4 -0.055 REMARK 500 6 DG A 1 N1 DG A 1 C2 -0.063 REMARK 500 6 DG A 2 N1 DG A 2 C2 -0.049 REMARK 500 6 DC A 3 C4 DC A 3 N4 -0.056 REMARK 500 6 DC A 8 C4 DC A 8 N4 -0.058 REMARK 500 6 DG A 9 N1 DG A 9 C2 -0.054 REMARK 500 6 DG A 10 N1 DG A 10 C2 -0.049 REMARK 500 6 DC B 11 C4 DC B 11 N4 -0.055 REMARK 500 6 DC B 12 C4 DC B 12 N4 -0.056 REMARK 500 6 DC B 19 C4 DC B 19 N4 -0.057 REMARK 500 7 DG A 1 N1 DG A 1 C2 -0.061 REMARK 500 REMARK 500 THIS ENTRY HAS 89 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 DG A 1 N1 - C2 - N3 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DG A 1 C2 - N3 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DG A 1 N1 - C2 - N2 ANGL. DEV. = -13.7 DEGREES REMARK 500 1 DG A 1 N3 - C2 - N2 ANGL. DEV. = 8.6 DEGREES REMARK 500 1 DG A 2 N1 - C2 - N3 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DG A 2 N1 - C2 - N2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DC A 3 C2 - N3 - C4 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DC A 3 N3 - C4 - C5 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DC A 3 N3 - C4 - N4 ANGL. DEV. = -7.1 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = -9.3 DEGREES REMARK 500 1 DA A 4 C5 - C6 - N6 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = -9.4 DEGREES REMARK 500 1 DA A 5 C5 - C6 - N6 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DA A 6 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA A 6 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 6 N1 - C6 - N6 ANGL. DEV. = -10.0 DEGREES REMARK 500 1 DA A 6 C5 - C6 - N6 ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DA A 7 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 7 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DA A 7 C4 - C5 - C6 ANGL. DEV. = -3.3 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. = -11.6 DEGREES REMARK 500 1 DA A 7 C5 - C6 - N6 ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DC A 8 C2 - N3 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DC A 8 N3 - C4 - C5 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DC A 8 N3 - C4 - N4 ANGL. DEV. = -7.8 DEGREES REMARK 500 1 DG A 9 N1 - C2 - N3 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG A 10 N1 - C2 - N3 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 10 N1 - C2 - N2 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC B 11 C2 - N3 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DC B 11 N3 - C4 - C5 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DC B 11 N3 - C4 - N4 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DC B 12 C2 - N3 - C4 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC B 12 N3 - C4 - C5 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DC B 12 N3 - C4 - N4 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DG B 13 N1 - C2 - N3 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT B 14 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT B 14 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT B 15 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DT B 15 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT B 16 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT B 16 O4' - C1' - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT B 17 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG B 18 N1 - C2 - N3 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG B 18 N1 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 613 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 5 0.06 SIDE_CHAIN REMARK 500 1 DC B 11 0.07 SIDE_CHAIN REMARK 500 1 DG B 13 0.05 SIDE_CHAIN REMARK 500 1 DC B 20 0.09 SIDE_CHAIN REMARK 500 2 DA A 5 0.06 SIDE_CHAIN REMARK 500 2 DC B 11 0.09 SIDE_CHAIN REMARK 500 3 DA A 5 0.06 SIDE_CHAIN REMARK 500 3 DC A 8 0.06 SIDE_CHAIN REMARK 500 3 DC B 11 0.09 SIDE_CHAIN REMARK 500 3 DG B 13 0.05 SIDE_CHAIN REMARK 500 3 DC B 20 0.11 SIDE_CHAIN REMARK 500 4 DG A 10 0.05 SIDE_CHAIN REMARK 500 4 DC B 20 0.12 SIDE_CHAIN REMARK 500 5 DA A 5 0.06 SIDE_CHAIN REMARK 500 5 DC B 11 0.09 SIDE_CHAIN REMARK 500 5 DG B 13 0.05 SIDE_CHAIN REMARK 500 6 DA A 5 0.06 SIDE_CHAIN REMARK 500 6 DG A 10 0.06 SIDE_CHAIN REMARK 500 6 DC B 12 0.06 SIDE_CHAIN REMARK 500 7 DA A 5 0.05 SIDE_CHAIN REMARK 500 7 DG A 10 0.10 SIDE_CHAIN REMARK 500 7 DC B 20 0.10 SIDE_CHAIN REMARK 500 8 DA A 5 0.07 SIDE_CHAIN REMARK 500 8 DG A 10 0.05 SIDE_CHAIN REMARK 500 8 DC B 11 0.09 SIDE_CHAIN REMARK 500 9 DA A 4 0.07 SIDE_CHAIN REMARK 500 9 DG A 10 0.05 SIDE_CHAIN REMARK 500 10 DC A 3 0.06 SIDE_CHAIN REMARK 500 10 DG A 10 0.05 SIDE_CHAIN REMARK 500 10 DC B 11 0.08 SIDE_CHAIN REMARK 500 10 DC B 20 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1NEV A 1 10 PDB 1NEV 1NEV 1 10 DBREF 1NEV B 11 20 PDB 1NEV 1NEV 11 20 SEQRES 1 A 10 DG DG DC DA DA DA DA DC DG DG SEQRES 1 B 10 DC DC DG DT DT DT DT DG DC DC 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 239 0 0 0 0 0 0 6 0 0 0 2 END