PDB Short entry for 2K67 HEADER DNA 04-JUL-08 2K67 TITLE NMR SOLUTION STRUCTURE OF MODIFIED DNA CONTAINING IMIDAZOLE TITLE 2 NUCLEOSIDES AT ACIDIC PH COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*DTP*DTP*DAP*DAP*DTP*DTP*DTP*(D33)P*(D33)P*(D33) COMPND 3 P*DAP*DAP*DAP*DTP*DTP*DAP*DA)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: DIH-DNA-17-MER SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA 17-MER, HAIRPIN, ARTIFICIAL NUCLEOBASE, IMIDAZOLE NUCLEOSIDE, KEYWDS 2 SHIFTED PKA, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.JOHANNSEN,D.BOEHME,N.DUEPRE,J.MUELLER,R.K.O.SIGEL REVDAT 3 01-MAY-24 2K67 1 REMARK LINK REVDAT 2 04-MAY-11 2K67 1 ATOM REVDAT 1 07-JUL-09 2K67 0 JRNL AUTH S.JOHANNSEN,D.BOEHME,N.DUEPRE,J.MUELLER,R.K.O.SIGEL JRNL TITL SOLUTION STRUCTURE AT DIFFERENT PHS OF A DNA HAIRPIN JRNL TITL 2 CONTAINING ARTIFICIAL NUCLEOTIDES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, 2.0, 2.1, X-PLOR NIH 2.15 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K67 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000100726. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 278 REMARK 210 PH : 4.7; 4.7 REMARK 210 IONIC STRENGTH : 120 MM; 120 MM REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM DIH DNA 17-MER, 120 MM REMARK 210 SODIUM PERCHLORATE, 100% D2O; REMARK 210 0.5 MM DIH DNA 17-MER, 120 MM REMARK 210 SODIUM PERCHLORATE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.1, DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: 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 OP2 D33 A 8 H44 D33 A 9 1.56 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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA A 11 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 14 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 15 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA A 16 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA A 17 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DA A 11 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA A 13 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT A 14 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT A 15 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DA A 16 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DA A 17 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 3 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 3 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DA A 11 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DA A 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DT A 14 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DT A 15 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DA A 16 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DA A 17 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 4 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 4 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 4 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 4 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 306 ANGLE DEVIATIONS. 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 D33 A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D33 A 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D33 A 10 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K68 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF MODIFIED DNA CONTAINING IMIDAZOLE REMARK 900 NUCLEOSIDES AT NEUTRAL PH REMARK 900 RELATED ID: 2K69 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF MODIFIED DNA CONTAINING IMIDAZOLE REMARK 900 NUCLEOSIDES AT BASIC PH DBREF 2K67 A 1 17 PDB 2K67 2K67 1 17 SEQRES 1 A 17 DT DT DA DA DT DT DT D33 D33 D33 DA DA DA SEQRES 2 A 17 DT DT DA DA HET D33 A 8 27 HET D33 A 9 27 HET D33 A 10 27 HETNAM D33 1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 D33 PENTOFURANOSYL)-1H-IMIDAZOLE FORMUL 1 D33 3(C8 H13 N2 O6 P) LINK O3' DT A 7 P D33 A 8 1555 1555 1.61 LINK O3' D33 A 8 P D33 A 9 1555 1555 1.61 LINK O3' D33 A 9 P D33 A 10 1555 1555 1.61 LINK O3' D33 A 10 P DA A 11 1555 1555 1.61 SITE 1 AC1 1 DT A 7 SITE 1 AC2 1 DT A 7 SITE 1 AC3 2 DT A 6 DA A 11 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