Header list of 1s88.pdb file
Complete list - r 2 2 Bytes
HEADER DNA 31-JAN-04 1S88 TITLE NMR STRUCTURE OF A DNA DUPLEX WITH TWO INA NUCLEOTIDES INSERTED TITLE 2 OPPOSITE EACH OTHER, DCTCAACXCAAGCT:DAGCTTGXGTTGAG COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*TP*CP*AP*AP*CP*(2DM)P*CP*AP*AP*GP*CP*T)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*AP*GP*CP*TP*TP*GP*(2DM)P*GP*TP*TP*GP*AP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.B.NIELSEN,M.PETERSEN,E.B.PEDERSEN,P.E.HANSEN,U.B.CHRISTENSEN REVDAT 3 02-MAR-22 1S88 1 REMARK LINK REVDAT 2 24-FEB-09 1S88 1 VERSN REVDAT 1 25-MAY-04 1S88 0 JRNL AUTH C.B.NIELSEN,M.PETERSEN,E.B.PEDERSEN,P.E.HANSEN, JRNL AUTH 2 U.B.CHRISTENSEN JRNL TITL NMR STRUCTURE DETERMINATION OF A MODIFIED DNA JRNL TITL 2 OLIGONUCLEOTIDE CONTAINING A NEW INTERCALATING NUCLEIC ACID. JRNL REF BIOCONJUG.CHEM. V. 15 260 2004 JRNL REFN ISSN 1043-1802 JRNL PMID 15025521 JRNL DOI 10.1021/BC0341932 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 6 REMARK 3 AUTHORS : CASE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1S88 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000021490. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.9MM DNA, 10MM SODIUM PHOSPHATE REMARK 210 BUFFER, 100MM NACL, 0.05MM EDTA, REMARK 210 100% D2O; 1.9MM DNA, 10MM SODIUM REMARK 210 PHOSPHATE BUFFER, 100MM NACL, REMARK 210 0.05MM EDTA, 90% H2O 10% D20 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 98 REMARK 210 METHOD USED : RESTRAINT MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 DA B 14 C5' DA B 14 C4' 0.054 REMARK 500 2 DA B 14 C5' DA B 14 C4' 0.054 REMARK 500 3 DA B 14 C5' DA B 14 C4' 0.054 REMARK 500 4 DA B 14 C5' DA B 14 C4' 0.053 REMARK 500 5 DA B 14 C5' DA B 14 C4' 0.054 REMARK 500 6 DA B 14 C5' DA B 14 C4' 0.053 REMARK 500 7 DA B 14 C5' DA B 14 C4' 0.055 REMARK 500 8 DA B 14 C5' DA B 14 C4' 0.054 REMARK 500 9 DA B 14 C5' DA B 14 C4' 0.054 REMARK 500 10 DA B 14 C5' DA B 14 C4' 0.054 REMARK 500 11 DA B 14 C5' DA B 14 C4' 0.053 REMARK 500 12 DA B 14 C5' DA B 14 C4' 0.053 REMARK 500 13 DA B 14 C5' DA B 14 C4' 0.055 REMARK 500 14 DA B 14 C5' DA B 14 C4' 0.053 REMARK 500 15 DA B 14 C5' DA B 14 C4' 0.054 REMARK 500 16 DA B 14 C5' DA B 14 C4' 0.053 REMARK 500 17 DA B 14 C5' DA B 14 C4' 0.053 REMARK 500 18 DA B 14 C5' DA B 14 C4' 0.054 REMARK 500 19 DA B 14 C5' DA B 14 C4' 0.055 REMARK 500 20 DA B 14 C5' DA B 14 C4' 0.054 REMARK 500 REMARK 500 REMARK: NULL 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 1 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 2 C4 - C5 - C7 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT A 2 C6 - C5 - C7 ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC A 6 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 1 2DM A 7 C3' - O3' - P ANGL. DEV. = -14.2 DEGREES REMARK 500 1 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG B 15 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DC B 16 C5 - C4 - N4 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 2DM B 20 C3' - O3' - P ANGL. DEV. = -16.8 DEGREES REMARK 500 1 DG B 21 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT B 22 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT B 22 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT B 23 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG B 24 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DA B 25 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DT A 2 C4 - C5 - C7 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DT A 2 C6 - C5 - C7 ANGL. DEV. = -6.4 DEGREES REMARK 500 2 DC A 6 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 2DM A 7 C3' - O3' - P ANGL. DEV. = -11.1 DEGREES REMARK 500 2 DC A 12 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG B 15 