PDB Short entry for 1K1H HEADER DNA 25-SEP-01 1K1H TITLE HETERODUPLEX OF CHIRALLY PURE METHYLPHOSPHONATE/DNA DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*GP*TP*TP*TP*GP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*(CMR)P*(RMP)P*(RMP)P*(SMP)P*(CMR)P*(RMP))-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS METHYL PHOSPHONATE, ANTI SENSE, DNA EXPDTA SOLUTION NMR AUTHOR V.THIVIYANATHAN,K.V.VYAZOVKINA,E.K.GOZANSKY,E.BICHENCHOVA, AUTHOR 2 T.V.ABRAMOVA,B.A.LUXON,A.V.LEBEDEV,D.G.GORENSTEIN REVDAT 4 23-FEB-22 1K1H 1 REMARK LINK REVDAT 3 24-FEB-09 1K1H 1 VERSN REVDAT 2 01-APR-03 1K1H 1 JRNL REVDAT 1 19-JUN-02 1K1H 0 JRNL AUTH V.THIVIYANATHAN,K.V.VYAZOVKINA,E.K.GOZANSKY,E.BICHENCHOVA, JRNL AUTH 2 T.V.ABRAMOVA,B.A.LUXON,A.V.LEBEDEV,D.G.GORENSTEIN JRNL TITL STRUCTURE OF HYBRID BACKBONE METHYLPHOSPHONATE DNA JRNL TITL 2 HETERODUPLEXES: EFFECT OF R AND S STEREOCHEMISTRY. JRNL REF BIOCHEMISTRY V. 41 827 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 11790104 JRNL DOI 10.1021/BI011551K REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 5.1, AMBER 5.0 REMARK 3 AUTHORS : VARIAN (VNMR), UCSF (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NO DIHEDRAL RESTRAINTS WERE USED. REMARK 4 REMARK 4 1K1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000014441. 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 : 100 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : DNA, 100 MM NACL, 10 MM REMARK 210 PHOSPHATE, 0.1 MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MORASS 2.1 REMARK 210 METHOD USED : MOLECULAR DYNAMICS MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES 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 DG A 7 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K1R RELATED DB: PDB REMARK 900 HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE / DNA DUPLEX DBREF 1K1H A 1 8 PDB 1K1H 1K1H 1 8 DBREF 1K1H B 9 15 PDB 1K1H 1K1H 9 15 SEQRES 1 A 8 DT DG DT DT DT DG DG DC SEQRES 1 B 7 DC CMR RMP RMP SMP CMR RMP MODRES 1K1H CMR B 10 DC MODRES 1K1H RMP B 11 DA MODRES 1K1H RMP B 12 DA MODRES 1K1H SMP B 13 DA MODRES 1K1H CMR B 14 DC MODRES 1K1H RMP B 15 DA HET CMR B 10 33 HET RMP B 11 35 HET RMP B 12 35 HET SMP B 13 35 HET CMR B 14 33 HET RMP B 15 36 HETNAM CMR 2'-DEOXY-CYTIDINE-5'-RP-MONOMETHYLPHOSPHONATE HETNAM RMP 2'-DEOXY-ADENOSINE-5'-RP-MONOMETHYLPHOSPHONATE HETNAM SMP 2'-DEOXY-ADENOSINE-5'-SP-MONOMETHYLPHOSPHONATE FORMUL 2 CMR 2(C10 H16 N3 O6 P) FORMUL 2 RMP 3(C11 H16 N5 O5 P) FORMUL 2 SMP C11 H16 N5 O5 P LINK O3' DC B 9 P CMR B 10 1555 1555 1.60 LINK O3' CMR B 10 P RMP B 11 1555 1555 1.61 LINK O3' RMP B 11 P RMP B 12 1555 1555 1.59 LINK O3' RMP B 12 P SMP B 13 1555 1555 1.59 LINK O3' SMP B 13 P CMR B 14 1555 1555 1.60 LINK O3' CMR B 14 P RMP B 15 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