HEADER DNA 04-JAN-04 1S0T TITLE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING AN ALPHA-ANOMERIC TITLE 2 ADENOSINE: INSIGHTS INTO SUBSTRATE RECOGNITION BY ENDONUCLEASE IV COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*TP*CP*CP*(A3A)P*CP*GP*AP*CP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*GP*TP*CP*GP*TP*GP*GP*AP*C)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE CORE OF THE SEQUENCE CORRESPONDS TO THE SOURCE 4 RECOGNITION SITE OF E. COLI ENDONUCLEASE IV; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES KEYWDS DNA DOUBLE HELIX WITH ENLARGED MINER GROOVE AND HELICAL KINK, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR J.M.ARAMINI,S.H.CLEAVER,R.T.PON,R.P.CUNNINGHAM,M.W.GERMANN REVDAT 4 22-MAY-24 1S0T 1 REMARK REVDAT 3 02-MAR-22 1S0T 1 REMARK LINK REVDAT 2 24-FEB-09 1S0T 1 VERSN REVDAT 1 20-APR-04 1S0T 0 JRNL AUTH J.M.ARAMINI,S.H.CLEAVER,R.T.PON,R.P.CUNNINGHAM,M.W.GERMANN JRNL TITL SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING AN JRNL TITL 2 ALPHA-ANOMERIC ADENOSINE: INSIGHTS INTO SUBSTRATE JRNL TITL 3 RECOGNITION BY ENDONUCLEASE IV. JRNL REF J.MOL.BIOL. V. 338 77 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15050824 JRNL DOI 10.1016/J.JMB.2004.02.035 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, AMBER 6.0 REMARK 3 AUTHORS : GUNTERT ET AL (DYANA), CASE ET AL. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE IS BASED ON A TOTAL OF 502 RESTRAINTS: 284 DISTANCE REMARK 3 RESTRAINTS, 80 ENDOCYCLIC TORSION ANGLE RESTRAINTS, 50 WATSON- REMARK 3 CRICK DISTANCE AND ANGLE RESTRAINTS, REMARK 3 AND 88 BACKBONE TORSION ANGLE RESTRAINTS. THE ALPHAA DUPLEX REMARK 3 STRUCTURE WAS ELUCIDATED BY A COMBINATION OF DYANA AND RMD/REM IN REMARK 3 AMBER. ALL CALCULATIONS WERE PERFORMED IN VACUO. THE FINAL REMARK 3 STRUCTURE DEPOSITED HERE WAS OBTAINED BY COORDINATE AVERAGING THE REMARK 3 FINAL ENSEMBLE OF 10 RMD/REM STRUCTURES FOLLOWED BY RESTRAINED REMARK 3 ENERGY MINIMIZATION. REMARK 4 REMARK 4 1S0T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021223. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 283 REMARK 210 PH : 6.6; 6.6 REMARK 210 IONIC STRENGTH : 50 MM NACL; 50 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM ALPHAA DUPLEX, 10 MM REMARK 210 PHOSPHATE BUFFER, 50 MM NACL, REMARK 210 0.1 MM EDTA, PH 6.6; 1.0 MM REMARK 210 ALPHAA DUPLEX, 10 MM PHOSPHATE REMARK 210 BUFFER, 50 MM NACL, 0.1 MM EDTA, REMARK 210 PH 6.6 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 2D TOCSY; 2D REMARK 210 31P,1H CORRELATION; HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MARDIGRAS 3.2, CORMA 5.2, CURVES REMARK 210 5.1, MOLMOL 2.0 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: REMARK 210 FOR NON-EXCHANGEABLE PROTONS, NOESY EXPERIMENTS IN D2O WERE REMARK 210 PERFORMED WITH 10S RELAXATION DELAYS AND MIXING TIMES OF 75MS, REMARK 210 150MS AND 250 MS. REMARK 210 FOR EXCHANGEABLE PROTONS, A WATERGATE NOESY WAS PERFORMED WITH A REMARK 210 RELAXATION DELAY OF 4S AND 150MS MIXING TIME. 