HEADER DNA 19-SEP-00 1FV8 TITLE NMR STUDY OF AN HETEROCHIRAL HAIRPIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*AP*TP*CP*AP*(0DT)P*CP*GP*AP*TP*A)-3'; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: AT(L)C HAIRPIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE COMES FROM A PBR322 TOPOISOMERASE II SOURCE 4 CLEAVAGE SITE KEYWDS HAIRPIN, HETEROCHIRAL LOOP, FLEXIBILTY, ANTISENSE DNA, DNA EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR C.EL AMRI,O.MAUFFRET,F.SANTAMARIA,B.RAYNER,S.FERMANDJIAN REVDAT 5 23-FEB-22 1FV8 1 REMARK LINK REVDAT 4 07-APR-10 1FV8 1 HET HETATM REVDAT 3 24-FEB-09 1FV8 1 VERSN REVDAT 2 25-MAY-04 1FV8 1 JRNL REMARK MODRES HETNAM REVDAT 1 11-OCT-00 1FV8 0 JRNL AUTH C.EL AMRI,O.MAUFFRET,F.SANTAMARIAR,G.TEVANIAN,B.RAYNER, JRNL AUTH 2 S.FERMANDJIAN JRNL TITL NMR STUDY OF A HETEROCHIRAL DNA HAIRPIN:IMPACT OF JRNL TITL 2 L-ENANTIOMERY IN THE LOOP. JRNL REF J.BIOMOL.STRUCT.DYN. V. 19 459 2001 JRNL REFN ISSN 0739-1102 JRNL PMID 11790144 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX, CNS XPLOR 3.8 REMARK 3 AUTHORS : MSI (SAN DIEGO) (FELIX), BRUNGER ET AL., 1998 REMARK 3 (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 252 RESTRAINTS, DISTANCE CONSTRAINTS, 56 DIHEDRAL ANGLE REMARK 3 RESTRAINTS,9 DISTANCE RESTRAINTS FROM HYDROGEN BONDS, AND 4 REMARK 3 PLANARITY CONSTRAINTS. THE CALCULATIONS WERE PERFORMED ON THE 11 REMARK 3 CENTRAL RESIDUES. REMARK 4 REMARK 4 1FV8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000011930. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 0.025 REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : AT(L)C; AT(L)C REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; P-COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS XPLOR 3.8, XWINNMR REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 11 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES, AND PFG TO MEASURE THE DIFFUSION CONSTANT 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 O2 DC A 4 H21 DG A 8 1.57 REMARK 500 O4 DT A 1 H61 DA A 11 1.57 REMARK 500 N1 DA A 2 H3 DT A 10 1.58 REMARK 500 H3 DT A 3 N1 DA A 9 1.58 REMARK 500 REMARK 500 REMARK: NULL 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 11 DT A 1 O5' DT A 1 C5' -0.780 REMARK 500 11 DC A 4 P DC A 4 O5' -0.091 REMARK 500 11 DC A 7 C4 DC A 7 C5 -0.062 REMARK 500 11 DG A 8 P DG A 8 OP1 -0.131 REMARK 500 11 DG A 8 P DG A 8 OP2 -0.213 REMARK 500 11 DG A 8 P DG A 8 O5' -0.220 REMARK 500 11 DG A 8 O5' DG A 8 C5' -0.226 REMARK 500 11 DA A 11 O5' DA A 11 C5' -0.177 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 11 DT A 1 O5' - C5' - C4' ANGL. DEV. = 27.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1FV8 A 1 11 PDB 1FV8 1FV8 1 11 SEQRES 1 A 11 DT DA DT DC DA 0DT DC DG DA DT DA HET 0DT A 6 32 HETNAM 0DT 2'-DEOXY-L-RIBO-FURANOSYL THYMIDINE-5'-MONOPHOSPHATE FORMUL 1 0DT C10 H15 N2 O8 P LINK O3' DA A 5 P 0DT A 6 1555 1555 1.61 LINK O3' 0DT A 6 P DC A 7 1555 1555 1.61 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