HEADER DNA 02-NOV-10 2L5K TITLE SOLUTION STRUCTURE OF TRUNCATED 23-MER DNA MUC1 APTAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-R(*(N68)P*G)- COMPND 3 D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP* COMPND 4 GP*GP*T)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS NMR SOLUTION STRUCTURE, DYANA AND BCE MODELS, TTT TRILOOP CONTAINING KEYWDS 2 DNA, TRUNCATED DNA MUC1 APTAMER SEQUENCE, BINDING NUCLEOTIDES, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.COGNET,M.BAOUENDI,E.HANTZ,S.MISSAILIDIS,C.HERVE DU PENHOAT,M.PIOTTO REVDAT 3 01-FEB-12 2L5K 1 JRNL REVDAT 2 21-DEC-11 2L5K 1 JRNL REVDAT 1 07-DEC-11 2L5K 0 JRNL AUTH M.BAOUENDI,J.A.COGNET,C.S.FERREIRA,S.MISSAILIDIS,J.COUTANT, JRNL AUTH 2 M.PIOTTO,E.HANTZ,C.HERVE DU PENHOAT JRNL TITL SOLUTION STRUCTURE OF A TRUNCATED ANTI-MUC1 DNA APTAMER JRNL TITL 2 DETERMINED BY MESOSCALE MODELING AND NMR. JRNL REF FEBS J. V. 279 479 2012 JRNL REFN ISSN 1742-464X JRNL PMID 22129448 JRNL DOI 10.1111/J.1742-4658.2011.08440.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5 REMARK 3 AUTHORS : GUNTERT, BRAUN AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 100 STRUCTURES WERE CALCULATED WITH REMARK 3 DYANA AND THE 20 STRUCTURES WITH THE SMALLEST RESIDUAL TARGET REMARK 3 FUNCTION HAVE BEEN REFINED BY ENERGY MINIMIZATION WITH AMBER REMARK 3 BEFORE BEING DEPOSITED., A MODEL WITH THE NMR-DEFINED TORSION REMARK 3 ANGLES WAS CONSTRUCTED WITH THE BCE METHOD AND AMBER ENERGY REMARK 3 REFINED. IT CONTAINS 2 BRIDGING WATER MOLECULES (COORDINATES REMARK 3 AVAILABLE UPON REQUEST TO J. COGNET). REMARK 4 REMARK 4 2L5K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-10. REMARK 100 THE RCSB ID CODE IS RCSB101984. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 264.5 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 50; 50 REMARK 210 PRESSURE : AMBIENT; 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM DNA (5'-D(*CP*AP*GP*TP*TP* REMARK 210 GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 MM REMARK 210 SODIUM PHOSPHATE, 5 UM SODIUM AZIDE, 50 MM SODIUM CHLORIDE, 90% REMARK 210 H2O/10% D2O; 2 MM DNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP* REMARK 210 TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 MM SODIUM PHOSPHATE, 50 REMARK 210 MM SODIUM CHLORIDE, 5 UM SODIUM AZIDE, 100% D2O; 1 MM DNA (5'-D(* REMARK 210 CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP* REMARK 210 TP*G)-3'), 20 MM SODIUM PHOSPHATE, 50 MM SODIUM CHLORIDE, 5 UM REMARK 210 SODIUM AZIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-13C HSQC; REMARK 210 2D 1H-31P COSY; 2D DQF-COSY; 2D REMARK 210 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PROSA 6.0.2, XEASY 1.2, NMRPIPE REMARK 210 1998, AMBER 8, SMOL 1 REMARK 210 METHOD USED : SIMULATED ANNEALING, BIOPLYMER REMARK 210 CHAIN ELASTICITY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : 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: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 N68 A -1 REMARK 465 DG A 0 REMARK 465 DG A 24 REMARK 465 DT A 25 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 DC A 1 P OP1 OP2 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 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DT A 11 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA A 16 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 17 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC A 19 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC A 20 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 23 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DA A 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT A 11 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DT A 12 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DT A 12 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DT A 13 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA A 