HEADER DNA 01-APR-04 1SY8 TITLE STRUCTURE OF DNA SEQUENCE D-TGATCA BY TWO-DIMENSIONAL NUCLEAR MAGNETIC TITLE 2 RESONANCE SPEC AND RESTRAINED MOLECULAR DYNAMICS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*TP*GP*AP*TP*CP*A)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS TPG/CPA BASEPAIR STEP, 2D-NMR OF D-TGATCA, RESTRAINED MOLECULAR KEYWDS 2 DYNAMICS, SEQUENCE RELATED CONFORMATION, DNA FLEXIBILITY, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR R.BARTHWAL,P.AWASTHI,M.NARANG,U.SHARMA,N.SRIVASTAVA REVDAT 3 22-FEB-12 1SY8 1 JRNL VERSN REVDAT 2 24-FEB-09 1SY8 1 VERSN REVDAT 1 04-JAN-05 1SY8 0 JRNL AUTH R.BARTHWAL,P.AWASTHI,M.NARANG,M.KAUR,U.SHARMA,N.SRIVASTAVA, JRNL AUTH 2 S.K.BARTHWAL,G.GOVIL JRNL TITL STRUCTURE OF DNA SEQUENCE D-TGATCA BY TWO-DIMENSIONAL JRNL TITL 2 NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED JRNL TITL 3 MOLECULAR DYNAMICS JRNL REF J.STRUCT.BIOL. V. 148 34 2004 JRNL REFN ISSN 1047-8477 JRNL PMID 15363786 JRNL DOI 10.1016/J.JSB.2004.05.005 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 97 REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON TOTAL 95 REMARK 3 INTRA RESIDUE AND 26 INTER RESIDUE NOESY RESTRAINTS AND 12 REMARK 3 TORSINAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1SY8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-APR-04. REMARK 100 THE RCSB ID CODE IS RCSB022089. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 20MM PHOSPHATE BUFFER; 15MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 3.68MM DUPLEX CONCENTRATION; REMARK 210 20MM PHOSPHATE BUFFER WITH 15MM REMARK 210 NACL; 4.57MM DUPLEX REMARK 210 CONCENTRATION; 20MM PHOSPHATE REMARK 210 BUFFER WITH 15MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AM REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 25 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: FOR IMINO PROTONS 1D WATER SPECTRA VS TEMPERATURE WAS ALSO REMARK 210 DONE 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 DT A 1 C5' DT A 1 C4' 0.044 REMARK 500 1 DC A 5 C4 DC A 5 N4 0.070 REMARK 500 1 DT B 1 C5' DT B 1 C4' 0.042 REMARK 500 1 DC B 5 C4 DC B 5 N4 0.070 REMARK 500 2 DT A 1 C5' DT A 1 C4' 0.043 REMARK 500 2 DC A 5 C4 DC A 5 N4 0.070 REMARK 500 2 DT B 1 C5' DT B 1 C4' 0.044 REMARK 500 2 DC B 5 C4 DC B 5 N4 0.070 REMARK 500 3 DT A 1 C5' DT A 1 C4' 0.043 REMARK 500 3 DC A 5 C4 DC A 5 N4 0.070 REMARK 500 3 DC B 5 C4 DC B 5 N4 0.070 REMARK 500 4 DT A 1 C5' DT A 1 C4' 0.044 REMARK 500 4 DC A 5 C4 DC A 5 N4 0.070 REMARK 500 4 DC B 5 C4 DC B 5 N4 0.070 REMARK 500 5 DC A 5 C4 DC A 5 N4 0.069 REMARK 500 5 DC B 5 C4 DC B 5 N4 0.069 REMARK 500 5 DA B 6 N7 DA B 6 C8 0.056 REMARK 500 6 DC A 5 C4 DC A 5 N4 0.069 REMARK 500 6 DC B 5 C4 DC B 5 N4 0.069 REMARK 500 6 DA B 6 N7 DA B 6 C8 0.060 REMARK 500 7 DC A 5 C4 DC A 5 N4 0.070 REMARK 