10 20 30 40 50 60 70 80 1PQT - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 19-JUN-03 1PQT
TITLE REFINEMENT OF D(GCGAAGC) HAIRPIN STRUCTURE USING ONE- AND TITLE 2 TWO-BOND RESIDUAL DIPOLAR COUPLINGS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*AP*AP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN SOURCE 4 REPLICATION ORIGINS OF PHAGE PHIX174, IN HERPES SIMPLEX SOURCE 5 VIRUS, IN E. COLI HEAT-SHOCK GENE AND RRNA GENES.
KEYWDS HAIRPIN, DNA, GA MISMATCH
EXPDTA SOLUTION NMR
NUMMDL 14
AUTHOR P.PADRTA,R.STEFL,L.ZIDEK,V.SKLENAR
REVDAT 2 24-FEB-09 1PQT 1 VERSN REVDAT 1 01-JUL-03 1PQT 0
JRNL AUTH P.PADRTA,R.STEFL,L.KRALIK,L.ZIDEK,V.SKLENAR JRNL TITL REFINEMENT OF D(GCGAAGC) HAIRPIN STRUCTURE USING JRNL TITL 2 ONE- AND TWO-BOND RESIDUAL DIPOLAR COUPLINGS JRNL REF J.BIOMOL.NMR V. 24 1 2002 JRNL REFN ISSN 0925-2738 JRNL PMID 12449414 JRNL DOI 10.1023/A:1020632900961
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 REMARK 3 AUTHORS : KOLLMAN, CASE ET. AL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1PQT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-03. REMARK 100 THE RCSB ID CODE IS RCSB019514.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 10 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 6MM NATURAL ABUNDANCE REMARK 210 D(GCGAAGC), 10MM PHOSPHATE REMARK 210 BUFFER NA, D2O; 6MM NATURAL REMARK 210 ABUNDANCE D(GCGAAGC), 10MM REMARK 210 PHOSPHATE BUFFER NA, 90% H2O, REMARK 210 10% D2O; U-15N,13C, 0.5MM REMARK 210 D(GCGAAGC), 10MM PHOSPHATE REMARK 210 BUFFER NA, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, E-COSY, DQF-COSY, REMARK 210 COUPLED HSQC, S3E E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.1, XWINNMR 3.0, REMARK 210 SPARKY 3.X, AMBER 7.0 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 14 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 7 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY IN ISOTROPIC AND LIQUID CRYSTALLINE PHASE.
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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 3 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 3 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 4 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 4 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 5 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 5 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 5 DG A 6 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 DG A 1 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 6 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 6 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 6 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 6 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 7 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 7 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 7 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 8 DG A 1 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 8 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 93 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 DA A 4 0.09 SIDE_CHAIN REMARK 500 1 DA A 5 0.06 SIDE_CHAIN REMARK 500 1 DG A 6 0.07 SIDE_CHAIN REMARK 500 2 DA A 4 0.09 SIDE_CHAIN REMARK 500 2 DA A 5 0.07 SIDE_CHAIN REMARK 500 3 DA A 4 0.09 SIDE_CHAIN REMARK 500 3 DA A 5 0.06 SIDE_CHAIN REMARK 500 4 DA A 4 0.08 SIDE_CHAIN REMARK 500 4 DA A 5 0.06 SIDE_CHAIN REMARK 500 5 DA A 4 0.09 SIDE_CHAIN REMARK 500 5 DA A 5 0.06 SIDE_CHAIN REMARK 500 5 DG A 6 0.06 SIDE_CHAIN REMARK 500 6 DA A 4 0.08 SIDE_CHAIN REMARK 500 6 DA A 5 0.07 SIDE_CHAIN REMARK 500 7 DA A 4 0.08 SIDE_CHAIN REMARK 500 7 DA A 5 0.07 SIDE_CHAIN REMARK 500 8 DA A 4 0.07 SIDE_CHAIN REMARK 500 8 DA A 5 0.06 SIDE_CHAIN REMARK 500 9 DA A 4 0.08 SIDE_CHAIN REMARK 500 9 DA A 5 0.07 SIDE_CHAIN REMARK 500 10 DA A 4 0.09 SIDE_CHAIN REMARK 500 10 DA A 5 0.08 SIDE_CHAIN REMARK 500 11 DA A 4 0.08 SIDE_CHAIN REMARK 500 11 DA A 5 0.07 SIDE_CHAIN REMARK 500 12 DA A 4 0.08 SIDE_CHAIN REMARK 500 12 DA A 5 0.06 SIDE_CHAIN REMARK 500 12 DG A 6 0.06 SIDE_CHAIN REMARK 500 13 DA A 4 0.08 SIDE_CHAIN REMARK 500 13 DA A 5 0.07 SIDE_CHAIN REMARK 500 14 DA A 4 0.08 SIDE_CHAIN REMARK 500 14 DA A 5 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KR8 RELATED DB: PDB REMARK 900 1KR8 IS THE SAME DNA HAIRPIN BUT CALCULATED WITH THE SIMPLE REMARK 900 PARABOLIC POTENTIAL AS THE PENALTY FUNCTION FOR RDC REMARK 900 RESTRAINTS, UNLIKE THIS ENTRY WHERE THE FLAT-BOTTOM REMARK 900 POTENTIAL WAS USED FOR RDCS INSTEAD.
DBREF 1PQT A 1 7 PDB 1PQT 1PQT 1 7
SEQRES 1 A 7 DG DC DG DA DA DG DC
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