10 20 30 40 50 60 70 80 1IEY - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 11-APR-01 1IEY
TITLE SOLUTION STRUCTURE OF THE DNA DUPLEX D(CCACCGGAAC) TITLE 2 .(GTTCCGGTGG) WITH A CHIRAL ALKYL-PHOSPHONATE MOIETY TITLE 3 (DIAESTEREOISOMER R)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*CP*CP*AP*CP*CP*(OCT)GP*GP*AP*AP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*TP*TP*CP*CP*GP*GP*TP*GP*G)-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 DOUBLE HELIX, DNA BENDING, MODIFIED OLIGONUCLEOTIDE, CHARGE KEYWDS 2 NEUTRALIZATION
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR R.SOLIVA,V.MONACO,I.GOMEZ-PINTO,N.J.MEEUWENOORD,G.A.VAN DER AUTHOR 2 MAREL,J.H.VAN BOOM,C.GONZALEZ,M.OROZCO
REVDAT 3 24-FEB-09 1IEY 1 VERSN REVDAT 2 01-APR-03 1IEY 1 JRNL REVDAT 1 25-JUL-01 1IEY 0
JRNL AUTH R.SOLIVA,V.MONACO,I.GOMEZ-PINTO,N.J.MEEUWENOORD, JRNL AUTH 2 G.A.MAREL,J.H.BOOM,C.GONZALEZ,M.OROZCO JRNL TITL SOLUTION STRUCTURE OF A DNA DUPLEX WITH A CHIRAL JRNL TITL 2 ALKYL PHOSPHONATE MOIETY. JRNL REF NUCLEIC ACIDS RES. V. 29 2973 2001 JRNL REFN ISSN 0305-1048 JRNL PMID 11452022 JRNL DOI 10.1093/NAR/29.14.2973
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 5.0 REMARK 3 AUTHORS : KOLLMAN, P.A. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 280 NOE-DERIVED DISTANCE CONSTRAINTS OBTAINED FROM A REMARK 3 COMPLETE RELAXATION MATRIX REFINEMENT. THE STRUCTURES WERE REMARK 3 CALCULATED BY USING RESTRAINED MOLECULAR DYNAMICS WITH REMARK 3 EXPLICIT SOLVENT, AND APPLYING THE PARTICLE MESH EWALD METHOD.
REMARK 4 REMARK 4 1IEY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-01. REMARK 100 THE RCSB ID CODE IS RCSB013220.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 298 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 2MM DUPLEX; 10MM PHOSPHATE, REMARK 210 100MM NACL; 2MM DUPLEX; 10MM REMARK 210 PHOSPHATE, 100MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MARDIGRAS 5.2, XWINNMR 1.3 REMARK 210 METHOD USED : SIMULATED, ANNEALING REMARK 210 MOLECULAR DYNAMICS, MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-10 REMARK 470 RES CSSEQI ATOMS REMARK 470 DG A 6 OP1
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 DC A 1 P DC A 1 O5' 10.673 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 DC A 1 P - O5' - C5' ANGL. DEV. = -48.5 DEGREES REMARK 500 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT B 12 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT B 13 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT B 13 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT B 18 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG B 19 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC A 10 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DG B 11 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DT B 12 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DT B 13 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DT B 13 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DG B 16 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DT B 18 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DT B 18 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DG B 19 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG B 20 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DG A 6 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 3 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DC