HEADER DNA 02-NOV-99 1DB6 TITLE SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' TITLE 2 COMPLEXED WITH ARGININAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE IS DERIVED FROM IN-VITRO SELECTION SOURCE 4 EXPERIMENTS. SEQUENCES WERE CHEMICALLY SYTHETHESIZED. KEYWDS APTAMER, ARGININE, ARGININAMIDE, SINGLE-STRAND, HAIRPIN, SELEX, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.A.ROBERTSON,K.HARADA,A.D.FRANKEL,D.E.WEMMER REVDAT 4 16-FEB-22 1DB6 1 REMARK REVDAT 3 24-FEB-09 1DB6 1 VERSN REVDAT 2 01-MAY-00 1DB6 1 REMARK ATOM REVDAT 1 03-FEB-00 1DB6 0 JRNL AUTH S.A.ROBERTSON,K.HARADA,A.D.FRANKEL,D.E.WEMMER JRNL TITL STRUCTURE DETERMINATION AND BINDING KINETICS OF A DNA JRNL TITL 2 APTAMER-ARGININAMIDE COMPLEX. JRNL REF BIOCHEMISTRY V. 39 946 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10653638 JRNL DOI 10.1021/BI9915061 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.HARADA,A.D.FRANKEL REMARK 1 TITL IDENTIFICATION OF TWO NOVEL ARGININE BINDING DNAS REMARK 1 REF EMBO J. V. 14 5798 1995 REMARK 1 REFN ISSN 0261-4189 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 950, DISCOVER 2.97 REMARK 3 AUTHORS : MOLECULAR SIMULATIONS, INC (FELIX), MOLECULAR REMARK 3 SIMULATIONS, INC (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DB6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-99. REMARK 100 THE DEPOSITION ID IS D_1000009942. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 278 REMARK 210 PH : 6.2; 6.2 REMARK 210 IONIC STRENGTH : 0-25 MM NACL; 0-25 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.44 MM DNA, 10 MM SODIUM REMARK 210 PHOSPHATE BUFFER, PH 6.2, 0.05 REMARK 210 MM EDTA, 0-25 MM NACL, 8-10 REMARK 210 EQUIVALENTS ARGININAMIDE; 1.44 REMARK 210 MM DNA, 10 MM SODIUM PHOSPHATE REMARK 210 BUFFER, PH 6.2, 0.05 MM EDTA, 0- REMARK 210 25 MM NACL, 8-10 EQUIVALENTS REMARK 210 ARGININAMIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : OMEGA; AMX REMARK 210 SPECTROMETER MANUFACTURER : GE; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MARDIGRAS 3.2 REMARK 210 METHOD USED : DISTANCE RESTRAINTS WERE REMARK 210 OBTAINED FROM RELAXATION RATE REMARK 210 MATRIX CALCULATIONS. STRUCTURES REMARK 210 WERE CALCULATED USING SIMULATED REMARK 210 ANNEALING AND MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON- BOND ENERGY, REMARK 210 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 : 6 REMARK 210 REMARK 210 REMARK: DATA WERE ALSO COLLECTED FOR SEQUENCES CONTAINING 5-METHYL REMARK 210 CYTOSINE SUBSTITUTED INDEPENDENTLY AT POSITIONS 15 AND 16, AND REMARK 210 FOR THE SEQUENCE WITH INOSINE SUBSTITUTED AT POSTION 14. 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 H3 DT A 10 O6 DG A 14 1.57 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 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 16 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 17 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 20 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DC A 21 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DC A 13 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC A 16 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG A 18 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DC A 21 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG A 22 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DA A 7 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DC A 8 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DT A 12 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 3 DT A 12 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 DC A 13 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DC A 16 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DG A 18 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DC A 21 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DG A 22 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 4 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DA A 6 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 152 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DC A 1 0.07 SIDE CHAIN REMARK 500 1 DC A 15 0.07 SIDE CHAIN REMARK 500 1 DC A 16 0.11 SIDE CHAIN REMARK 500 2 DC A 1 0.07 SIDE CHAIN REMARK 500 2 DG A 14 0.07 SIDE CHAIN REMARK 500 2 DC A 15 0.08 SIDE CHAIN REMARK 500 2 DC A 16 0.06 SIDE CHAIN REMARK 500 3 DC A 1 0.07 SIDE CHAIN REMARK 500 3 DT A 10 0.07 SIDE CHAIN REMARK 500 3 DG A 14 0.08 SIDE CHAIN REMARK 500 3 DC A 15 0.09 SIDE CHAIN REMARK 500 3 DC A 16 0.07 SIDE CHAIN REMARK 500 4 DC A 1 0.07 SIDE CHAIN REMARK 500 4 DG A 14 0.08 SIDE CHAIN REMARK 500 4 DC A 15 0.06 SIDE CHAIN REMARK 500 4 DC A 16 0.06 SIDE CHAIN REMARK 500 5 DC A 8 0.06 SIDE CHAIN REMARK 500 5 DT A 12 0.07 SIDE CHAIN REMARK 500 5 DG A 14 0.08 SIDE CHAIN REMARK 500 5 DC A 15 0.08 SIDE CHAIN REMARK 500 5 DC A 16 0.08 SIDE CHAIN REMARK 500 6 DC A 1 0.06 SIDE CHAIN REMARK 500 6 DG A 14 0.08 SIDE CHAIN REMARK 500 6 DC A 15 0.06 SIDE CHAIN REMARK 500 7 DC A 1 0.07 SIDE CHAIN REMARK 500 7 DG A 14 0.07 SIDE CHAIN REMARK 500 7 DC A 15 0.10 SIDE CHAIN REMARK 500 7 DC A 16 0.09 SIDE CHAIN REMARK 500 8 DC A 1 0.07 SIDE CHAIN REMARK 500 8 DG A 14 0.09 SIDE CHAIN REMARK 500 8 DC A 15 0.11 SIDE CHAIN REMARK 500 8 DC A 16 0.10 SIDE CHAIN REMARK 500 9 DC A 1 0.07 SIDE CHAIN REMARK 500 9 DG A 14 0.06 SIDE CHAIN REMARK 500 9 DC A 15 0.09 SIDE CHAIN REMARK 500 9 DC A 16 0.09 SIDE CHAIN REMARK 500 10 DC A 1 0.06 SIDE CHAIN REMARK 500 10 DG A 14 0.09 SIDE CHAIN REMARK 500 10 DC A 15 0.08 SIDE CHAIN REMARK 500 10 DC A 16 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AAR A 23 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ARG RELATED DB: PDB REMARK 900 2ARG CONTAINS A DIFFERENT DNA APTAMER COMPLEXED WITH ARGININAMIDE REMARK 900 RELATED ID: 1OLD RELATED DB: PDB REMARK 900 1OLD IS A SIMILAR DNA APTAMER DBREF 1DB6 A 1 22 PDB 1DB6 1DB6 1 22 SEQRES 1 A 22 DC DG DA DC DC DA DA DC DG DT DG DT DC SEQRES 2 A 22 DG DC DC DT DG DG DT DC DG HET AAR A 23 28 HETNAM AAR ARGININEAMIDE FORMUL 2 AAR C6 H16 N5 O 1+ SITE 1 AC1 8 DC A 8 DG A 9 DT A 12 DC A 13 SITE 2 AC1 8 DG A 14 DC A 16 DT A 17 DG A 18 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