HEADER DNA 15-NOV-93 148D TITLE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE THROMBIN BINDING DNA TITLE 2 APTAMER D(GGTTGGTGTGGTTGG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)- COMPND 3 3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR P.SCHULTZE,R.F.MACAYA,J.FEIGON REVDAT 5 16-FEB-22 148D 1 REMARK REVDAT 4 07-APR-09 148D 1 REMARK REVDAT 3 24-FEB-09 148D 1 VERSN REVDAT 2 01-APR-03 148D 1 JRNL REVDAT 1 30-APR-94 148D 0 JRNL AUTH P.SCHULTZE,R.F.MACAYA,J.FEIGON JRNL TITL THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE THROMBIN-BINDING JRNL TITL 2 DNA APTAMER D(GGTTGGTGTGGTTGG). JRNL REF J.MOL.BIOL. V. 235 1532 1994 JRNL REFN ISSN 0022-2836 JRNL PMID 8107090 JRNL DOI 10.1006/JMBI.1994.1105 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.F.MACAYA,P.SCHULTZE,F.W.SMITH,J.A.ROE,J.FEIGON REMARK 1 TITL THROMBIN-BINDING DNA APTAMER FORMS A UNIMOLECULAR QUADRUPLEX REMARK 1 TITL 2 STRUCTURE IN SOLUTION REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 90 3745 1993 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STEP (1) SUBSTRUCTURE EMBEDDING ON 20 REMARK 3 STRUCTURES STEP (2) TEMPLATE FITTING AND REGULARIZATION BY REMARK 3 SIMULATED ANNEALING (20 STRUCTURES) STEP (3) SIMULATED ANNEALING REMARK 3 AND ENERGY MINIMIZATION (20 STRUCTURES) STEP (4) RELAXATION REMARK 3 MATRIX REFINEMENT ON THE BEST 6 OF 20 STRUCTURES THIS PROCEDURE REMARK 3 WAS CARRIED OUT SEPARATELY WITH DISTANCE RESTRAINTS ENFORCING REMARK 3 HYDROGEN BONDING BETWEEN T4 AND T13 INVOLVING O2 ATOMS IN ONE REMARK 3 CASE (MODELS 1-6) AND O4 ATOMS IN THE OTHER (MODELS 7-12). ALL REMARK 3 MODELS WERE SUPERIMPOSED ON MODEL 1, USING ALL NON-HYDROGEN REMARK 3 ATOMS OF G1, G2, G5, G6, G10, G11, G14, G15; I.E., ALL G REMARK 3 RESIDUES PARTICIPATING IN TETRAD FORMATION. REMARK 4 REMARK 4 148D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170109. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : 6.1 REMARK 210 IONIC STRENGTH : 0.11M REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING, MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: 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: 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 1 DT A 4 C5 DT A 4 C7 0.041 REMARK 500 1 DT A 7 C5 DT A 7 C7 0.047 REMARK 500 1 DG A 8 C5' DG A 8 C4' 0.050 REMARK 500 1 DT A 9 C5' DT A 9 C4' 0.119 REMARK 500 1 DT A 9 C5 DT A 9 C7 0.048 REMARK 500 1 DG A 10 C5' DG A 10 C4' 0.054 REMARK 500 1 DT A 12 C5 DT A 12 C7 0.038 REMARK 500 2 DT A 3 C5 DT A 3 C7 0.037 REMARK 500 2 DT A 4 C5 DT A 4 C7 0.042 REMARK 500 2 DG A 5 C8 DG A 5 N9 -0.043 REMARK 500 2 DT A 7 C5 DT A 7 C7 0.045 REMARK 500 2 DG A 8 C5' DG A 8 C4' 0.061 REMARK 500 2 DT A 9 C5' DT A 9 C4' 0.129 REMARK 500 2 DT A 12 C5 DT A 12 C7 0.038 REMARK 500 3 DT A 4 C5 DT A 4 C7 0.040 REMARK 500 3 DT A 7 C5 DT A 7 C7 0.043 REMARK 500 3 DG A 8 C5' DG A 8 C4' 0.051 REMARK 500 3 DT A 9 C5' DT A 9 C4' 0.121 REMARK 500 3 DT A 9 C5 DT A 9 C7 0.041 REMARK 500 3 DT A 12 C5 DT A 12 C7 0.039 REMARK 500 4 DT A 3 C5 DT A 3 C7 0.040 REMARK 500 4 DT A 4 C5' DT A 4 C4' 0.043 REMARK 500 4 DG A 5 C5' DG A 5 C4' 0.047 REMARK 500 4 DT A 7 C5 DT A 7 C7 0.041 REMARK 500 4 DG A 8 C5' DG A 8 C4' 0.061 REMARK 500 4 DT A 9 C5' DT A 9 C4' 0.134 REMARK 500 4 DT A 12 C5 DT A 12 C7 0.038 REMARK 500 5 DT A 3 C5 DT A 3 C7 0.036 REMARK 500 5 DT A 4 C5 DT