10 20 30 40 50 60 70 80 1YBL - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 21-DEC-04 1YBL
TITLE NMR STRUCTURE OF THE I-MOTIF TETRAMER OF D(AACCCC)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*AP*CP*CP*CP*C)-3'; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS DNA; I-MOTIF; HEMIPROTONATED CYTIDINE; TETRAHYMENA; TELOMER
EXPDTA SOLUTION NMR
AUTHOR N.ESMAILI,J.-L.LEROY
REVDAT 3 24-FEB-09 1YBL 1 VERSN REVDAT 2 15-FEB-05 1YBL 1 JRNL REVDAT 1 11-JAN-05 1YBL 0
JRNL AUTH N.ESMAILI,J.-L.LEROY JRNL TITL I-MOTIF SOLUTION STRUCTURE AND DYNAMICS OF THE JRNL TITL 2 D(AACCCC) AND D(CCCCAA) TETRAHYMENA TELOMERIC JRNL TITL 3 REPEATS JRNL REF NUCLEIC ACIDS RES. V. 33 213 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 15647504 JRNL DOI 10.1093/NAR/GKI160
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER A.T. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 96 NOE-DERIVED DISTANCES CONSTRAINTS REMARK 3 AND 12 DISTANCE RESTRAINTS FOR HYDROGEN BONDS DERIVED FROM REMARK 3 PROTON EXCHANGE MEASUREMENTS
REMARK 4 REMARK 4 1YBL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-DEC-04. REMARK 100 THE RCSB ID CODE IS RCSB031347.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 0 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : NO ADDED SALT REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : PH 4.5 TO 6 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.851 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE REMARK 210 WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES
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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA A 1 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DA A 2 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA A 2 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA B 1 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA B 1 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA B 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DA B 2 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA B 2 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC B 3 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC B 4 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DC B 5 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC B 6 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA C 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA C 1 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA C 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DA C 2 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DA C 2 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC C 3 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC C 4 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC C 5 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC C 6 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA D 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA D 1 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA D 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DA D 2 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA D 2 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC D 3 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DC D 4 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC D 5 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC D 6 O4' - C1' - N1 ANGL. DEV. = 2.8 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 DA A 1 0.09 SIDE_CHAIN REMARK 500 DA A 2 0.06 SIDE_CHAIN REMARK 500 DC A 3 0.06 SIDE_CHAIN REMARK 500 DC A 4 0.08 SIDE_CHAIN REMARK 500 DA B 1 0.09 SIDE_CHAIN REMARK 500 DA B 2 0.06 SIDE_CHAIN REMARK 500 DC B 3 0.07 SIDE_CHAIN REMARK 500 DC B 4 0.08 SIDE_CHAIN REMARK 500 DA C 1 0.09 SIDE_CHAIN REMARK 500 DA C 2 0.06 SIDE_CHAIN REMARK 500 DC C 3 0.06 SIDE_CHAIN REMARK 500 DC C 4 0.08 SIDE_CHAIN REMARK 500 DA D 1 0.09 SIDE_CHAIN REMARK 500 DA D 2 0.06 SIDE_CHAIN REMARK 500 DC D 3 0.07 SIDE_CHAIN REMARK 500 DC D 4 0.09 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 294D RELATED DB: PDB REMARK 900 THE X-RAY STRUCTURE OF THE SAME I-MOTIF TETRAMER REMARK 900 RELATED ID: 1YBN RELATED DB: PDB REMARK 900 I-MOTIF, DIFFERENT SEQUENCE, TOPOLOGY 1 REMARK 900 RELATED ID: 1YBR RELATED DB: PDB REMARK 900 I-MOTIF, DIFFERENT SEQUENCE, TOPOLOGY 2
DBREF 1YBL A 1 6 PDB 1YBL 1YBL 1 6 DBREF 1YBL B 1 6 PDB 1YBL 1YBL 1 6 DBREF 1YBL C 1 6 PDB 1YBL 1YBL 1 6 DBREF 1YBL D 1 6 PDB 1YBL 1YBL 1 6
SEQRES 1 A 6 DA DA DC DC DC DC SEQRES 1 B 6 DA DA DC DC DC DC SEQRES 1 C 6 DA DA DC DC DC DC SEQRES 1 D 6 DA DA DC DC DC 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