HEADER DNA 28-AUG-01 1JUU TITLE NMR STRUCTURE OF A PARALLEL STRANDED DNA DUPLEX AT ATOMIC RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*CP*CP*AP*TP*AP*AP*TP*TP*TP*AP*CP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(P*CP*CP*TP*AP*TP*TP*AP*AP*AP*TP*CP*C)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE DNA DUPLEX WAS SYNTHESIZED WITH AN APPLIED SOURCE 4 BIOSYSTEMS MODEL 380B DNA SYNTHESIZER USING SOLID STATE SOURCE 5 PHOSPHORAMIDATE CHEMISTRY; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES KEYWDS PARALLEL STRANDED, DNA DUPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR V.R.PARVATHY,S.R.BHAUMIK,K.V.R.CHARY,G.GOVIL,K.LIU,F.B.HOWARD, AUTHOR 2 H.T.MILES REVDAT 4 23-FEB-22 1JUU 1 REMARK REVDAT 3 24-FEB-09 1JUU 1 VERSN REVDAT 2 01-APR-03 1JUU 1 JRNL REVDAT 1 03-APR-02 1JUU 0 JRNL AUTH V.R.PARVATHY,S.R.BHAUMIK,K.V.CHARY,G.GOVIL,K.LIU,F.B.HOWARD, JRNL AUTH 2 H.T.MILES JRNL TITL NMR STRUCTURE OF A PARALLEL-STRANDED DNA DUPLEX AT ATOMIC JRNL TITL 2 RESOLUTION. JRNL REF NUCLEIC ACIDS RES. V. 30 1500 2002 JRNL REFN ISSN 0305-1048 JRNL PMID 11917010 JRNL DOI 10.1093/NAR/30.7.1500 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 3.1, DISCOVER 3.1 REMARK 3 AUTHORS : MSI (DISCOVER), MSI (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE WAS CALCULATED USING 78 NOE REMARK 3 CONSTRAINTS, 28 HYDROGEN BOND CONSTRAINTS, AND 162 DIHEDRAL REMARK 3 ANGLE CONSTRAINTS. REMARK 4 REMARK 4 1JUU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1000014208. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 100MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 5 MM CONCENTRATION OF EACH REMARK 210 DODECAMER STRAND, 0.05 M REMARK 210 DEUTERATED SODIUM ACETATE BUFFER REMARK 210 AND 0.1 M NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : COSY, NOESY, TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN 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 : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 20 REMARK 210 REMARK 210 REMARK: STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR EXPERIMENTS. 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 DC A 1 C4 DC A 1 N4 0.099 REMARK 500 1 DC A 1 N1 DC A 1 C6 0.109 REMARK 500 1 DC A 1 C4 DC A 1 C5 -0.068 REMARK 500 1 DC A 2 C4 DC A 2 N4 0.099 REMARK 500 1 DC A 2 N1 DC A 2 C6 0.107 REMARK 500 1 DC A 2 C4 DC A 2 C5 -0.069 REMARK 500 1 DC A 11 C4 DC A 11 N4 0.103 REMARK 500 1 DC A 11 N1 DC A 11 C6 0.112 REMARK 500 1 DC A 11 C4 DC A 11 C5 -0.068 REMARK 500 1 DC A 12 C4 DC A 12 N4 0.098 REMARK 500 1 DC A 12 N1 DC A 12 C6 0.107 REMARK 500 1 DC A 12 C4 DC A 12 C5 -0.069 REMARK 500 1 DT B 5 C5 DT B 5 C7 0.040 REMARK 500 2 DC A 1 C4 DC A 1 N4 0.100 REMARK 500 2 DC A 1 N1 DC A 1 C6 0.110 REMARK 500 2 DC A 1 C4 DC A 1 C5 -0.069 REMARK 500 2 DC A 2 C4 DC A 2 N4 0.099 REMARK 500 2 DC A 2 N1 DC A 2 C6 0.109 REMARK 500 2 DC A 2 C4 DC A 2 C5 -0.068 REMARK 500 2 DT A 9 C5 DT A 9 C7 0.036 REMARK 500 2 DC A 11 C4 DC A 11 N4 0.103 REMARK 500 2 DC A 11 N1 DC A 11 C6 0.113 REMARK 500 2 DC A 11 C4 DC A 11 C5 -0.066 REMARK 500 2 DC A 12 C4 DC A 12 N4 0.098 REMARK 500 2 DC A 12 N1 DC A 12 C6 0.108 REMARK 500 2 DC A 12 C4 DC A 12 C5 -0.070 REMARK 500 2 DT B 5 C5 DT B 5 C7 0.040 REMARK 500 3 DC A 1 C4 DC A 1 N4 0.098 REMARK 500 3 DC A 1 N1 DC A 1 C6 0.109 REMARK 500 3 DC A 1 C4 DC A 1 C5 -0.067 REMARK 500 3 DC A 2 C4 DC A 2 N4 0.099 REMARK 500 3 DC A 2 N1 DC A 2 C6 0.108 REMARK 500 3 DC A 2 C4 DC A 2 C5 -0.068 REMARK 500 3 DT A 9 C5 DT A 9 C7 0.036 REMARK 500 3 DC A 11 C4 DC A 11 N4 0.103 REMARK 500 3 DC A 11 N1 DC A 11 C6 0.112 REMARK 500 3 DC A 11 C4 DC A 11 C5 -0.068 REMARK 500 3 DC A 12 C4 DC A 12 N4 0.098 REMARK 500 3 DC A 12 N1 DC A 12 C6 0.107 REMARK 500 3 DC A 12 C4 DC A 12 C5 -0.069 REMARK 500 3 DT B 5 C5 DT B 5 C7 0.040 REMARK 500 4 DC A 1 C4 DC A 1 N4 0.099 REMARK 500 4 DC A 1 N1 DC A 1 C6 0.109 REMARK 500 4 DC A 1 C4 DC A 1 C5 -0.069 REMARK 500 4 DC A 2 C4 DC A 2 N4 0.100 REMARK 500 4 DC A 2 N1 DC A 2 C6 0.107 REMARK 500 4 DC A 2 C4 DC A 2 C5 -0.068 REMARK 500 4 DC A 11 C4 DC A 11 N4 0.098 REMARK 500 4 DC A 11 N1 DC A 11 C6 0.111 REMARK 500 4 DC A 11 C4 DC A 11 C5 -0.068 REMARK 500 REMARK 500 THIS ENTRY HAS 262 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC A 1 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC A 2 C6 - N1 - C2 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 4 N3 - C2 - O2 ANGL. DEV. = -6.8 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DA A 6 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 7 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT A 8 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT A 9 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 10 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 10 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC A 11 C6 - N1 - C2 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT B 3 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT B 3 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DA B 4 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA B 4 N1 - C6 - N6 ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DT B 5 O4' - C1' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 1 DT B 5 O4' - C1' - N1 ANGL. DEV. = 8.8 DEGREES REMARK 500 1 DT B 5 N3 - C2 - O2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 DT B 6 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DT B 6 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA B 7 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA B 7 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DA B 8 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA B 8 N1 - C6 - N6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA B 9 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT B 10 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT B 10 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC A 1 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DC A 2 C6 - N1 - C2 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DA A 3 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 825 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 3 0.23 SIDE CHAIN REMARK 500 1 DA A 5 0.06 SIDE CHAIN REMARK 500 1 DA A 6 0.07 SIDE CHAIN REMARK 500 1 DT A 7 0.10 SIDE CHAIN REMARK 500 1 DC B 2 0.08 SIDE CHAIN REMARK 500 1 DT B 3 0.08 SIDE CHAIN REMARK 500 1 DA B 4 0.13 SIDE CHAIN REMARK 500 1 DA B 7 0.07 SIDE CHAIN REMARK 500 2 DA A 3 0.22 SIDE CHAIN REMARK 500 2 DA A 5 0.06 SIDE CHAIN REMARK 500 2 DA A 6 0.07 SIDE CHAIN REMARK 500 2 DT A 7 0.10 SIDE CHAIN REMARK 500 2 DC B 1 0.06 SIDE CHAIN REMARK 500 2 DC B 2 0.08 SIDE CHAIN REMARK 500 2 DT B 3 0.08 SIDE CHAIN REMARK 500 2 DA B 4 0.13 SIDE CHAIN REMARK 500 2 DA B 7 0.07 SIDE CHAIN REMARK 500 3 DA A 3 0.23 SIDE CHAIN REMARK 500 3 DA A 5 0.06 SIDE CHAIN REMARK 500 3 DA A 6 0.08 SIDE CHAIN REMARK 500 3 DT A 7 0.10 SIDE CHAIN REMARK 500 3 DC B 2 0.08 SIDE CHAIN REMARK 500 3 DT B 3 0.09 SIDE CHAIN REMARK 500 3 DA B 4 0.13 SIDE CHAIN REMARK 500 3 DA B 7 0.07 SIDE CHAIN REMARK 500 4 DA A 3 0.22 SIDE CHAIN REMARK 500 4 DA A 5 0.06 SIDE CHAIN REMARK 500 4 DA A 6 0.08 SIDE CHAIN REMARK 500 4 DT A 7 0.11 SIDE CHAIN REMARK 500 4 DC B 2 0.09 SIDE CHAIN REMARK 500 4 DT B 3 0.09 SIDE CHAIN REMARK 500 4 DA B 4 0.12 SIDE CHAIN REMARK 500 4 DA B 7 0.07 SIDE CHAIN REMARK 500 5 DA A 3 0.23 SIDE CHAIN REMARK 500 5 DA A 5 0.06 SIDE CHAIN REMARK 500 5 DA A 6 0.08 SIDE CHAIN REMARK 500 5 DT A 7 0.10 SIDE CHAIN REMARK 500 5 DC B 2 0.07 SIDE CHAIN REMARK 500 5 DT B 3 0.08 SIDE CHAIN REMARK 500 5 DA B 4 0.14 SIDE CHAIN REMARK 500 5 DA B 7 0.07 SIDE CHAIN REMARK 500 6 DA A 3 0.22 SIDE CHAIN REMARK 500 6 DA A 5 0.06 SIDE CHAIN REMARK 500 6 DA A 6 0.08 SIDE CHAIN REMARK 500 6 DT A 7 0.10 SIDE CHAIN REMARK 500 6 DC B 1 0.06 SIDE CHAIN REMARK 500 6 DC B 2 0.08 SIDE CHAIN REMARK 500 6 DT B 3 0.08 SIDE CHAIN REMARK 500 6 DA B 4 0.12 SIDE CHAIN REMARK 500 6 DA B 7 0.08 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 171 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1JUU A 1 12 PDB 1JUU 1JUU 1 12 DBREF 1JUU B 1 12 PDB 1JUU 1JUU 1 12 SEQRES 1 A 12 DC DC DA DT DA DA DT DT DT DA DC DC SEQRES 1 B 12 DC DC DT DA DT DT DA DA DA DT DC DC CRYST1 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 MODEL 1