HEADER DNA 24-OCT-01 1K8N TITLE NMR STRUCTURE OF THE XBY2 DNA DUPLEX, AN ANALOG OF CK14 CONTAINING TITLE 2 PHOSPHORODITHIOATE GROUPS AT C22 AND C24 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIRST STRAND OF CK14 DNA DUPLEX; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SECOND STRAND OF CK14 DNA DUPLEX; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: DITHIOATED AT C22 AND C24; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES; COMPND 12 OTHER_DETAILS: CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED WITH NORMAL PHOSPHOROAMIDITE CHEMISTRY; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHESIZED WITH BOTH NORMAL PHOSPHOROAMIDITE SOURCE 7 CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY KEYWDS PHOSPHORODITHIOATE, CK14, CK1, NF-KB, XBY6, XBY2, THIOPHOSPHATE, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR D.E.VOLK,X.YANG,S.M.FENNEWALD,D.J.KING,S.E.BASSETT,S.VENKITACHALAM, AUTHOR 2 N.HERZOG,B.A.LUXON,D.G.GORENSTEIN REVDAT 3 23-FEB-22 1K8N 1 REMARK LINK REVDAT 2 24-FEB-09 1K8N 1 VERSN REVDAT 1 15-APR-03 1K8N 0 JRNL AUTH D.E.VOLK,X.YANG,S.M.FENNEWALD,D.J.KING,S.E.BASSETT, JRNL AUTH 2 S.VENKITACHALAM,N.HERZOG,B.A.LUXON,D.G.GORENSTEIN JRNL TITL SOLUTION STRUCTURE AND DESIGN OF DITHIOPHOSPHATE BACKBONE JRNL TITL 2 APTAMERS TARGETING TRANSCRIPTION FACTOR NF-KAPPAB JRNL REF BIOORG.CHEM. V. 30 396 2002 JRNL REFN ISSN 0045-2068 JRNL PMID 12642125 JRNL DOI 10.1016/S0045-2068(02)00510-2 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : MORASS 2.5, AMBER 5 REMARK 3 AUTHORS : GORENSTEIN (MORASS), CASE AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 DISTANCE RESTRAINTS WERE DERIVED BY MORASS 2.5 USING A TOTAL REMARK 3 RELAXATION REMARK 3 MATRIX METHOD. THE DEPOSITED STRUCTURE REPRESENTS THE AVERAGE OF REMARK 3 10 FINAL REMARK 3 STRUCTURES REMARK 4 REMARK 4 1K8N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014697. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 288 REMARK 210 PH : 6.7; 6.7 REMARK 210 IONIC STRENGTH : 100 MM; 100 MM REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM DUPLEX, 12 MM NA2HPO4, 8 MM REMARK 210 NAH2PO4, 56 MM NACL, 50 UM NAN3; REMARK 210 1 MM DUPLEX, 12 MM NA2HPO4,8 MM REMARK 210 NAH2PO4, 56 MM NACL, 50 UM NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER 5 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 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: STANDARD 2D HOMONUCLEAR METHODS WERE USED 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: 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 HO5' DC A 1 OP2 DC A 2 1.33 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA A 6 N1 - C6 - N6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DC A 12 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG B 15 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT B 21 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT B 21 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT B 23 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT B 23 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC B 25 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT B 26 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 27 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 DG B 28 O4' - C1' - N9 ANGL. DEV. = 2.5 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 DC A 1 0.06 SIDE CHAIN REMARK 500 DC A 2 0.07 SIDE CHAIN REMARK 500 DG A 4 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K8J RELATED DB: PDB REMARK 900 NMR STRUCTURE OF CK14, THE NON-THIOATED ANALOG OF XBY6 REMARK 900 RELATED ID: 1K8L RELATED DB: PDB REMARK 900 NMR STRUCTURE OF CK14, AN ANALOG WITH 6 PHOSPHORODITHIOATES DBREF 1K8N A 1 14 PDB 1K8N 1K8N 1 14 DBREF 1K8N B 15 28 PDB 1K8N 1K8N 15 28 SEQRES 1 A 14 DC DC DA DG DG DA DG DA DT DT DC DC DA SEQRES 2 A 14 DC SEQRES 1 B 14 DG DT DG DG DA DA DT C2S DT C2S DC DT DG SEQRES 2 B 14 DG MODRES 1K8N C2S B 22 DC CYTIDINE-5'-DITHIOPHOSPHORATE MODRES 1K8N C2S B 24 DC CYTIDINE-5'-DITHIOPHOSPHORATE HET C2S B 22 30 HET C2S B 24 30 HETNAM C2S CYTIDINE-5'-DITHIOPHOSPHORATE FORMUL 2 C2S 2(C9 H14 N3 O5 P S2) LINK O3' DT B 21 P C2S B 22 1555 1555 1.62 LINK O3' C2S B 22 P DT B 23 1555 1555 1.62 LINK O3' DT B 23 P C2S B 24 1555 1555 1.62 LINK O3' C2S B 24 P DC B 25 1555 1555 1.62 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