HEADER DNA 23-MAR-04 1SS7 TITLE COMPENSATING BENDS IN A 16 BASE-PAIR DNA OLIGOMER CONTAINING A T3A3 TITLE 2 SEGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*AP*GP*GP*TP*TP*TP*AP*AP*AP*CP*CP*TP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS B-DNA; DOUBLE HELIX; RESIDUAL DIPOLAR COUPLINGS, DNA EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR K.MCATEER,A.ACEVES-GAONA,R.MICHALCZYK,G.W.BUCHKO,N.G.ISERN,L.A.SILKS, AUTHOR 2 J.H.MILLER,M.A.KENNEDY REVDAT 4 22-MAY-24 1SS7 1 REMARK REVDAT 3 02-MAR-22 1SS7 1 REMARK REVDAT 2 24-FEB-09 1SS7 1 VERSN REVDAT 1 07-DEC-04 1SS7 0 JRNL AUTH K.MCATEER,A.ACEVES-GAONA,R.MICHALCZYK,G.W.BUCHKO,N.G.ISERN, JRNL AUTH 2 L.A.SILKS,J.H.MILLER,M.A.KENNEDY JRNL TITL COMPENSATING BENDS IN A 16-BASE-PAIR DNA OLIGOMER CONTAINING JRNL TITL 2 A T(3)A(3) SEGMENT: A NMR STUDY OF GLOBAL DNA CURVATURE JRNL REF BIOPOLYMERS V. 75 497 2004 JRNL REFN ISSN 0006-3525 JRNL PMID 15526287 JRNL DOI 10.1002/BIP.20168 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 98, X-PLOR 3.85 REMARK 3 AUTHORS : MSI (FELIX), BRUNGER, TJANDRA (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURES ARE BASED ON A TOTAL OF 316 NOE, 90 TORSION ANGLE, AND 6 REMARK 3 DISTANCE RESTRAINTS REPRESENTED EACH W-C BASE-PAIR. FOR THE RDC REMARK 3 STRUCTURES AN ADDITIONAL 88 ONE-BOND C-H AND 14 ONE-BOND N-H REMARK 3 RESIDUAL REMARK 3 DIPOLAR COUPLING RESTRAINTS WERE USED REMARK 4 REMARK 4 1SS7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000021958. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 400 MM NACL, 40MM PHOSPHATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM DNA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 2D 13C-1H CT REMARK 210 -TROSY-HSQC; 2D 15N-1H TROSY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : BIRDER 96 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 45 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: REMARK 210 HETERONUCLEAR DIPOLAR COUPLINGS WERE MEASURED IN SAMPLES ALIGNED REMARK 210 WITH REMARK 210 FILAMENTOUS PF1 BACTERIOPHAGE 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA A 9 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA A 10 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 11 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA A 11 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 13 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 14 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 15 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 16 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 16 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DC B 17 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG B 18 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG B 18 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG B 18 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DA B 19 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA B 19 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG B 20 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG B 20 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG B 20 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DG B 21 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 21 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG B 21 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DT B 22 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT B 23 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT B 24 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA B 25 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA B 25 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA B 26 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA B 26 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA B 27 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA B 27 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC B 28 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 830 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SSV RELATED DB: PDB REMARK 900 THE SAME SEQUENCE, DIFFERENT NMR SOLUTION DBREF 1SS7 A 1 16 PDB 1SS7 1SS7 1 16 DBREF 1SS7 B 17 32 PDB 1SS7 1SS7 17 32 SEQRES 1 A 16 DC DG DA DG DG DT DT DT DA DA DA DC DC SEQRES 2 A 16 DT DC DG SEQRES 1 B 16 DC DG DA DG DG DT DT DT DA DA DA DC DC SEQRES 2 B 16 DT DC DG 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 MODEL 1