PDB Short entry for 1FC8 HEADER RNA/DNA CHIMERA 18-JUL-00 1FC8 TITLE NMR SOLUTION STRUCTURE OF A CHIMERIC OLIGONUCLEOTIDE HAIRPIN R(GGAC) TITLE 2 D(TTCG)2'F-A(GTCC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*AP*CP)D(*TP*TP*CP*GP*(GFL)P*(TAF)P*(CFL) COMPND 3 P*(CFL))-3'; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: RNA/2'F-ANA HAIRPIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SOLID PHASE SYNTHESIS; PHOSPHORAMIDITE CHEMISTRY KEYWDS 2'F-ARABINONUCLEIC ACID, RNA, DNA, HYBRID DUPLEX, HAIRPIN, RNA-DNA KEYWDS 2 CHIMERA COMPLEX EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR J.-F.TREMPE,K.GEHRING REVDAT 4 23-FEB-22 1FC8 1 REMARK LINK REVDAT 3 24-FEB-09 1FC8 1 VERSN REVDAT 2 01-APR-03 1FC8 1 JRNL REVDAT 1 30-MAY-01 1FC8 0 JRNL AUTH J.F.TREMPE,C.J.WILDS,A.Y.DENISOV,R.T.PON,M.J.DAMHA,K.GEHRING JRNL TITL NMR SOLUTION STRUCTURE OF AN OLIGONUCLEOTIDE HAIRPIN WITH A JRNL TITL 2 2'F-ANA/RNA STEM: IMPLICATIONS FOR RNASE H SPECIFICITY JRNL TITL 3 TOWARD DNA/RNA HYBRID DUPLEXES. JRNL REF J.AM.CHEM.SOC. V. 123 4896 2001 JRNL REFN ISSN 0002-7863 JRNL PMID 11457316 JRNL DOI 10.1021/JA003859P REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843, X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 SA AT 15000K FOR 15 PSEC FROM RANDOM COORDINATES. REMARK 3 REFINEMENT FROM LOWER ENERGY STRUCTURE AT 3000K FRO 9 PSEC. REMARK 3 5 STRUCTURES GENERATED. REMARK 3 REMARK 3 TOTAL OF 305 RESTRAINTS: REMARK 3 98 INTRARESIDUE NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 94 SEQUENTIAL NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 3 LONG RANGE NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 15 DISTANCE RESTRAINTS FROM HYDROGEN BONDS, REMARK 3 91 DIHEDRAL ANGLE RESTRAINTS, REMARK 3 4 PLANARITY CONSTRAINTS FOR BASE PAIRS REMARK 4 REMARK 4 1FC8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-00. REMARK 100 THE DEPOSITION ID IS D_1000011473. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0.066 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM OLIGONUCLEOTIDE HAIRPIN; REMARK 210 90% H2O, 10% D2O; 0.5 MM REMARK 210 OLIGONUCLEOTIDE HAIRPIN; D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 2D 1H-13C REMARK 210 HMQC; 2D 1H-31P HETCOR; 2D 1H- REMARK 210 19F HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 400 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 5 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : RMSD FROM AVERAGE LOWER THAN 0.7 REMARK 210 ANGSTROM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 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 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 4 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 4 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 4 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 4 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 4 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 5 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 5 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 5 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 C A 4 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 5 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 5 DT A 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 5 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 5 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1FC8 A 1 12 PDB 1FC8 1FC8 1 12 SEQRES 1 A 12 G G A C DT DT DC DG GFL TAF CFL CFL MODRES 1FC8 GFL A 9 DG MODRES 1FC8 TAF A 10 DT MODRES 1FC8 CFL A 11 DC MODRES 1FC8 CFL A 12 DC HET GFL A 9 33 HET TAF A 10 32 HET CFL A 11 30 HET CFL A 12 31 HETNAM GFL 2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D- HETNAM 2 GFL ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE HETNAM TAF 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE-5'- HETNAM 2 TAF PHOSPHATE HETNAM CFL 4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D- HETNAM 2 CFL ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE HETSYN GFL 2'-FLUORO-2-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN CFL 2'-FLUORO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 GFL C10 H13 F N5 O7 P FORMUL 1 TAF C10 H14 F N2 O8 P FORMUL 1 CFL 2(C9 H13 F N3 O7 P) LINK O3' DG A 8 P GFL A 9 1555 1555 1.62 LINK O3' GFL A 9 P TAF A 10 1555 1555 1.62 LINK O3' TAF A 10 P CFL A 11 1555 1555 1.62 LINK O3' CFL A 11 P CFL A 12 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