A 10 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 DG B 11 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 3 DT B 12 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 3 DT B 13 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DT B 13 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 3 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DG B 17 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 3 DT B 18 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DT B 18 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 3 DG B 19 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 164 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 1 DG A 6 0.10 SIDE_CHAIN REMARK 500 1 DC A 10 0.08 SIDE_CHAIN REMARK 500 1 DG B 11 0.10 SIDE_CHAIN REMARK 500 1 DT B 13 0.07 SIDE_CHAIN REMARK 500 1 DG B 16 0.13 SIDE_CHAIN REMARK 500 1 DG B 19 0.06 SIDE_CHAIN REMARK 500 2 DG A 6 0.10 SIDE_CHAIN REMARK 500 2 DC A 10 0.08 SIDE_CHAIN REMARK 500 2 DG B 11 0.08 SIDE_CHAIN REMARK 500 2 DT B 13 0.07 SIDE_CHAIN REMARK 500 2 DG B 16 0.12 SIDE_CHAIN REMARK 500 2 DG B 19 0.06 SIDE_CHAIN REMARK 500 3 DG A 6 0.12 SIDE_CHAIN REMARK 500 3 DC A 10 0.08 SIDE_CHAIN REMARK 500 3 DG B 11 0.07 SIDE_CHAIN REMARK 500 3 DT B 13 0.08 SIDE_CHAIN REMARK 500 3 DG B 16 0.06 SIDE_CHAIN REMARK 500 3 DG B 19 0.07 SIDE_CHAIN REMARK 500 4 DG A 6 0.09 SIDE_CHAIN REMARK 500 4 DC A 10 0.08 SIDE_CHAIN REMARK 500 4 DT B 13 0.07 SIDE_CHAIN REMARK 500 4 DG B 16 0.13 SIDE_CHAIN REMARK 500 4 DG B 17 0.07 SIDE_CHAIN REMARK 500 5 DG A 6 0.10 SIDE_CHAIN REMARK 500 5 DC A 10 0.09 SIDE_CHAIN REMARK 500 5 DT B 13 0.09 SIDE_CHAIN REMARK 500 5 DG B 16 0.12 SIDE_CHAIN REMARK 500 5 DG B 17 0.07 SIDE_CHAIN REMARK 500 5 DG B 19 0.07 SIDE_CHAIN REMARK 500 6 DA A 9 0.07 SIDE_CHAIN REMARK 500 6 DC A 10 0.10 SIDE_CHAIN REMARK 500 6 DT B 13 0.08 SIDE_CHAIN REMARK 500 6 DG B 16 0.06 SIDE_CHAIN REMARK 500 6 DG B 19 0.07 SIDE_CHAIN REMARK 500 7 DG A 6 0.07 SIDE_CHAIN REMARK 500 7 DC A 10 0.09 SIDE_CHAIN REMARK 500 7 DG B 11 0.07 SIDE_CHAIN REMARK 500 7 DT B 13 0.07 SIDE_CHAIN REMARK 500 7 DG B 16 0.08 SIDE_CHAIN REMARK 500 7 DG B 19 0.07 SIDE_CHAIN REMARK 500 8 DG A 6 0.06 SIDE_CHAIN REMARK 500 8 DC A 10 0.08 SIDE_CHAIN REMARK 500 8 DG B 11 0.07 SIDE_CHAIN REMARK 500 8 DT B 13 0.07 SIDE_CHAIN REMARK 500 8 DG B 16 0.05 SIDE_CHAIN REMARK 500 8 DG B 17 0.07 SIDE_CHAIN REMARK 500 8 DG B 19 0.07 SIDE_CHAIN REMARK 500 9 DG A 6 0.06 SIDE_CHAIN REMARK 500 9 DC A 10 0.09 SIDE_CHAIN REMARK 500 9 DT B 13 0.07 SIDE_CHAIN REMARK 500 9 DG B 16 0.12 SIDE_CHAIN REMARK 500 9 DG B 17 0.07 SIDE_CHAIN REMARK 500 9 DG B 19 0.06 SIDE_CHAIN REMARK 500 10 DC A 10 0.10 SIDE_CHAIN REMARK 500 10 DG B 11 0.07 SIDE_CHAIN REMARK 500 10 DT B 13 0.09 SIDE_CHAIN REMARK 500 10 DC B 14 0.09 SIDE_CHAIN REMARK 500 10 DG B 16 0.13 SIDE_CHAIN REMARK 500 10 DG B 17 0.08 SIDE_CHAIN REMARK 500 10 DG B 19 0.06 SIDE_CHAIN 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 OCT A 11
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IEK RELATED DB: PDB REMARK 900 DIAESTEREOISOMER S
DBREF 1IEY A 1 10 PDB 1IEY 1IEY 1 10 DBREF 1IEY B 11 20 PDB 1IEY 1IEY 11 20
SEQRES 1 A 10 DC DC DA DC DC DG DG DA DA DC SEQRES 1 B 10 DG DT DT DC DC DG DG DT DG DG
HET OCT A 11 25
HETNAM OCT N-OCTANE
FORMUL 3 OCT C8 H18
LINK P DG A 6 C1 OCT A 11 1555 1555 1.86
SITE 1 AC1 2 DC A 5 DG A 6
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