10 20 30 40 50 60 70 80 2HK4 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 03-JUL-06 2HK4
TITLE DIMERIC SOLUTION STRUCTURE OF THE CYCLIC OCTAMER D(CCGTCCGT)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*CP*CP*GP*TP*CP*CP*GP*T)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS CYCLIC OLIGONUCLEOTIDE, QUADRUPLEX, MINOR GROOVE TETRADS, KEYWDS 2 DNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR N.ESCAJA,I.GOMEZ-PINTO,E.PEDROSO,C.GONZALEZ
REVDAT 2 24-FEB-09 2HK4 1 VERSN REVDAT 1 20-MAR-07 2HK4 0
JRNL AUTH N.ESCAJA,I.GOMEZ-PINTO,E.PEDROSO,C.GONZALEZ JRNL TITL FOUR-STRANDED DNA STRUCTURES CAN BE STABILIZED BY JRNL TITL 2 TWO DIFFERENT TYPES OF MINOR GROOVE G:C:G:C JRNL TITL 3 TETRADS. JRNL REF J.AM.CHEM.SOC. V. 129 2004 2007 JRNL REFN ISSN 0002-7863 JRNL PMID 17260988 JRNL DOI 10.1021/JA066172Z
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 REMARK 3 AUTHORS : KOLLMAN ET AL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2HK4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-06. REMARK 100 THE RCSB ID CODE IS RCSB038436.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 289 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 100 MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 5MM OLIGONUCLEOTIDE REMARK 210 CONCENTRATION, 100MM NACL REMARK 210 BUFFER, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MARDIGRAS 1.5 REMARK 210 METHOD USED : RELAXATION MATRIX CALCULATION REMARK 210 RESTRAINED MOLECULAR DYNAMICS 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 : 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 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 2 C5' - C4' - O4' ANGL. DEV. = 8.2 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DC B 2 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC B 2 C5' - C4' - O4' ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DT B 4 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DC B 6 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DT B 8 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DC A 5 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DC B 2 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DC B 2 C5' - C4' - O4' ANGL. DEV. = 7.3 DEGREES REMARK 500 2 DT B 4 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DC B 6 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 2 DT B 8 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 DT A 8 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 DC B 2 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DC B 2 C5' - C4' - O4' ANGL. DEV. = 7.3 DEGREES REMARK 500 3 DT B 4 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 3 DT B 8 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 4 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 DT A 8 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 DC B 2 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 4 DC B 2 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES REMARK 500 4 DT B 4 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 4 DC B 6 C5' - C4' - O4' ANGL. DEV. = 7.0 DEGREES REMARK 500 4 DT B 8 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 5 DC A 2 C5' - C4' - O4' ANGL. DEV. = 7.1 DEGREES REMARK 500 5 DT A 4 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 5 DC A 6 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 5 DC A 6 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES REMARK 500 5 DT A 8 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 DC B 2 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 5 DC B 2 C5' - C4' - O4' ANGL. DEV. = 6.8 DEGREES REMARK 500 5 DT B 4 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 5 DC B 6 C5' - C4' - O4' ANGL. DEV. = 7.5 DEGREES REMARK 500 5 DT B 8 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 6 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 6 DC A 2 C5' - C4' - O4' ANGL. DEV. = 7.5 DEGREES REMARK 500 6 DT A 4 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 6 DT A 8 