500 7 DC B 5 C4 DC B 5 N4 0.070 REMARK 500 8 DC A 5 C4 DC A 5 N4 0.069 REMARK 500 8 DC B 5 C4 DC B 5 N4 0.069 REMARK 500 9 DT A 1 C5' DT A 1 C4' 0.043 REMARK 500 9 DC A 5 C4 DC A 5 N4 0.069 REMARK 500 9 DC B 5 C4 DC B 5 N4 0.069 REMARK 500 10 DT A 1 C5' DT A 1 C4' 0.042 REMARK 500 10 DC A 5 C4 DC A 5 N4 0.070 REMARK 500 10 DC B 5 C4 DC B 5 N4 0.069 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 DT A 1 O5' - P - OP1 ANGL. DEV. = 8.4 DEGREES REMARK 500 1 DT A 1 O5' - P - OP2 ANGL. DEV. = 8.3 DEGREES REMARK 500 1 DT A 1 C4 - C5 - C7 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DT A 1 C6 - C5 - C7 ANGL. DEV. = -8.8 DEGREES REMARK 500 1 DG A 2 OP1 - P - OP2 ANGL. DEV. = -9.3 DEGREES REMARK 500 1 DG A 2 N1 - C6 - O6 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG A 2 C5 - C6 - O6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DA A 3 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES REMARK 500 1 DA A 3 O4' - C4' - C3' ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 4 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES REMARK 500 1 DT A 4 O4' - C4' - C3' ANGL. DEV. = 5.6 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DC A 5 OP1 - P - OP2 ANGL. DEV. = -9.2 DEGREES REMARK 500 1 DC A 5 O4' - C4' - C3' ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DC A 5 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA A 6 OP1 - P - OP2 ANGL. DEV. = -9.3 DEGREES REMARK 500 1 DT B 1 O5' - P - OP1 ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DT B 1 O5' - P - OP2 ANGL. DEV. = 8.7 DEGREES REMARK 500 1 DT B 1 C4 - C5 - C7 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DT B 1 C6 - C5 - C7 ANGL. DEV. = -9.8 DEGREES REMARK 500 1 DG B 2 OP1 - P - OP2 ANGL. DEV. = -9.3 DEGREES REMARK 500 1 DG B 2 N1 - C6 - O6 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG B 2 C5 - C6 - O6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DA B 3 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES REMARK 500 1 DA B 3 O4' - C4' - C3' ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DA B 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT B 4 OP1 - P - OP2 ANGL. DEV. = -9.0 DEGREES REMARK 500 1 DT B 4 O4' - C4' - C3' ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DT B 4 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DT B 4 C6 - C5 - C7 ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DC B 5 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES REMARK 500 1 DC B 5 O4' - C4' - C3' ANGL. DEV. = 5.6 DEGREES REMARK 500 1 DC B 5 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA B 6 OP1 - P - OP2 ANGL. DEV. = -9.3 DEGREES REMARK 500 2 DT A 1 O5' - P - OP1 ANGL. DEV. = 8.0 DEGREES REMARK 500 2 DT A 1 O5' - P - OP2 ANGL. DEV. = 8.1 DEGREES REMARK 500 2 DT A 1 C4 - C5 - C7 ANGL. DEV. = 6.3 DEGREES