HEADER DNA 24-SEP-93 142D TITLE SOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE FROM THE HIV- TITLE 2 1 GENOME: RESTRAINED MOLECULAR DYNAMICS SIMULATION WITH TITLE 3 DISTANCE AND TORSION ANGLE RESTRAINTS DERIVED FROM TWO- TITLE 4 DIMENSIONAL NMR SPECTRA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*AP*GP*CP*TP*TP*GP*CP*CP*TP*TP*GP*AP*G)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(*CP*TP*CP*AP*AP*GP*GP*CP*AP*AP*GP*CP*T)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, NMR, DOUBLE HELIX,CONSERVED SEQUENCE OF HIV-1 GENOME EXPDTA SOLUTION NMR AUTHOR A.MUJEEB,T.L.JAMES REVDAT 3 24-FEB-09 142D 1 VERSN REVDAT 2 15-JAN-95 142D 1 SEQRES REVDAT 1 30-APR-94 142D 0 JRNL AUTH A.MUJEEB,S.M.KERWIN,G.L.KENYON,T.L.JAMES JRNL TITL SOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE JRNL TITL 2 FROM THE HIV-1 GENOME: RESTRAINED MOLECULAR JRNL TITL 3 DYNAMICS SIMULATION WITH DISTANCE AND TORSION JRNL TITL 4 ANGLE RESTRAINTS DERIVED FROM TWO-DIMENSIONAL NMR JRNL TITL 5 SPECTRA. JRNL REF BIOCHEMISTRY V. 32 13419 1993 JRNL REFN ISSN 0006-2960 JRNL PMID 8257678 JRNL DOI 10.1021/BI00212A007 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER4 REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON, REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ALL COORDINATES AROSE FROM ENERGY REMARK 3 MINIMIZED AMBER4 FILES THAT WERE REFORMATTED FOR THE HELIX REMARK 3 ANALYSIS PROGRAM CURVES. THEREFORE, ALL HYDROGEN ATOMS WERE REMARK 3 REMOVED. THE DEPOSITORS HAVE PROVIDED THREE COORDINATE SETS REMARK 3 FOR THIS STRUCTURE. THE FIRST TWO COORDINATE SETS (PROTEIN REMARK 3 DATA BANK ENTRIES 140D AND 141D) CONTAIN THE RESULTS OF THE REMARK 3 NMR/RESTRAINED MOLECULAR DYNAMICS REFINEMENT WHERE A-DNA AND B REMARK 3 -DNA WERE USED AS STARTING MODELS, RESPECTIVELY. THE AUTHORS REMARK 3 DENOTED THESE STRUCTURES AS RMD-A AND RMD-B, RESPECTIVELY. THE REMARK 3 THIRD COORDINATE SET (PROTEIN DATA BANK ENTRY 142D) REPRESENTS REMARK 3 THE FINAL STRUCTURE, DENOTED RMD-FINAL BY THE AUTHORS. ALL REMARK 3 STRUCTURES WERE DERIVED BY AVERAGING THE LAST 4 PS OF 30 PS REMARK 3 RESTRAINED MD (AMBER4) AND SUBSEQUENT RESTRAINED ENERGY REMARK 3 MINIMIZATION. FIVE RMD RUNS WERE AVERAGED TO EACH INTERIM REMARK 3 STRUCTURE RMD-A AND RMD-B, DEPENDING ON THE STARTING GEOMETRY. REMARK 3 ALL TEN STRUCTURES WERE AVERAGED, RESTRAINED ENERGY MINIMIZED REMARK 3 AND A FINAL 20PS RMD RUN WAS PERFORMED, THE LAST 4PS OF WHICH, REMARK 3 AFTER AVERAGING AND RESTRAINED ENERGY MINIMIZATION LEAD TO THE REMARK 3 FINAL STRUCTURE: RMD-FINAL. REMARK 4 REMARK 4 142D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. 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 : AMBER4 REMARK 210 METHOD USED : MOLECULAR DYNAMICS, ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: SUGAR PUCKER OF DEOXYRIBOSES HAS BEEN DETERMINED BY REMARK 210 SIMULATION OF 2QF-COSY SPECTRA. A LIST OF TORSION ANGLE AND REMARK 210 NOE DISTANCE RESTRAINTS IS AVAILABLE FROM THE PROTEIN DATA REMARK 210 BANK AS ENTRY R140DMR. 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 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 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 DT A 4 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 4 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT A 5 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 DA A 12 O4' - C4' - C3' ANGL. DEV. = 5.2 DEGREES REMARK 500 DG A 13 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DT B 15 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC B 16 O4' - C4' - C3' ANGL. DEV. = 6.6 DEGREES REMARK 500 DC B 16 C5' - C4' - O4' ANGL. DEV. = 7.9 DEGREES REMARK 500 DC B 16 C3' - C2' - C1' ANGL. DEV. = 9.1 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DA B 18 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DA B 18 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 DG B 19 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DG B 19 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 20 O4' - C4' - C3' ANGL. DEV. = 5.6 DEGREES REMARK 500 DG B 20 C5' - C4' - O4' ANGL. DEV. = 6.8 DEGREES REMARK 500 DC B 21 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES REMARK 500 DC B 21 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES REMARK 500 DA B 22 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG B 24 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DC B 25 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 DC B 25 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT B 26 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES 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 DC A 3 0.11 SIDE_CHAIN REMARK 500 DT A 4 0.07 SIDE_CHAIN REMARK 500 DG A 6 0.12 SIDE_CHAIN REMARK 500 DC B 16 0.10 SIDE_CHAIN REMARK 500 DG B 24 0.09 SIDE_CHAIN REMARK 500 DC B 25 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 140D RELATED DB: PDB REMARK 900 1 STRUCTURE (A DNA USED AS STARTING STRUCTURE) REMARK 900 RELATED ID: 141D RELATED DB: PDB REMARK 900 1 STRUCTURE (B DNA USED AS STARTING STRUCTURE) DBREF 142D A 1 13 PDB 142D 142D 1 13 DBREF 142D B 14 26 PDB 142D 142D 14 26 SEQRES 1 A 13 DA DG DC DT DT DG DC DC DT DT DG DA DG SEQRES 1 B 13 DC DT DC DA DA DG DG DC DA DA DG DC 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 MASTER 144 0 0 0 0 0 0 6 0 0 0 2 END