HEADER DNA 24-SEP-93 141D TITLE SOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE FROM THE HIV-1 GENOME: TITLE 2 RESTRAINED MOLECULAR DYNAMICS SIMULATION WITH DISTANCE AND TORSION TITLE 3 ANGLE RESTRAINTS DERIVED FROM TWO-DIMENSIONAL NMR SPECTRA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*GP*CP*TP*TP*GP*CP*CP*TP*TP*GP*AP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*TP*CP*AP*AP*GP*GP*CP*AP*AP*GP*CP*T)-3'); COMPND 7 CHAIN: B; COMPND 8 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, DOUBLE HELIX, CONSERVED SEQUENCE OF HIV-1 GENOME EXPDTA SOLUTION NMR AUTHOR A.MUJEEB,T.L.JAMES REVDAT 4 16-FEB-22 141D 1 REMARK REVDAT 3 24-FEB-09 141D 1 VERSN REVDAT 2 15-JAN-95 141D 1 SEQRES REVDAT 1 30-APR-94 141D 0 JRNL AUTH A.MUJEEB,S.M.KERWIN,G.L.KENYON,T.L.JAMES JRNL TITL SOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE FROM THE JRNL TITL 2 HIV-1 GENOME: RESTRAINED MOLECULAR DYNAMICS SIMULATION WITH JRNL TITL 3 DISTANCE AND TORSION ANGLE RESTRAINTS DERIVED FROM JRNL TITL 4 TWO-DIMENSIONAL NMR SPECTRA. JRNL REF BIOCHEMISTRY V. 32 13419 1993 JRNL REFN ISSN 0006-2960 JRNL PMID 8257678 JRNL DOI 10.1021/BI00212A007 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 ALL COORDINATES AROSE FROM ENERGY MINIMIZED AMBER4 FILES THAT WERE REMARK 3 REFORMATTED FOR THE HELIX ANALYSIS PROGRAM CURVES. THEREFORE, ALL REMARK 3 HYDROGEN ATOMS WERE REMOVED. THE DEPOSITORS HAVE PROVIDED THREE REMARK 3 COORDINATE SETS FOR THIS REMARK 3 STRUCTURE. THE FIRST TWO COORDINATE SETS (PROTEIN DATA REMARK 3 BANK ENTRIES 140D AND 141D) CONTAIN THE RESULTS OF THE REMARK 3 NMR/RESTRAINED MOLECULAR DYNAMICS REFINEMENT WHERE A-DNA REMARK 3 AND B-DNA WERE USED AS STARTING MODELS, RESPECTIVELY. THE REMARK 3 AUTHORS DENOTED THESE STRUCTURES AS RMD-A AND RMD-B, REMARK 3 RESPECTIVELY. THE THIRD COORDINATE SET (PROTEIN DATA BANK REMARK 3 ENTRY 142D) REPRESENTS THE FINAL STRUCTURE, DENOTED REMARK 3 RMD-FINAL BY THE AUTHORS. ALL STRUCTURES WERE DERIVED BY REMARK 3 AVERAGING THE LAST 4 PS OF 30 PS RESTRAINED MD (AMBER4) AND REMARK 3 SUBSEQUENT RESTRAINED ENERGY MINIMIZATION. FIVE RMD RUNS REMARK 3 WERE AVERAGED TO EACH INTERIM STRUCTURE RMD-A AND RMD-B, REMARK 3 DEPENDING ON THE STARTING GEOMETRY. ALL TEN STRUCTURES REMARK 3 WERE AVERAGED, RESTRAINED ENERGY MINIMIZED AND A FINAL 20PS REMARK 3 RMD RUN WAS PERFORMED, THE LAST 4PS OF WHICH, AFTER REMARK 3 AVERAGING AND RESTRAINED ENERGY MINIMIZATION LEAD TO THE FINAL REMARK 3 STRUCTURE: RMD-FINAL. REMARK 4 REMARK 4 141D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170096. 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 : 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 NOE REMARK 210 DISTANCE RESTRAINTS IS AVAILABLE FROM THE PROTEIN DATA BANK AS REMARK 210 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 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 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. = 5.8 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 DT A 4 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT A 5 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 DA A 12 O4' - C4' - C3' ANGL. DEV. = 5.2 DEGREES REMARK 500 DG A 13 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 DC B 14 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT B 15 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC B 16 O4' - C4' - C3' ANGL. DEV. = 6.8 DEGREES REMARK 500 DC B 16 C5' - C4' - O4' ANGL. DEV. = 8.6 DEGREES REMARK 500 DC B 16 C3' - C2' - C1' ANGL. DEV. = 9.1 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DA B 18 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 DA B 18 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 DG B 19 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DG B 19 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG B 20 O4' - C4' - C3' ANGL. DEV. = 5.3 DEGREES REMARK 500 DG B 20 C5' - C4' - O4' ANGL. DEV. = 6.9 DEGREES REMARK 500 DC B 21 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 DC B 21 C5' - C4' - O4' ANGL. DEV. = 7.1 DEGREES REMARK 500 DA B 22 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DA B 23 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG B 24 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DC B 25 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 25 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 26 O4' - C1' - N1 ANGL. DEV. = 3.2 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 0.07 SIDE CHAIN REMARK 500 DG A 6 0.07 SIDE CHAIN REMARK 500 DC A 7 0.07 SIDE CHAIN REMARK 500 DG A 11 0.07 SIDE CHAIN REMARK 500 DC B 16 0.10 SIDE CHAIN REMARK 500 DG B 24 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: 142D RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE DBREF 141D A 1 13 PDB 141D 141D 1 13 DBREF 141D B 14 26 PDB 141D 141D 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