HEADER DNA 12-JUL-04 1U01 TITLE HIGH RESOLUTION NMR STRUCTURE OF 5-D(GCGT*GCG)-3/5-D(CGCACGC)-3 TITLE 2 (T*REPRESENTS A CYCLOHEXENYL NUCLEOTIDE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*(XTR)P*GP*CP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CYCLOHEXENYL NUCLEOTIDE, PHOSPHORAMIDITE CHEMISTRY; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES KEYWDS NUCLEIC ACID, RNA MIMIC, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR K.NAUWELAERTS,E.LESCRINIER,G.SCLEP,P.HERDEWIJN REVDAT 4 02-MAR-22 1U01 1 REMARK LINK REVDAT 3 07-APR-10 1U01 1 HET HETATM HETNAM REVDAT 2 24-FEB-09 1U01 1 VERSN REVDAT 1 31-MAY-05 1U01 0 JRNL AUTH K.NAUWELAERTS,E.LESCRINIER,G.SCLEP,P.HERDEWIJN JRNL TITL CYCLOHEXENYL NUCLEIC ACIDS: CONFORMATIONALLY FLEXIBLE JRNL TITL 2 OLIGONUCLEOTIDES. JRNL REF NUCLEIC ACIDS RES. V. 33 2452 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 15863723 JRNL DOI 10.1093/NAR/GKI538 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 97.0, X-PLOR 3.8.5 REMARK 3 AUTHORS : A (FELIX), A (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1U01 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000023075. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 283 REMARK 210 PH : 7.2; 7.2 REMARK 210 IONIC STRENGTH : 0; 0 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 5-D(GCGT*GCG)-3/5-D(CGCACGC)-3 REMARK 210 2.8MM; 100% D2; 5-D(GCGT*GCG)-3/ REMARK 210 5-D(CGCACGC)-3 2.8MM; 10% D20,90% REMARK 210 H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; P REMARK 210 -COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 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 FOLLOWED BY REMARK 210 A MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 25 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM, REMARK 210 STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A 1 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 7 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC B 8 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG B 9 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 9 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG B 9 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA B 11 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA B 11 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 13 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 13 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC B 14 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1U01 A 1 7 PDB 1U01 1U01 1 7 DBREF 1U01 B 8 14 PDB 1U01 1U01 8 14 SEQRES 1 A 7 DG DC DG XTR DG DC DG SEQRES 1 B 7 DC DG DC DA DC DG DC MODRES 1U01 XTR A 4 DT HET XTR A 4 35 HETNAM XTR [(1R,4S,6S)-6-HYDROXY-4-(5-METHYL-2,4-DIOXO-3,4- HETNAM 2 XTR DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOHEX-2-EN-1-YL]METHYL HETNAM 3 XTR DIHYDROGEN PHOSPHATE FORMUL 1 XTR C12 H17 N2 O7 P LINK O3' DG A 3 P XTR A 4 1555 1555 1.62 LINK O3' XTR A 4 P DG A 5 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