HEADER DNA 26-JAN-00 1ECU TITLE SOLUTION STRUCTURE OF E2F BINDING DNA FRAGMENT GCGCGAAAC-T-GTTTCGCGC COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*GP*CP*GP*CP*GP*AP*AP*AP*CP*TP*GP*TP*TP*TP*CP*GP*CP*GP*C)-3'); COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: FRAGMENT OF E2F BINDING DNA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE SEQUENCE IS FORMED BY ADDING CTG LOOP TO ENDS OF SOURCE 4 DS(GCGCGAAA:TTTCGCGC), WHICH OCCURS NATURALLY IN HUMANS. KEYWDS DOUBLE STRANDS, LOOP, DNA EXPDTA SOLUTION NMR NUMMDL 2 AUTHOR J.H.WU,C.CHANG,J.M.PEI,Q.XIAO,Y.Y.SHI REVDAT 3 16-FEB-22 1ECU 1 REMARK REVDAT 2 24-FEB-09 1ECU 1 VERSN REVDAT 1 02-FEB-00 1ECU 0 JRNL AUTH J.H.WU,C.CHANG,J.M.PEI,Q.XIAO,Y.Y.SHI JRNL TITL SOLUTION STRUCTURE OF E2F BINDING DNA FRAGMENT JRNL TITL 2 GCGCGAAAC-T-GTTTCGCGC STUDIED BY MOLECULAR DYNAMICS JRNL TITL 3 SIMULATION AND TWO DIMENSIONAL NMR EXPERIMENT JRNL REF TO BE PUBLISHED 2000 JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 1.1, GROMOS 96 REMARK 3 AUTHORS : BRUKER (XWINNMR), W.F.VAN GUNSTEREN (GROMOS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INITIAL STRUCTURE FOR MODEL 1 IS A-DNA, REMARK 3 WHILE THAT FOR MODEL 2 IS B-DNA. FIRST WE APPLIED 640PS FREE MD REMARK 3 WITH 18 NA+ COUNTERIONS AND 2789 WATERS FOR A-DNA AND 2303 REMARK 3 WATERS FOR B-DNA. THEN WE APPLIED 4 CYCLES OF IRMA WITH 174 NOE REMARK 3 RESTRAINTS AND 19 HYDROGEN BOND RESTRAINTS REMARK 4 REMARK 4 1ECU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1000010455. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 150MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 3.5MM DNA FRAGMENT; 50MM REMARK 210 PHOSPHATE BUFFER, PH 7.0; 150MM REMARK 210 NACL; 1MM EDTA; 1MM NAN3; 90% REMARK 210 H2O, 10% D2O; SAME AS 1 EXCEPT REMARK 210 IN D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : IRMA 0.1 REMARK 210 METHOD USED : MOLECULAR DYNAMICS WITH PARTICLE REMARK 210 -PARTICLE PARTICLE-MESH METHOD; REMARK 210 ITERATIVE RELAXATION MATRIX REMARK 210 APPROACH WITH GENERALIZED ORDER REMARK 210 PARAMETERS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 2 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 2 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: SOLVENT SUPPRESSION WAS REALIZED BY WATERGATE METHOD. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 DG A 1 C5 DG A 1 N7 -0.076 REMARK 500 1 DG A 1 C8 DG A 1 N9 -0.061 REMARK 500 1 DG A 1 N9 DG A 1 C4 -0.060 REMARK 500 1 DG A 3 C5 DG A 3 N7 -0.068 REMARK 500 1 DG A 3 C8 DG A 3 N9 -0.053 REMARK 500 1 DG A 3 N9 DG A 3 C4 -0.054 REMARK 500 1 DG A 3 O3' DC A 4 P -0.090 REMARK 500 1 DC A 4 P DC A 4 OP1 -0.109 REMARK 500 1 DG A 5 C5 DG A 5 N7 -0.066 REMARK 500 1 DG A 5 C8 DG A 5 N9 -0.053 REMARK 500 1 DG A 5 N9 DG A 5 C4 -0.052 REMARK 500 1 DA A 6 C5 DA A 6 N7 -0.069 REMARK 500 1 DA A 6 C8 DA A 6 N9 -0.053 REMARK 500 1 DA A 6 N9 DA A 6 C4 -0.054 REMARK 500 1 DA A 7 C5 DA A 7 N7 -0.069 REMARK 500 1 DA A 7 C8 DA A 7 N9 -0.051 REMARK 500 1 DA A 7 N9 DA A 7 C4 -0.053 REMARK 500 1 DA A 8 C5 DA A 8 N7 -0.067 REMARK 500 1 DA A 8 C8 DA A 8 N9 -0.051 REMARK 500 1 DA A 8 N9 DA A 8 C4 -0.051 REMARK 500 1 DT A 10 C4 DT A 10 C5 -0.072 REMARK 500 1 DG A 11 C5 DG A 11 N7 -0.070 REMARK 500 1 DG A 11 C8 DG A 11 N9 -0.053 REMARK 500 1 DG A 11 N9 DG A 11 C4 -0.058 REMARK 500 1 DT A 12 C4 DT A 12 C5 -0.070 REMARK 500 1 DT A 13 C4 DT A 13 C5 -0.069 REMARK 500 1 DT A 14 C4 DT A 14 C5 -0.066 REMARK 500 1 DC A 15 C4 DC A 15 C5 -0.051 REMARK 500 1 DG A 16 C5 DG A 16 N7 -0.070 REMARK 500 1 DG A 16 C8 DG A 16 N9 -0.058 REMARK 500 1 DG A 16 N9 DG A 16 C4 -0.055 REMARK 500 1 DG A 18 C5 DG A 18 N7 -0.072 REMARK 500 1 DG A 18 C8 DG A 18 N9 -0.057 REMARK 500 1 DG A 18 N9 DG A 18 C4 -0.059 REMARK 500 1 DC A 19 C4 DC A 19 C5 -0.055 REMARK 500 2 DG A 1 C5 DG A 1 N7 -0.072 REMARK 500 2 DG A 1 C8 DG A 1 N9 -0.057 REMARK 500 2 DG A 1 N9 DG A 1 C4 -0.058 REMARK 500 2 DC A 2 C4 DC A 2 C5 -0.049 REMARK 500 2 DG A 3 C5 DG A 3 N7 -0.069 REMARK 500 2 DG A 3 C8 DG A 3 N9 -0.054 REMARK 500 2 DG A 3 N9 DG A 3 C4 -0.054 REMARK 500 2 DG A 3 O3' DC A 4 P -0.096 REMARK 500 2 DG A 5 P DG A 5 OP1 -0.125 REMARK 500 2 DG A 5 P DG A 5 OP2 -0.118 REMARK 500 2 DG A 5 P DG A 5 O5' -0.127 REMARK 500 2 DG A 5 C5 DG A 5 N7 -0.068 REMARK 500 2 DG A 5 C8 DG A 5 N9 -0.053 REMARK 500 2 DG A 5 N9 DG A 5 C4 -0.052 REMARK 500 2 DA A 6 C5 DA A 6 N7 -0.068 REMARK 500 REMARK 500 THIS ENTRY HAS 77 BOND DEVIATIONS. 