REMARK 500 2 DT A 1 C6 - C5 - C7 ANGL. DEV. = -9.0 DEGREES REMARK 500 2 DG A 2 OP1 - P - OP2 ANGL. DEV. = -9.2 DEGREES REMARK 500 2 DG A 2 N1 - C6 - O6 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG A 2 C5 - C6 - O6 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DA A 3 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES REMARK 500 2 DA A 3 O4' - C4' - C3' ANGL. DEV. = 6.7 DEGREES REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT A 4 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES REMARK 500 2 DT A 4 O4' - C4' - C3' ANGL. DEV. = 5.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 361 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 DT A 4 0.09 SIDE CHAIN REMARK 500 1 DA A 6 0.07 SIDE CHAIN REMARK 500 1 DA B 3 0.05 SIDE CHAIN REMARK 500 1 DT B 4 0.09 SIDE CHAIN REMARK 500 1 DA B 6 0.05 SIDE CHAIN REMARK 500 2 DT A 4 0.10 SIDE CHAIN REMARK 500 2 DA A 6 0.05 SIDE CHAIN REMARK 500 2 DT B 1 0.07 SIDE CHAIN REMARK 500 2 DT B 4 0.09 SIDE CHAIN REMARK 500 2 DA B 6 0.05 SIDE CHAIN REMARK 500 3 DT A 1 0.08 SIDE CHAIN REMARK 500 3 DA A 3 0.05 SIDE CHAIN REMARK 500 3 DT A 4 0.10 SIDE CHAIN REMARK 500 3 DA A 6 0.07 SIDE CHAIN REMARK 500 3 DT B 4 0.10 SIDE CHAIN REMARK 500 3 DA B 6 0.06 SIDE CHAIN REMARK 500 4 DT A 1 0.07 SIDE CHAIN REMARK 500 4 DA A 3 0.05 SIDE CHAIN REMARK 500 4 DT A 4 0.10 SIDE CHAIN REMARK 500 4 DT B 4 0.10 SIDE CHAIN REMARK 500 5 DT A 4 0.10 SIDE CHAIN REMARK 500 5 DT B 4 0.09 SIDE CHAIN REMARK 500 6 DT A 4 0.09 SIDE CHAIN REMARK 500 6 DA A 6 0.05 SIDE CHAIN REMARK 500 6 DT B 1 0.06 SIDE CHAIN REMARK 500 6 DT B 4 0.08 SIDE CHAIN REMARK 500 7 DT A 1 0.06 SIDE CHAIN REMARK 500 7 DT A 4 0.10 SIDE CHAIN REMARK 500 7 DT B 1 0.06 SIDE CHAIN REMARK 500 7 DT B 4 0.09 SIDE CHAIN REMARK 500 7 DA B 6 0.06 SIDE CHAIN REMARK 500 8 DT A 4 0.10 SIDE CHAIN REMARK 500 8 DT B 1 0.07 SIDE CHAIN REMARK 500 8 DT B 4 0.10 SIDE CHAIN REMARK 500 9 DT A 4 0.09 SIDE CHAIN REMARK 500 9 DT B 4 0.10 SIDE CHAIN REMARK 500 9 DA B 6 0.06 SIDE CHAIN REMARK 500 10 DT A 1 0.06 SIDE CHAIN REMARK 500 10 DT A 4 0.08 SIDE CHAIN REMARK 500 10 DA A 6 0.06 SIDE CHAIN REMARK 500 10 DT B 4 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D54 RELATED DB: PDB REMARK 900 ANTHRACYCLINE BINDING TO DNA. HIGH-RESOLUTION STRUCTURE OF REMARK 900 D(TGTACA) COMPLEXED WITH 4'-EPIADRIAMYCIN REMARK 900 RELATED ID: 1D58 RELATED DB: PDB REMARK 900 THE MOLECULAR STRUCTURE OF A 4'-EPIADRIAMYCIN COMPLEX WITH REMARK 900 D(TGATCA) AT 1.7A RESOLUTION: COMPARISON WITH THE STRUCTURE REMARK 900 OF 4'-EPIADRIAMYCIN D(TGTACA) AND D(CGATCG) COMPLEXES DBREF 1SY8 A 1 6 PDB 1SY8 1SY8 1 6 DBREF 1SY8 B 1 6 PDB 1SY8 1SY8 1 6 SEQRES 1 A 6 DT DG DA DT DC DA SEQRES 1 B 6 DT DG DA DT DC DA 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 255 0 0 0 0 0 0 6 0 0 0 2 END