10 20 30 40 50 60 70 80 2K8Z - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 29-SEP-08 2K8Z
TITLE DIMERIC SOLUTION STRUCTURE OF THE DNA LOOP D(TCGTTGCT)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*CP*GP*TP*TP*GP*CP*T)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS DNA, QUADRUPLEX, DNA-LOOP, MINOR GROOVE TETRAD
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR J.VILADOMS,N.ESCAJA,M.FRIEDEN,I.GOMEZ-PINTO,E.PEDROSO, AUTHOR 2 C.GONZALEZ
REVDAT 2 23-JUN-09 2K8Z 1 JRNL REVDAT 1 28-APR-09 2K8Z 0
JRNL AUTH J.VILADOMS,N.ESCAJA,M.FRIEDEN,I.GOMEZ-PINTO, JRNL AUTH 2 E.PEDROSO,C.GONZALEZ JRNL TITL SELF-ASSOCIATION OF SHORT DNA LOOPS THROUGH MINOR JRNL TITL 2 GROOVE C:G:G:C TETRADS. JRNL REF NUCLEIC ACIDS RES. V. 37 3264 2009 JRNL REFN ISSN 0305-1048 JRNL PMID 19321501 JRNL DOI 10.1093/NAR/GKP191
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA REMARK 3 AUTHORS : GUNTERT, BRAUN AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2K8Z COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-08. REMARK 100 THE RCSB ID CODE IS RCSB100826.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.1-2.0 MM DNA (5'-D(*DTP* REMARK 210 DCP*DGP*DTP*DTP*DGP*DCP*DT)-3'), 25 MM SODIUM PHOSPHATE, 100 REMARK 210 MM SODIUM CHLORIDE, 10 MM MAGNESIUM CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H REMARK 210 TOCSY; 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX; DPX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER, DYANA, SPARKY REMARK 210 METHOD USED : 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 DT A 1 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 6 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DG A 6 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DT B 9 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT B 9 O4' - C1' - C2' ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT B 9 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DC B 10 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT B 12 O4' - C1' - N1 ANGL. DEV. = 8.0 DEGREES REMARK 500 1 DT B 13 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG B 14 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT B 16 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DT A 1 C5 - C6 - N1 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT A 1 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 2 DT A 4 C5 - C6 - N1 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DG A 6 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = -7.2 DEGREES REMARK 500 2 DG A 6 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DT A 8 C6 - C5 - C7 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DT B 9 C5 - C6 - N1 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DT B 9 C4 - C5 - C7 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DT B 9 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DC B 10 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 DT B 12 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DT B 12 C5 - C6 - N1 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DT B 12 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DT B 13 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DT B 13 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DG B 14 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DG B 14 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT B 16 C4 - C5 - C6 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DT B 16 C5 - C6 - N1 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT B 16 C6 - C5 - C7 ANGL. DEV. = -6.3 DEGREES REMARK 500 3 DT A 1 C5 - C6 - N1 ANGL. DEV. = -4.0 DEGREES REMARK 500 3 DT A 1 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 3 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 7.5 DEGREES REMARK 500 3 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 180 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 3 0.05 SIDE_CHAIN REMARK 500 1 DG B 11 0.06 SIDE_CHAIN REMARK 500 2 DG A 3 0.05 SIDE_CHAIN REMARK 500 2 DG B 11 0.07 SIDE_CHAIN REMARK 500 2 DT B 13 0.06 SIDE_CHAIN REMARK 500 2 DC B 15 0.08 SIDE_CHAIN REMARK 500 3 DC A 2 0.07 SIDE_CHAIN REMARK 500 3 DG A 3 0.08 SIDE_CHAIN REMARK 500 3 DG A 6 0.06 SIDE_CHAIN REMARK 500 4 DC A 7 0.07 SIDE_CHAIN REMARK 500 4 DG B 11 0.07 SIDE_CHAIN REMARK 500 5 DG A 3 0.05 SIDE_CHAIN REMARK 500 5 DC B 15 0.08 SIDE_CHAIN REMARK 500 6 DG A 3 0.07 SIDE_CHAIN REMARK 500 6 DT A 5 0.07 SIDE_CHAIN REMARK 500 6 DC A 7 0.06 SIDE_CHAIN REMARK 500 6 DG B 14 0.07 SIDE_CHAIN REMARK 500 7 DG A 3 0.06 SIDE_CHAIN REMARK 500 7 DC A 7 0.06 SIDE_CHAIN REMARK 500 8 DG A 3 0.07 SIDE_CHAIN REMARK 500 8 DT B 9 0.10 SIDE_CHAIN REMARK 500 8 DG B 11 0.07 SIDE_CHAIN REMARK 500 9 DG A 6 0.05 SIDE_CHAIN REMARK 500 9 DT B 12 0.07 SIDE_CHAIN REMARK 500 9 DG B 14 0.06 SIDE_CHAIN REMARK 500 10 DG A 3 0.05 SIDE_CHAIN REMARK 500 10 DG B 11 0.06 SIDE_CHAIN REMARK 500 10 DC B 15 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K90 RELATED DB: PDB REMARK 900 STRUCTURE OF THE LINEAL ANALOGUE D(TGCTTCGT) REMARK 900 RELATED ID: 2K97 RELATED DB: PDB REMARK 900 STRUCTURE OF CYCLIC OCTAMER D(CGCTCCGT) REMARK 900 RELATED ID: 16212 RELATED DB: BMRB
DBREF 2K8Z A 1 8 PDB 2K8Z 2K8Z 1 8 DBREF 2K8Z B 9 16 PDB 2K8Z 2K8Z 9 16
SEQRES 1 A 8 DT DC DG DT DT DG DC DT SEQRES 1 B 8 DT DC DG DT DT DG DC DT
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