16 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT A 17 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC A 19 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC A 20 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT A 22 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DG A 23 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DT A 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 3 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DA A 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DT A 11 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 DT A 12 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 DT A 12 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 3 DT A 13 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DA A 16 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DT A 17 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DC A 20 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DG A 23 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DT A 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 4 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 4 DT A 11 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 DT A 12 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 4 DT A 12 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 4 DT A 13 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DG A 14 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 4 DA A 16 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DT A 17 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 294 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 DT A 8 0.07 SIDE CHAIN REMARK 500 1 DT A 12 0.08 SIDE CHAIN REMARK 500 1 DG A 23 0.06 SIDE CHAIN REMARK 500 2 DT A 8 0.07 SIDE CHAIN REMARK 500 2 DT A 12 0.07 SIDE CHAIN REMARK 500 2 DG A 23 0.06 SIDE CHAIN REMARK 500 3 DT A 8 0.07 SIDE CHAIN REMARK 500 3 DT A 12 0.08 SIDE CHAIN REMARK 500 3 DG A 23 0.05 SIDE CHAIN REMARK 500 4 DT A 8 0.08 SIDE CHAIN REMARK 500 4 DT A 12 0.07 SIDE CHAIN REMARK 500 4 DG A 23 0.05 SIDE CHAIN REMARK 500 5 DT A 8 0.07 SIDE CHAIN REMARK 500 5 DT A 12 0.08 SIDE CHAIN REMARK 500 5 DG A 23 0.05 SIDE CHAIN REMARK 500 6 DT A 4 0.09 SIDE CHAIN REMARK 500 6 DT A 8 0.08 SIDE CHAIN REMARK 500 6 DT A 12 0.07 SIDE CHAIN REMARK 500 6 DG A 23 0.05 SIDE CHAIN REMARK 500 7 DT A 8 0.07 SIDE CHAIN REMARK 500 7 DT A 12 0.08 SIDE CHAIN REMARK 500 7 DG A 23 0.06 SIDE CHAIN REMARK 500 8 DT A 8 0.07 SIDE CHAIN REMARK 500 8 DT A 12 0.07 SIDE CHAIN REMARK 500 8 DG A 23 0.06 SIDE CHAIN REMARK 500 9 DT A 8 0.07 SIDE CHAIN REMARK 500 9 DT A 12 0.08 SIDE CHAIN REMARK 500 9 DG A 23 0.06 SIDE CHAIN REMARK 500 10 DT A 8 0.07 SIDE CHAIN REMARK 500 10 DT A 12 0.07 SIDE CHAIN REMARK 500 10 DG A 23 0.06 SIDE CHAIN REMARK 500 11 DT A 8 0.07 SIDE CHAIN REMARK 500 11 DT A 12 0.08 SIDE CHAIN REMARK 500 11 DG A 23 0.05 SIDE CHAIN REMARK 500 12 DT A 8 0.08 SIDE CHAIN REMARK 500 12 DT A 12 0.08 SIDE CHAIN REMARK 500 12 DG A 23 0.05 SIDE CHAIN REMARK 500 13 DT A 8 0.07 SIDE CHAIN REMARK 500 13 DT A 12 0.08 SIDE CHAIN REMARK 500 13 DG A 23 0.06 SIDE CHAIN REMARK 500 14 DT A 8 0.07 SIDE CHAIN REMARK 500 14 DT A 12 0.08 SIDE CHAIN REMARK 500 14 DG A 23 0.06 SIDE CHAIN REMARK 500 15 DT A 8 0.07 SIDE CHAIN REMARK 500 15 DT A 12 0.08 SIDE CHAIN REMARK 500 15 DG A 23 0.06 SIDE CHAIN REMARK 500 16 DT A 8 0.07 SIDE CHAIN REMARK 500 16 DT A 12 0.07 SIDE CHAIN REMARK 500 16 DG A 23 0.06 SIDE CHAIN REMARK 500 17 DT A 8 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 60 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17129 RELATED DB: BMRB REMARK 900 TRUNCATED 25MER DNA APTAMER DBREF 2L5K A 1 23 PDB 2L5K 2L5K 1 23 SEQRES 1 A 27 N68 DG DC DA DG DT DT DG DA DT DC DC DT SEQRES 2 A 27 DT DT DG DG DA DT DA DC DC DC DT DG DG SEQRES 3 A 27 DT 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 241 0 0 0 0 0 0 6 0 0 0 3 END