HEADER 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 4 29-MAY-24 2F1Q 1 REMARK REVDAT 3 09-MAR-22 2F1Q 1 REMARK 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 THE JRNL TITL 2 PRESENCE OF COBALT ION JRNL REF TO BE PUBLISHED JRNL REFN 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 DEPOSITION ID IS D_1000035343. 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, 6MM REMARK 210 CO(NH3)6CL3, 50 MM NACL, 0.1 MM REMARK 210 NA2EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 400 MHZ; 500 MHZ; 800 REMARK 210 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 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 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. = 4.7 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 MODEL 1