HEADER DNA 13-SEP-06 2ICZ TITLE NMR STRUCTURES OF THE EXPANDED DNA 10BP TITLE 2 XTGXTAXCXGCXAXGT:XACTXGCGXTAXCA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*(XTY)P*GP*(XTY)P*AP*(XCS)P*(XGA)P*CP*(XAE)P*(XGA) COMPND 3 P*T)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*(XAE)P*CP*TP*(XGA)P*CP*GP*(XTY)P*AP*(XCS)P*A)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS EXPANDED DNA, XDNA, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.R.LYNCH REVDAT 3 09-MAR-22 2ICZ 1 REMARK LINK ATOM REVDAT 2 24-FEB-09 2ICZ 1 VERSN REVDAT 1 21-NOV-06 2ICZ 0 JRNL AUTH S.R.LYNCH,H.LIU,J.GAO,E.T.KOOL JRNL TITL TOWARD A DESIGNED, FUNCTIONING GENETIC SYSTEM WITH JRNL TITL 2 EXPANDED-SIZE BASE PAIRS: SOLUTION STRUCTURE OF THE JRNL TITL 3 EIGHT-BASE XDNA DOUBLE HELIX. JRNL REF J.AM.CHEM.SOC. V. 128 14704 2006 JRNL REFN ISSN 0002-7863 JRNL PMID 17090058 JRNL DOI 10.1021/JA065606N REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CNS 1.1 REMARK 3 AUTHORS : BRUNGER A. T. ETALL (CNS), BRUNGER A. T. ETALL REMARK 3 (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 635 NOE, 25 HYDROGEN BONDS, 180 TORSION REMARK 3 ANGLE RESTRAINTS REMARK 4 REMARK 4 2ICZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039428. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 20 MM NAP REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM DNA, 20 MM NA PHOSPHATE; REMARK 210 90% H2O/10% D2O; 1.0 MM DNA, 20 REMARK 210 MM NA PHOSPHATE; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1C, SPARKY 3.106 REMARK 210 METHOD USED : SIMULATED ANNEALING MOLECULAR REMARK 210 DYNAMICS TORSION ANGLE DYNAMICS REMARK 210 CARTESIAN DYNAMICS 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 5 DT B 13 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 7 DT B 13 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 16 DA B 18 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 2ICZ A 1 10 PDB 2ICZ 2ICZ 1 10 DBREF 2ICZ B 11 20 PDB 2ICZ 2ICZ 11 20 SEQRES 1 A 10 XTY DG XTY DA XCS XGA DC XAE XGA DT SEQRES 1 B 10 XAE DC DT XGA DC DG XTY DA XCS DA HET XTY A 1 36 HET XTY A 3 38 HET XCS A 5 39 HET XGA A 6 39 HET XAE A 8 38 HET XGA A 9 39 HET XAE B 11 36 HET XGA B 14 39 HET XTY B 17 38 HET XCS B 19 39 HETNAM XTY (1R)-1,4-ANHYDRO-2-DEOXY-1-(6-METHYL-2,4-DIOXO-1,2,3,4- HETNAM 2 XTY TETRAHYDROQUINAZOLIN-8-YL)-5-O-PHOSPHONO-D-ERYTHRO- HETNAM 3 XTY PENTITOL HETNAM XCS (1R)-1-(4-AMINO-6-METHYL-2-OXO-1,2-DIHYDROQUINAZOLIN-8- HETNAM 2 XCS YL)-1,4-ANHYDRO-2-DEOXY-5-O-PHOSPHONO-D-ERYTHRO- HETNAM 3 XCS PENTITOL HETNAM XGA 6-AMINO-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 XGA PENTOFURANOSYL)-3,7-DIHYDRO-8H-IMIDAZO[4,5- HETNAM 3 XGA G]QUINAZOLIN-8-ONE HETNAM XAE 3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 XAE PENTOFURANOSYL)-3H-IMIDAZO[4,5-G]QUINAZOLIN-8-AMINE FORMUL 1 XTY 3(C14 H17 N2 O8 