HEADER DNA, RNA 07-AUG-02 1ME0 TITLE CHIMERIC HAIRPIN WITH 2',5'-LINKED RNA LOOP AND DNA STEM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA (5'-D(*GP*GP*AP*C)-R(P*(U25)P*(U25)P*(C25)P*(5GP))- COMPND 3 D(P*GP*TP*CP*C)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SOLID PHASE SYNTHESIS, PHOSPHORAMIDITE CHEMISTRY KEYWDS HAIRPIN, (2', 5')-RNA, DNA, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.Y.DENISOV,R.N.HANNOUSH,K.GEHRING,M.J.DAMHA REVDAT 5 01-MAY-24 1ME0 1 LINK REVDAT 4 24-AUG-11 1ME0 1 HETATM REMARK VERSN REVDAT 3 24-FEB-09 1ME0 1 VERSN REVDAT 2 23-SEP-03 1ME0 1 JRNL REVDAT 1 19-AUG-03 1ME0 0 JRNL AUTH A.Y.DENISOV,R.N.HANNOUSH,K.GEHRING,M.J.DAMHA JRNL TITL A NOVEL RNA MOTIF BASED ON THE STRUCTURE OF UNUSUALLY STABLE JRNL TITL 2 2',5'-LINKED R(UUCG) LOOPS JRNL REF J.AM.CHEM.SOC. V. 125 11525 2003 JRNL REFN ISSN 0002-7863 JRNL PMID 13129354 JRNL DOI 10.1021/JA036207K REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE REFINED BY NMR REMARK 3 -RESTRAINED MOLECULAR DYNAMICS (12 PS, 300-1000 K) WITH FINAL REMARK 3 ENERGY MINIMIZATION REMARK 4 REMARK 4 1ME0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016842. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.5 MM HAIRPIN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: STRUCTURE WAS DETERMINED USING STANDARD 2D HOMO- AND REMARK 210 HETERONUCLEAR TECHNIQUES: 2D-NOESY, DQF-COSY, TOCSY, H,C-HMQC, H, REMARK 210 P-HETCOSY 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 400 REMARK 400 COMPOUND REMARK 400 NUCLEOTIDES 5(U25), 6(U25), 7(C25), 8(5GP) REMARK 400 HAS A NON-STANDARD 2'-5' LINKAGE. 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 H22 DG A 1 O2 DC A 12 1.59 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA A 3 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DA A 3 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 3 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DA A 3 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 DC A 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 4 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 4 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 4 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 4 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DA A 3 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 DC A 4 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 4 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 4 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 131 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ME1 RELATED DB: PDB REMARK 900 CHIMERIC HAIRPIN WITH 2',5'-LINKED RNA LOOP AND RNA STEM DBREF 1ME0 A 1 12 PDB 1ME0 1ME0 1 12 SEQRES 1 A 12 DG DG DA DC U5P U5P C5P 5GP DG DT DC DC HET U5P A 5 30 HET U5P A 6 30 HET C5P A 7 31 HET 5GP A 8 34 HETNAM U5P URIDINE-5'-MONOPHOSPHATE HETNAM C5P CYTIDINE-5'-MONOPHOSPHATE HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE FORMUL 1 U5P 2(C9 H13 N2 O9 P) FORMUL 1 C5P C9 H14 N3 O8 P FORMUL 1 5GP C10 H14 N5 O8 P LINK O3' DC A 4 P U5P A 5 1555 1555 1.62 LINK O2' U5P A 5 P U5P A 6 1555 1555 1.61 LINK O2' U5P A 6 P C5P A 7 1555 1555 1.61 LINK O2' C5P A 7 P 5GP A 8 1555 1555 1.62 LINK O2' 5GP A 8 P DG A 9 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