Header list of 1ybn.pdb file
Complete list - 6 201 Bytes
HEADER DNA 21-DEC-04 1YBN TITLE SOLUTION STRUCTURE OF THE 3'E TOPOLOGY OF THE I-MOTIF TETRAMER OF TITLE 2 D(CCCCAA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*CP*CP*AP*A)-3'; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: I-MOTIF WITH A DISTINCT TOPOLOGY SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DNA; I-MOTIF; HEMIPROTONATED CYTIDINE; TETRAHYMENA; TELOMER, DNA EXPDTA SOLUTION NMR AUTHOR N.ESMAILI,J.-L.LEROY REVDAT 4 06-JUN-18 1YBN 1 SOURCE REMARK REVDAT 3 24-FEB-09 1YBN 1 VERSN REVDAT 2 15-FEB-05 1YBN 1 JRNL REVDAT 1 11-JAN-05 1YBN 0 JRNL AUTH N.ESMAILI,J.-L.LEROY JRNL TITL I-MOTIF SOLUTION STRUCTURE AND DYNAMICS OF THE D(AACCCC) AND JRNL TITL 2 D(CCCCAA) TETRAHYMENA TELOMERIC 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR, X-PLOR REMARK 3 AUTHORS : BRUNGER, A.T. (X-PLOR), BRUNGER, A.T. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 54 NOE-DERIVED DISTANCE CONSTRAINTS AND REMARK 3 12 DISTANCES CONSTRAINTS FOR H-BONDING DERIVED FROM PROTON REMARK 3 EXCHANGE MEASUREMENTS REMARK 4 REMARK 4 1YBN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031349. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : NO ADDED SALT REMARK 210 PRESSURE : NORMAL REMARK 210 SAMPLE CONTENTS : PH 4.5 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; HMBC 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 : NULL 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 WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: STANDARD 2 D METHODS 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 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 5 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA A 5 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA A 6 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC B 1 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC B 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC B 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC B 4 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA B 5 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA B 5 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 DA B 6 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 6 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC C 1 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC C 2 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC C 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC C 4 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA C 5 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA C 6 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA C 6 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC D 1 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC D 2 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC D 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC D 4 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA D 5 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA D 5 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DA D 6 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA D 6 N7 - C8 - N9 ANGL. DEV. = 3.7 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 DC A 1 0.06 SIDE CHAIN REMARK 500 DC B 1 0.06 SIDE CHAIN REMARK 500 DC C 1 0.06 SIDE CHAIN REMARK 500 DC D 1 0.06 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: 1YBL RELATED DB: PDB REMARK 900 I-MOTIF, DIFFERENT SEQUENCE REMARK 900 RELATED ID: 1YBR RELATED DB: PDB REMARK 900 I-MOTIF, DISTINCT TOPOLOGY, SAME SEQUENCE DBREF 1YBN A 1 6 PDB 1YBN 1YBN 1 6 DBREF 1YBN B 1 6 PDB 1YBN 1YBN 1 6 DBREF 1YBN C 1 6 PDB 1YBN 1YBN 1 6 DBREF 1YBN D 1 6 PDB 1YBN 1YBN 1 6 SEQRES 1 A 6 DC DC DC DC DA DA SEQRES 1 B 6 DC DC DC DC DA DA SEQRES 1 C 6 DC DC DC DC DA DA SEQRES 1 D 6 DC DC DC DC DA DA 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
Complete list - 6 201 Bytes