P) FORMUL 1 XCS 2(C14 H18 N3 O7 P) FORMUL 1 XGA 3(C14 H16 N5 O7 P) FORMUL 1 XAE 2(C14 H16 N5 O6 P) LINK O3' XTY A 1 P DG A 2 1555 1555 1.61 LINK O3' DG A 2 P XTY A 3 1555 1555 1.61 LINK O3' XTY A 3 P DA A 4 1555 1555 1.61 LINK O3' DA A 4 P XCS A 5 1555 1555 1.61 LINK O3' XCS A 5 P XGA A 6 1555 1555 1.61 LINK O3' XGA A 6 P DC A 7 1555 1555 1.61 LINK O3' DC A 7 P XAE A 8 1555 1555 1.61 LINK O3' XAE A 8 P XGA A 9 1555 1555 1.61 LINK O3' XGA A 9 P DT A 10 1555 1555 1.61 LINK O3' XAE B 11 P DC B 12 1555 1555 1.61 LINK O3' DT B 13 P XGA B 14 1555 1555 1.61 LINK O3' XGA B 14 P DC B 15 1555 1555 1.61 LINK O3' DG B 16 P XTY B 17 1555 1555 1.61 LINK O3' XTY B 17 P DA B 18 1555 1555 1.61 LINK O3' DA B 18 P XCS B 19 1555 1555 1.61 LINK O3' XCS B 19 P DA B 20 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 HETATM 1 C5' XTY A 1 -14.871 -9.039 -8.856 1.00 0.00 C HETATM 2 C4' XTY A 1 -14.157 -10.098 -8.016 1.00 0.00 C HETATM 3 O4' XTY A 1 -12.924 -10.453 -8.661 1.00 0.00 O HETATM 4 C3' XTY A 1 -13.748 -9.642 -6.622 1.00 0.00 C HETATM 5 C2' XTY A 1 -12.348 -9.096 -6.841 1.00 0.00 C HETATM 6 C1' XTY A 1 -11.789 -10.102 -7.851 1.00 0.00 C HETATM 7 O5' XTY A 1 -15.027 -7.811 -8.139 1.00 0.00 O HETATM 8 C2 XTY A 1 -10.411 -12.336 -11.019 1.00 0.00 C HETATM 9 O2 XTY A 1 -10.841 -13.473 -11.194 1.00 0.00 O HETATM 10 N3 XTY A 1 -9.475 -11.786 -11.875 1.00 0.00 N HETATM 11 C4 XTY A 1 -8.949 -10.515 -11.753 1.00 0.00 C HETATM 12 O4 XTY A 1 -8.120 -10.103 -12.562 1.00 0.00 O HETATM 13 C5 XTY A 1 -9.395 -9.728 -10.685 1.00 0.00 C HETATM 14 C6 XTY A 1 -10.354 -10.268 -9.792 1.00 0.00 C HETATM 15 N XTY A 1 -10.858 -11.558 -9.956 1.00 0.00 N HETATM 16 CP XTY A 1 -8.898 -8.416 -10.501 1.00 0.00 C HETATM 17 CD XTY A 1 -10.318 -8.193 -8.537 1.00 0.00 C HETATM 18 C8 XTY A 1 -10.830 -9.508 -8.706 1.00 0.00 C HETATM 19 C7 XTY A 1 -9.364 -7.658 -9.427 1.00 0.00 C HETATM 20 C7A XTY A 1 -8.837 -6.241 -9.215 1.00 0.00 C HETATM 21 O3' XTY A 1 -13.629 -10.821 -5.818 1.00 0.00 O HETATM 22 H5'1 XTY A 1 -15.856 -9.412 -9.138 1.00 0.00 H HETATM 23 H5'2 XTY A 1 -14.291 -8.850 -9.759 1.00 0.00 H HETATM 24 H4' XTY A 1 -14.790 -10.983 -7.956 1.00 0.00 H HETATM 25 H3' XTY A 1 -14.433 -8.917 -6.183 1.00 0.00 H HETATM 26 H2'1 XTY A 1 -12.383 -8.090 -7.254 1.00 0.00 H HETATM 27 H2'2 XTY A 1 -11.771 -9.096 -5.915 1.00 0.00 H HETATM 28 H1' XTY A 1 -11.456 -11.000 -7.327 1.00 0.00 H HETATM 29 HN3 XTY A 1 -9.155 -12.353 -12.646 1.00 0.00 H HETATM 30 HN XTY A 1 -11.544 -11.933 -9.317 1.00 0.00 H HETATM 31 HP XTY A 1 -8.166 -8.003 -11.184 1.00 0.00 H HETATM 32 HD XTY A 1 -10.660 -7.594 -7.711 1.00 0.00 H HETATM 33 H7A1 XTY A 1 -8.278 -5.924 -10.096 1.00 0.00 H HETATM 34 H7A2 XTY A 1 -8.183 -6.225 -8.344 1.00 0.00 H HETATM 35 H7A3 XTY A 1 -9.675 -5.562 -9.053 1.00 0.00 H HETATM 36 HO5' XTY A 1 -14.154 -7.541 -7.846 1.00 0.00 H