10 20 30 40 50 60 70 80 2F1Q - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 15-NOV-05 2F1Q
TITLE SOLUTION STRUCTURE OF A DNA HOLLIDAY JUNCTION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 42-MER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS DNA, HOLLIDAY JUNCTION, BRANCHED NUCLEIC ACIDS,GENETIC KEYWDS 2 RECOMBINATION, FOUR-WAY JUNCTION
EXPDTA SOLUTION NMR
NUMMDL 13
AUTHOR B.WU,B.N.M.VAN BUUREN,J.SCHLEUCHER,S.S.WIJMENGA
REVDAT 2 24-FEB-09 2F1Q 1 VERSN REVDAT 1 20-MAR-07 2F1Q 0
JRNL AUTH B.WU,B.N.M VAN BUUREN,J.SCHLEUCHER,S.S.WIJMENGA JRNL TITL THE SOLUTION STRUCTURE OF A FOUR-WAY JUNCTION IN JRNL TITL 2 THE PRESENCE OF COBALT ION JRNL REF TO BE PUBLISHED JRNL REFN
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 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2F1Q COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-05. REMARK 100 THE RCSB ID CODE IS RCSB035343.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 0.5MM DNA HOLLIDAY JUNCTION, REMARK 210 6MM CO(NH3)6CL3, 50 MM NACL, REMARK 210 0.1 MM NA2EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 400 MHZ, 500 MHZ, REMARK 210 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 13 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 13 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 13 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 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 DT A 5 C5 DT A 5 C7 0.054 REMARK 500 1 DT A 9 C5 DT A 9 C7 0.056 REMARK 500 1 DC A 11 C5' DC A 11 C4' 0.043 REMARK 500 1 DT A 12 C5' DT A 12 C4' 0.043 REMARK 500 1 DT A 12 C5 DT A 12 C7 0.055 REMARK 500 1 DT A 13 C5 DT A 13 C7 0.056 REMARK 500 1 DG A 14 C5' DG A 14 C4' 0.046 REMARK 500 1 DC A 19 C5' DC A 19 C4' 0.045 REMARK 500 1 DT A 20 C5' DT A 20 C4' 0.045 REMARK 500 1 DT A 20 C5 DT A 20 C7 0.057 REMARK 500 1 DT A 21 C5 DT A 21 C7 0.055 REMARK 500 1 DG A 22 C5' DG A 22 C4' 0.047 REMARK 500 1 DT A 29 C5 DT A 29 C7 0.058 REMARK 500 1 DT A 30 C5 DT A 30 C7 0.056 REMARK 500 1 DG A 31 C5' DG A 31 C4' 0.045 REMARK 500 1 DT A 32 C5 DT A 32 C7 0.049 REMARK 500 1 DT A 35 C5 DT A 35 C7 0.055 REMARK 500 1 DT A 40 C5 DT A 40 C7 0.056 REMARK 500 2 DT A 5 C5 DT A 5 C7 0.054 REMARK 500 2 DT A 9 C5' DT A 9 C4' 0.045 REMARK 500 2 DT A 9 C5 DT A 9 C7 0.055 REMARK 500 2 DC A 11 C5' DC A 11 C4' 0.046 REMARK 500 2 DT A 12 C5 DT A 12 C7 0.055 REMARK 500 2 DT A 13 C5 DT A 13 C7 0.055 REMARK 500 2 DG A 14 C5' DG A 14 C4' 0.045 REMARK 500 2 DC A 19 C5' DC A 19 C4' 0.044 REMARK 500 2 DT A 20 C5' DT A 20 C4' 0.043 REMARK 500 2 DT A 20 C5 DT A 20 C7 0.056 REMARK 500 2 DT A 21 C5 DT A 21 C7 0.055 REMARK 500 2 DG A 22 C5' DG A 22 C4' 0.048 REMARK 500 2 DT A 29 C5 DT A 29 C7 0.054 REMARK 500 2 DT A 30 C5 DT A 30 C7 0.056 REMARK 500 2 DG A 31 C5' DG A 31 C4' 0.046 REMARK 500 2 DT A 32 C5 DT A 32 C7 0.053 REMARK 500 2 DT A 35 C5 DT A 35 C7 0.057 REMARK 500 2 DT A 40 C5 DT A 40 C7 0.056 REMARK 500 3 DT A 5 C5 DT A 5 C7 0.054 REMARK 500 3 DT A 9 C5' DT A 9 C4' 0.045 REMARK 500 3 DT A 9 C5 DT A 9 C7 0.056 REMARK 500 3 DC A 11 C5' DC A 11 C4' 0.047 REMARK 500 3 DT A 12 C5 DT A 12 C7 0.056 REMARK 500 3 DT A 13 C5 DT A 13 C7 0.057 REMARK 500 3 DG A 14 C5' DG A 14 C4' 0.045 REMARK 500 3 DC A 19 C5' DC A 19 C4' 0.044 REMARK 500 3 DT A 20 C5' DT A 20 C4' 0.044 REMARK 500 3 DT A 20 C5 DT A 20 C7 0.056 REMARK 500 3 DT A 21 C5 DT A 21 C7 0.056 REMARK 500 3 DG A 22 C5' DG A 22 C4' 0.047 REMARK 500 3 DT A 29 C5 DT A 29 C7 0.056 REMARK 500 3 DT A 30 C5 DT A 30 C7 0.055 REMARK 500 REMARK 500 THIS ENTRY HAS 212 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 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 1 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 6 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 6 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA A 8 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 8 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 14 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 15 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 15 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 16 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DA A 16 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 16 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DC A 17 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 18 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 18 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DC A 19 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 20 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 21 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DG A 22 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 22 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DC A 23 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 24 N7 - C8 - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DG A 24 C8 - N9 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DC A 25 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC A 26 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA A 27 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA A 27 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 27 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 DC A 28 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DT A 29 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 30 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 31 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 977 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 43
DBREF 2F1Q A 1 42 PDB 2F1Q 2F1Q 1 42
SEQRES 1 A 42 DG DC DA DC DT DG DC DA DT DC DC DT DT SEQRES 2 A 42 DG DG DA DC DG DC DT DT DG DC DG DC DC SEQRES 3 A 42 DA DC DT DT DG DT DG DG DT DG DC DA DG SEQRES 4 A 42 DT DG DC
HET NCO A 43 25
HETNAM NCO COBALT HEXAMMINE(III)
FORMUL 2 NCO CO H18 N6 3+
SITE 1 AC1 1 DG A 15
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