Header list of 1ecu.pdb file
Complete list - 16 202 Bytes
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
Complete list - 16 202 Bytes