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 6 DC B 2 C5' - C4' - O4' ANGL. DEV. = 7.3 DEGREES REMARK 500 6 DT B 4 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 6 DC B 6 C5' - C4' - O4' ANGL. DEV. = 7.6 DEGREES REMARK 500 6 DT B 8 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 7 DT A 4 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 7 DC A 6 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 7 DC A 6 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 76 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 DC A 2 0.08 SIDE_CHAIN REMARK 500 1 DG A 3 0.11 SIDE_CHAIN REMARK 500 1 DC A 6 0.07 SIDE_CHAIN REMARK 500 1 DG A 7 0.12 SIDE_CHAIN REMARK 500 1 DC B 2 0.08 SIDE_CHAIN REMARK 500 1 DG B 3 0.14 SIDE_CHAIN REMARK 500 1 DC B 6 0.09 SIDE_CHAIN REMARK 500 1 DG B 7 0.14 SIDE_CHAIN REMARK 500 2 DG A 3 0.12 SIDE_CHAIN REMARK 500 2 DC A 6 0.08 SIDE_CHAIN REMARK 500 2 DG A 7 0.13 SIDE_CHAIN REMARK 500 2 DC B 2 0.09 SIDE_CHAIN REMARK 500 2 DG B 3 0.14 SIDE_CHAIN REMARK 500 2 DC B 6 0.10 SIDE_CHAIN REMARK 500 2 DG B 7 0.14 SIDE_CHAIN REMARK 500 3 DG A 3 0.13 SIDE_CHAIN REMARK 500 3 DG A 7 0.13 SIDE_CHAIN REMARK 500 3 DC B 2 0.10 SIDE_CHAIN REMARK 500 3 DG B 3 0.14 SIDE_CHAIN REMARK 500 3 DC B 6 0.08 SIDE_CHAIN REMARK 500 3 DG B 7 0.14 SIDE_CHAIN REMARK 500 4 DC A 2 0.08 SIDE_CHAIN REMARK 500 4 DG A 3 0.12 SIDE_CHAIN REMARK 500 4 DG A 7 0.13 SIDE_CHAIN REMARK 500 4 DC B 2 0.08 SIDE_CHAIN REMARK 500 4 DG B 3 0.14 SIDE_CHAIN REMARK 500 4 DC B 6 0.09 SIDE_CHAIN REMARK 500 4 DG B 7 0.13 SIDE_CHAIN REMARK 500 5 DC A 2 0.07 SIDE_CHAIN REMARK 500 5 DG A 3 0.13 SIDE_CHAIN REMARK 500 5 DC A 6 0.07 SIDE_CHAIN REMARK 500 5 DG A 7 0.13 SIDE_CHAIN REMARK 500 5 DC B 2 0.08 SIDE_CHAIN REMARK 500 5 DG B 3 0.14 SIDE_CHAIN REMARK 500 5 DC B 6 0.09 SIDE_CHAIN REMARK 500 5 DG B 7 0.14 SIDE_CHAIN REMARK 500 6 DC A 2 0.08 SIDE_CHAIN REMARK 500 6 DG A 3 0.12 SIDE_CHAIN REMARK 500 6 DC A 6 0.07 SIDE_CHAIN REMARK 500 6 DG A 7 0.12 SIDE_CHAIN REMARK 500 6 DC B 2 0.08 SIDE_CHAIN REMARK 500 6 DG B 3 0.14 SIDE_CHAIN REMARK 500 6 DC B 6 0.09 SIDE_CHAIN REMARK 500 6 DG B 7 0.14 SIDE_CHAIN REMARK 500 7 DC A 2 0.07 SIDE_CHAIN REMARK 500 7 DG A 3 0.12 SIDE_CHAIN REMARK 500 7 DG A 7 0.13 SIDE_CHAIN REMARK 500 7 DC B 2 0.09 SIDE_CHAIN REMARK 500 7 DG B 3 0.15 SIDE_CHAIN REMARK 500 7 DC B 6 0.08 SIDE_CHAIN REMARK 500 7 DG B 7 0.14 SIDE_CHAIN REMARK 500 8 DC A 2 0.07 SIDE_CHAIN REMARK 500 8 DG A 3 0.12 SIDE_CHAIN REMARK 500 8 DC A 6 0.07 SIDE_CHAIN REMARK 500 8 DG A 7 0.13 SIDE_CHAIN REMARK 500 8 DC B 2 0.07 SIDE_CHAIN REMARK 500 8 DG B 3 0.15 SIDE_CHAIN REMARK 500 8 DC B 6 0.09 SIDE_CHAIN REMARK 500 8 DG B 7 0.14 SIDE_CHAIN REMARK 500 9 DC A 2 0.07 SIDE_CHAIN REMARK 500 9 DG A 3 0.13 SIDE_CHAIN REMARK 500 9 DC A 6 0.07 SIDE_CHAIN REMARK 500 9 DG A 7 0.13 SIDE_CHAIN REMARK 500 9 DC B 2 0.09 SIDE_CHAIN REMARK 500 9 DG B 3 0.14 SIDE_CHAIN REMARK 500 9 DC B 6 0.10 SIDE_CHAIN REMARK 500 9 DG B 7 0.14 SIDE_CHAIN REMARK 500 10 DC A 2 0.07 SIDE_CHAIN REMARK 500 10 DG A 3 0.12 SIDE_CHAIN REMARK 500 10 DC A 6 0.08 SIDE_CHAIN REMARK 500 10 DG A 7 0.12 SIDE_CHAIN REMARK 500 10 DC B 2 0.10 SIDE_CHAIN REMARK 500 10 DG B 3 0.14 SIDE_CHAIN REMARK 500 10 DC B 6 0.10 SIDE_CHAIN REMARK 500 10 DG B 7 0.14 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EU2 RELATED DB: PDB REMARK 900 BELONGS TO THE SAME FAMILY OF DNA STRUCTURES REMARK 900 RELATED ID: 1EU6 RELATED DB: PDB REMARK 900 BELONGS TO THE SAME FAMILY OF DNA STRUCTURES REMARK 900 RELATED ID: 1N96 RELATED DB: PDB REMARK 900 BELONGS TO THE SAME FAMILY OF DNA STRUCTURES REMARK 900 RELATED ID: 284D RELATED DB: PDB REMARK 900 BELONGS TO THE SAME FAMILY OF DNA STRUCTURES REMARK 900 RELATED ID: 184D RELATED DB: PDB REMARK 900 BELONGS TO THE SAME FAMILY OF DNA STRUCTURES
DBREF 2HK4 A 1 8 PDB 2HK4 2HK4 1 8 DBREF 2HK4 B 1 8 PDB 2HK4 2HK4 1 8
SEQRES 1 A 8 DC DC DG DT DC DC DG DT SEQRES 1 B 8 DC DC DG DT DC DC DG DT
LINK P DC A 1 O3' DT A 8 1555 1555 1.61 LINK P DC B 1 O3' DT B 8 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