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 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 A3A A 5 O3' - P - O5' ANGL. DEV. = -20.4 DEGREES REMARK 500 DA A 8 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC A 9 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 11 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 DC B 14 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT B 16 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG B 17 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 18 O4' - C4' - C3' ANGL. DEV. = 4.9 DEGREES REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.2 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 DG A 7 0.08 SIDE CHAIN REMARK 500 DA A 8 0.08 SIDE CHAIN REMARK 500 DT B 13 0.10 SIDE CHAIN REMARK 500 DA B 19 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1S74 RELATED DB: PDB REMARK 900 RELATED ID: 1S75 RELATED DB: PDB DBREF 1S0T A 1 10 PDB 1S0T 1S0T 1 10 DBREF 1S0T B 11 20 PDB 1S0T 1S0T 11 20 SEQRES 1 A 10 DG DT DC DC A3A DC DG DA DC DG SEQRES 1 B 10 DC DG DT DC DG DT DG DG DA DC MODRES 1S0T A3A A 5 DA HET A3A A 5 32 HETNAM A3A 2'DEOXY-ALPHA-ANOMERIC-ADENOSINE-5'-PHOSPHATE FORMUL 1 A3A C10 H14 N5 O6 P LINK O3' DC A 4 P A3A A 5 1555 1555 1.62 LINK O3' A3A A 5 P DC A 6 1555 1555 1.62 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 HETATM 124 C8A A3A A 5 5.903 1.463 1.322 1.00 10.00 C HETATM 125 N9A A3A A 5 5.175 1.605 0.177 1.00 10.00 N HETATM 126 C4A A3A A 5 3.859 1.627 0.567 1.00 10.00 C HETATM 127 C5A A3A A 5 3.875 1.565 1.933 1.00 10.00 C HETATM 128 N7A A3A A 5 5.187 1.468 2.416 1.00 10.00 N HETATM 129 N3A A3A A 5 2.766 1.690 -0.240 1.00 10.00 N HETATM 130 C2A A3A A 5 1.634 1.668 0.464 1.00 10.00 C HETATM 131 N1A A3A A 5 1.483 1.626 1.788 1.00 10.00 N HETATM 132 C6A A3A A 5 2.598 1.586 2.535 1.00 10.00 C HETATM 133 N6A A3A A 5 2.427 1.540 3.844 1.00 10.00 N HETATM 134 P A3A A 5 8.057 3.757 -5.175 1.00 10.00 P HETATM 135 OP1 A3A A 5 9.333 4.493 -5.031 1.00 10.00 O HETATM 136 OP2 A3A A 5 7.855 2.863 -6.335 1.00 10.00 O HETATM 137 O6' A3A A 5 7.821 2.885 -3.832 1.00 10.00 O HETATM 138 C5' A3A A 5 8.362 3.272 -2.582 1.00 10.00 C HETATM 139 C4' A3A A 5 7.924 2.396 -1.411 1.00 10.00 C HETATM 140 O5' A3A A 5 6.695 2.912 -0.970 1.00 10.00 O HETATM 141 C3' A3A A 5 7.754 0.916 -1.767 1.00 10.00 C HETATM 142 O3' A3A A 5 8.171 0.100 -0.697 1.00 10.00 O HETATM 143 C2' A3A A 5 6.253 0.801 -1.985 1.00 10.00 C HETATM 144 C1' A3A A 5 5.689 1.952 -1.155 1.00 10.00 C HETATM 145 H8A A3A A 5 6.982 1.389 1.263 1.00 10.00 H HETATM 146 H2A A3A A 5 0.727 1.648 -0.122 1.00 10.00 H HETATM 147 HN61 A3A A 5 1.477 1.491 4.212 1.00 10.00 H HETATM 148 HN62 A3A A 5 3.236 1.452 4.432 1.00 10.00 H HETATM 149 H5' A3A A 5 8.127 4.316 -2.371 1.00 10.00 H HETATM 150 H5'' A3A A 5 9.421 3.158 -2.644 1.00 10.00 H HETATM 151 H4' A3A A 5 8.630 2.480 -0.580 1.00 10.00 H HETATM 152 H3' A3A A 5 8.313 0.662 -2.671 1.00 10.00 H HETATM 153 H2' A3A A 5 6.020 0.954 -3.038 1.00 10.00 H HETATM 154 H2'' A3A A 5 5.873 -0.161 -1.652 1.00 10.00 H HETATM 155 H1' A3A A 5 4.910 2.435 -1.700 1.00 10.00 H TER 315 DG A 10 TER 633 DC B 20 CONECT 102 134 CONECT 124 125 128 145 CONECT 125 124 126 144 CONECT 126 125 127 129 CONECT 127 126 128 132 CONECT 128 124 127 CONECT 129 126 130 CONECT 130 129 131 146 CONECT 131 130 132 CONECT 132 127 131 133 CONECT 133 132 147 148 CONECT 134 102 135 136 137 CONECT 135 134 CONECT 136 134 CONECT 137 134 138 CONECT 138 137 139 149 150 CONECT 139 138 140 141 151 CONECT 140 139 144 CONECT 141 139 142 143 152 CONECT 142 141 156 CONECT 143 141 144 153 154 CONECT 144 125 140 143 155 CONECT 145 124 CONECT 146 130 CONECT 147 133 CONECT 148 133 CONECT 149 138 CONECT 150 138 CONECT 151 139 CONECT 152 141 CONECT 153 143 CONECT 154 143 CONECT 155 144 CONECT 156 142 MASTER 140 0 1 0 0 0 0 6 404 2 34 2 END