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 DG A 1 C6 - N1 - C2 ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DG A 1 C2 - N3 - C4 ANGL. DEV. = 9.5 DEGREES REMARK 500 1 DG A 1 N3 - C4 - C5 ANGL. DEV. = -9.1 DEGREES REMARK 500 1 DG A 1 C5 - C6 - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DG A 1 C4 - C5 - N7 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DG A 1 N3 - C4 - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DG A 1 N1 - C2 - N2 ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DG A 1 N3 - C2 - N2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 1 C5 - C6 - O6 ANGL. DEV. = -9.5 DEGREES REMARK 500 1 DG A 1 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 1 DC A 2 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DC A 2 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 3 C6 - N1 - C2 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DG A 3 C2 - N3 - C4 ANGL. DEV. = 9.3 DEGREES REMARK 500 1 DG A 3 N3 - C4 - C5 ANGL. DEV. = -8.4 DEGREES REMARK 500 1 DG A 3 C5 - C6 - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 DG A 3 C4 - C5 - N7 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DG A 3 C5 - N7 - C8 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 3 N3 - C4 - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DG A 3 N1 - C2 - N2 ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DG A 3 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 3 C5 - C6 - O6 ANGL. DEV. = -9.0 DEGREES REMARK 500 1 DG A 3 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 1 DC A 4 C5' - C4' - O4' ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DC A 4 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DC A 4 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC A 4 N3 - C4 - C5 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 5 C6 - N1 - C2 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DG A 5 C2 - N3 - C4 ANGL. DEV. = 9.5 DEGREES REMARK 500 1 DG A 5 N3 - C4 - C5 ANGL. DEV. = -8.3 DEGREES REMARK 500 1 DG A 5 C5 - C6 - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DG A 5 C4 - C5 - N7 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DG A 5 C5 - N7 - C8 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 5 N3 - C4 - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DG A 5 N1 - C2 - N2 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DG A 5 C5 - C6 - O6 ANGL. DEV. = -8.3 DEGREES REMARK 500 1 DA A 6 N1 - C2 - N3 ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DA A 6 C2 - N3 - C4 ANGL. DEV. = 9.9 DEGREES REMARK 500 1 DA A 6 N3 - C4 - C5 ANGL. DEV. = -8.6 DEGREES REMARK 500 1 DA A 6 N3 - C4 - N9 ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DA A 6 N1 - C6 - N6 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DA A 6 C5 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DA A 7 N1 - C2 - N3 ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DA A 7 C2 - N3 - C4 ANGL. DEV. = 9.6 DEGREES REMARK 500 1 DA A 7 N3 - C4 - C5 ANGL. DEV. = -8.2 DEGREES REMARK 500 1 DA A 7 N3 - C4 - N9 ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DA A 7 N1 - C6 - N6 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 8 N1 - C2 - N3 ANGL. DEV. = -6.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 216 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 5 0.06 SIDE CHAIN REMARK 500 1 DA A 6 0.06 SIDE CHAIN REMARK 500 1 DA A 8 0.12 SIDE CHAIN REMARK 500 1 DC A 9 0.16 SIDE CHAIN REMARK 500 1 DG A 11 0.19 SIDE CHAIN REMARK 500 1 DT A 12 0.09 SIDE CHAIN REMARK 500 1 DC A 19 0.11 SIDE CHAIN REMARK 500 2 DA A 6 0.08 SIDE CHAIN REMARK 500 2 DC A 9 0.18 SIDE CHAIN REMARK 500 2 DG A 11 0.08 SIDE CHAIN REMARK 500 2 DT A 12 0.09 SIDE CHAIN REMARK 500 2 DC A 17 0.06 SIDE CHAIN REMARK 500 2 DC A 19 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1ECU A 1 19 PDB 1ECU 1ECU 1 19 SEQRES 1 A 19 DG DC DG DC DG DA DA DA DC DT DG DT DT SEQRES 2 A 19 DT DC DG DC 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 MODEL 1