A 4 C7 0.036 REMARK 500 5 DG A 6 C2' DG A 6 C1' -0.063 REMARK 500 5 DG A 6 C8 DG A 6 N9 -0.048 REMARK 500 5 DT A 7 C5 DT A 7 C7 0.039 REMARK 500 5 DG A 8 C5' DG A 8 C4' 0.058 REMARK 500 5 DT A 9 C5' DT A 9 C4' 0.085 REMARK 500 5 DT A 9 C5 DT A 9 C7 0.039 REMARK 500 5 DG A 10 C5' DG A 10 C4' 0.057 REMARK 500 5 DT A 12 C5 DT A 12 C7 0.039 REMARK 500 6 DT A 3 C5 DT A 3 C7 0.038 REMARK 500 6 DG A 6 C8 DG A 6 N9 -0.046 REMARK 500 6 DT A 7 C5 DT A 7 C7 0.042 REMARK 500 6 DG A 8 C5' DG A 8 C4' 0.042 REMARK 500 6 DT A 9 C5' DT A 9 C4' 0.077 REMARK 500 6 DT A 9 C5 DT A 9 C7 0.039 REMARK 500 6 DG A 10 C5' DG A 10 C4' 0.060 REMARK 500 6 DT A 12 C5 DT A 12 C7 0.039 REMARK 500 7 DT A 3 C5 DT A 3 C7 0.036 REMARK 500 7 DT A 4 C5 DT A 4 C7 0.042 REMARK 500 7 DT A 7 C5 DT A 7 C7 0.042 REMARK 500 7 DG A 8 C5' DG A 8 C4' 0.058 REMARK 500 7 DT A 9 C5' DT A 9 C4' 0.115 REMARK 500 REMARK 500 THIS ENTRY HAS 84 BOND DEVIATIONS. 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. = 6.7 DEGREES REMARK 500 1 DG A 1 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 2 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT A 4 C5' - C4' - O4' ANGL. DEV. = 6.8 DEGREES REMARK 500 1 DT A 4 O4' - C1' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG A 5 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 6 C4' - C3' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DG A 6 O4' - C1' - C2' ANGL. DEV. = -7.3 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 6 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT A 7 O3' - P - O5' ANGL. DEV. = -16.7 DEGREES REMARK 500 1 DT A 7 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 7 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG A 8 C5' - C4' - O4' ANGL. DEV. = 12.8 DEGREES REMARK 500 1 DG A 8 C4' - C3' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG A 8 C3' - C2' - C1' ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DG A 8 O4' - C1' - C2' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 DG A 8 N9 - C1' - C2' ANGL. DEV. = -12.9 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 8 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT A 9 P - O5' - C5' ANGL. DEV. = 9.7 DEGREES REMARK 500 1 DT A 9 O4' - C4' - C3' ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT A 9 C1' - O4' - C4' ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 11 C5 - N7 - C8 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DG A 11 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG A 15 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 15 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DG A 1 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 4 C5' - C4' - O4' ANGL. DEV. = 10.3 DEGREES REMARK 500 2 DT A 4 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 2 DG A 5 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DG A 5 C5' - C4' - C3' ANGL. DEV. = 7.4 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DG A 5 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DG A 6 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES REMARK 500 2 DG A 6 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 402 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 148D A 1 15 PDB 148D 148D 1 15 SEQRES 1 A 15 DG DG DT DT DG DG DT DG DT DG DG DT DT SEQRES 2 A 15 DG DG 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