HEADER DNA 29-JUL-08 2K71 TITLE STRUCTURE AND DYNAMICS OF A DNA GNRA HAIRPIN SOLVED VY HIGH- TITLE 2 SENSITIVITY NMR WITH TWO INDEPENDENT CONVERGING METHODS, TITLE 3 SIMULATED ANNEALING (DYANA) AND MESOSCOPIC MOLECULAR TITLE 4 MODELLING (BCE/AMBER) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*DGP*DCP*DGP*DAP*DAP*DAP*DGP*DC)-3'; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA GNRA HAIRPIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS TETRALOOP HAIRPIN, B-DNA-LIKE, 2 NON CANONICAL TORSIONS, KEYWDS 2 UNUSUAL BIIZ+ TORSIONS EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR G.P.H.SANTINI,J.A.H.COGNET,D.XU,K.K.SINGARAPU,C.L.M.HERVE DU AUTHOR 2 PENHOAT REVDAT 1 21-JUL-09 2K71 0 JRNL AUTH G.P.SANTINI,J.A.COGNET,D.XU,K.K.SINGARAPU, JRNL AUTH 2 C.HERVE DU PENHOAT JRNL TITL NUCLEIC ACID FOLDING DETERMINED BY MESOSCALE JRNL TITL 2 MODELING AND NMR SPECTROSCOPY: SOLUTION STRUCTURE JRNL TITL 3 OF D(GCGAAAGC). JRNL REF J.PHYS.CHEM.B V. 113 6881 2009 JRNL REFN ISSN 1089-5647 JRNL PMID 19374420 JRNL DOI 10.1021/JP8100656 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA REMARK 3 AUTHORS : GUNTERT, BRAUN AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 100 STRUCTURES WERE USED IN DYANA REMARK 3 SIMULATED ANNEALING APPROACH TO GIVE MODELS 1 TO 20 THAT WERE REMARK 3 ENERGY-REFINED WITH AMBER, MODEL NUMBER 21 WAS CONSTRUCTED REMARK 3 WITH THE BCE APPROACH IN AGREEMENT WITH THE NMR DATA AND THEN REMARK 3 ENERGY-REFINED WITH AMBER REMARK 4 REMARK 4 2K71 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUL-08. REMARK 100 THE RCSB ID CODE IS RCSB100756. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 274 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 50; 50 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 4 MM DGCGAAAGC, 10 MM SODIUM REMARK 210 PHOSPHATE, 0.0025 MM SODIUM REMARK 210 AZIDE, 0.005 MM EDTA, 50 MM REMARK 210 SODIUM CHLORIDE, 100% D2O; 4 REMARK 210 MM DGCGAAAGC, 10 MM SODIUM REMARK 210 PHOSPHATE, 0.0025 MM SODIUM REMARK 210 AZIDE, 0.005 MM EDTA, 50 MM REMARK 210 SODIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D DQF-COSY; 2D 1H-13C HSQC; REMARK 210 2D 1H-31P COSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR, PROSA, DYANA, MOLMOL REMARK 210 METHOD USED : SIMULATED ANNEALING, REMARK 210 BIOPOLYMER CHAIN ELASTICITY REMARK 210 APPROACH REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 101 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 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 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' - C4' - C3' ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DG A 1 C1' - O4' - C4' ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 1 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 DG A 1 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DG A 1 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 3 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 DG A 3 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DG A 3 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DA A 4 O4' - C4' - C3' ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 4 C1' - O4' - C4' ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA A 6 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 6 C1' - O4' - C4' ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 7 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DG A 7 C1' - O4' - C4' ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 7 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 DG A 7 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DG A 7 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DC A 8 O4' - C4' - C3' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DC A 8 C1' - O4' - C4' ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 5 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 6 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 6 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 7 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 110 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 21 DC A 2 0.06 SIDE_CHAIN REMARK 500 21 DA A 6 0.09 SIDE_CHAIN REMARK 500 21 DG A 7 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2K71 A 1 8 PDB 2K71 2K71 1 8 SEQRES 1 A 8 DG DC DG DA DA DA DG DC 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 ENDMDL MASTER 149 0 0 0 0 0 0 6 0 0 0 1 END