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DC B 16 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC B 16 C5 - C4 - N4 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DT B 17 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 2DM B 20 C3' - O3' - P ANGL. DEV. = -16.6 DEGREES REMARK 500 2 DG B 21 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DT B 22 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DT B 23 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 DG B 24 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 2 DA B 25 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DT A 2 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DT A 2 C4 - C5 - C7 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DT A 2 C6 - C5 - C7 ANGL. DEV. = -6.5 DEGREES REMARK 500 3 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DC A 6 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 3 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 2DM A 7 C3' - O3' - P ANGL. DEV. = -9.7 DEGREES REMARK 500 3 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DT A 13 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 3 DG B 15 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 370 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 6 0.06 SIDE CHAIN REMARK 500 1 DC A 8 0.07 SIDE CHAIN REMARK 500 1 DC B 16 0.06 SIDE CHAIN REMARK 500 1 DT B 17 0.10 SIDE CHAIN REMARK 500 1 DG B 21 0.08 SIDE CHAIN REMARK 500 1 DA B 25 0.11 SIDE CHAIN REMARK 500 1 DG B 26 0.07 SIDE CHAIN REMARK 500 2 DT B 17 0.13 SIDE CHAIN REMARK 500 2 DG B 21 0.08 SIDE CHAIN REMARK 500 2 DT B 22 0.07 SIDE CHAIN REMARK 500 2 DG B 24 0.06 SIDE CHAIN REMARK 500 2 DA B 25 0.12 SIDE CHAIN REMARK 500 2 DG B 26 0.05 SIDE CHAIN REMARK 500 3 DA B 14 0.07 SIDE CHAIN REMARK 500 3 DC B 16 0.06 SIDE CHAIN REMARK 500 3 DT B 17 0.09 SIDE CHAIN REMARK 500 3 DG B 21 0.10 SIDE CHAIN REMARK 500 3 DT B 22 0.08 SIDE CHAIN REMARK 500 3 DG B 24 0.06 SIDE CHAIN REMARK 500 3 DA B 25 0.12 SIDE CHAIN REMARK 500 3 DG B 26 0.07 SIDE CHAIN REMARK 500 4 DC A 3 0.08 SIDE CHAIN REMARK 500 4 DA A 10 0.07 SIDE CHAIN REMARK 500 4 DT B 17 0.14 SIDE CHAIN REMARK 500 4 DG B 21 0.07 SIDE CHAIN REMARK 500 4 DG B 24 0.07 SIDE CHAIN REMARK 500 4 DA B 25 0.11 SIDE CHAIN REMARK 500 5 DC A 3 0.09 SIDE CHAIN REMARK 500 5 DA A 10 0.06 SIDE CHAIN REMARK 500 5 DT B 17 0.09 SIDE CHAIN REMARK 500 5 DG B 21 0.10 SIDE CHAIN REMARK 500 5 DG B 24 0.07 SIDE CHAIN REMARK 500 5 DA B 25 0.10 SIDE CHAIN REMARK 500 6 DA B 14 0.07 SIDE CHAIN REMARK 500 6 DC B 16 0.06 SIDE CHAIN REMARK 500 6 DT B 17 0.08 SIDE CHAIN REMARK 500 6 DG B 21 0.08 SIDE CHAIN REMARK 500 6 DG B 24 0.07 SIDE CHAIN REMARK 500 6 DA B 25 0.11 SIDE CHAIN REMARK 500 6 DG B 26 0.06 SIDE CHAIN REMARK 500 7 DA A 9 0.06 SIDE CHAIN REMARK 500 7 DA B 14 0.09 SIDE CHAIN REMARK 500 7 DT B 17 0.12 SIDE CHAIN REMARK 500 7 DG B 21 0.08 SIDE CHAIN REMARK 500 7 DG B 24 0.06 SIDE CHAIN REMARK 500 7 DA B 25 0.12 SIDE CHAIN REMARK 500 7 DG B 26 0.06 SIDE CHAIN REMARK 500 8 DA A 4 0.06 SIDE CHAIN REMARK 500 8 DC B 16 0.06 SIDE CHAIN REMARK 500 8 DT B 17 0.08 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 127 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1S88 A 1 13 PDB 1S88 1S88 1 13 DBREF 1S88 B 14 26 PDB 1S88 1S88 14 26 SEQRES 1 A 13 DC DT DC DA DA DC 2DM DC DA DA DG DC DT SEQRES 1 B 13 DA DG DC DT DT DG 2DM DG DT DT DG DA DG HET 2DM A 7 42 HET 2DM B 20 42 HETNAM 2DM 2-HYDROXY-3-(PYREN-1-YLMETHOXY)PROPYL DIHYDROGEN HETNAM 2 2DM PHOSPHATE FORMUL 1 2DM 2(C20 H19 O6 P) LINK O3' DC A 6 P 2DM A 7 1555 1555 1.62 LINK O3' 2DM A 7 P DC A 8 1555 1555 1.63 LINK O3' DG B 19 P 2DM B 20 1555 1555 1.61 LINK O3' 2DM B 20 P DG B 21 1555 1555 1.64 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 MODEL 1
Complete list - r 2 2 Bytes