HEADER DNA 11-MAY-00 1EZN TITLE SOLUTION STRUCTURE OF A DNA THREE-WAY JUNCTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA THREE-WAY JUNCTION; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA, THREE-WAY JUNCTION, FOUR-WAY JUNCTION, HMG-BOX PROTEIN, HOLLIDAY KEYWDS 2 JUNCTION, HAMMERHEAD EXPDTA SOLUTION NMR NUMMDL 26 AUTHOR B.N.M.VAN BUUREN,F.J.OVERMARS,J.H.IPPEL,C.ALTONA,S.S.WIJMENGA REVDAT 4 16-FEB-22 1EZN 1 REMARK REVDAT 3 24-FEB-09 1EZN 1 VERSN REVDAT 2 01-APR-03 1EZN 1 JRNL REVDAT 1 21-APR-01 1EZN 0 JRNL AUTH B.N.VAN BUUREN,F.J.OVERMARS,J.H.IPPEL,C.ALTONA,S.S.WIJMENGA JRNL TITL SOLUTION STRUCTURE OF A DNA THREE-WAY JUNCTION CONTAINING JRNL TITL 2 TWO UNPAIRED THYMIDINE BASES. IDENTIFICATION OF SEQUENCE JRNL TITL 3 FEATURES THAT DECIDE CONFORMER SELECTION. JRNL REF J.MOL.BIOL. V. 304 371 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 11090280 JRNL DOI 10.1006/JMBI.2000.4224 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.J.OVERMARS,J.A.PIKKEMAAT,H.VAN DEN ELST,J.H.VAN BOOM, REMARK 1 AUTH 2 C.ALTONA REMARK 1 TITL NMR STUDIES OF DNA THREE-WAY JUNCTIONS CONTAINING TWO REMARK 1 TITL 2 UNPAIRED THYMIDINE BASES: THE INFLUENCE OF THE SEQUENCE AT REMARK 1 TITL 3 THE JUNCTION ON THE STABILITY OF THE STACKING CONFORMERS. REMARK 1 REF J.MOL.BIOL. V. 255 702 1996 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1996.0057 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 1EZN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-00. REMARK 100 THE DEPOSITION ID IS D_1000011063. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 50MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM DNA 3H; 50MM NACL; REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX 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 : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 26 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM, REMARK 210 STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS,STRUCTURES WITH THE REMARK 210 LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL 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 3 C5 DT A 3 C7 0.056 REMARK 500 1 DT A 12 C5 DT A 12 C7 0.056 REMARK 500 1 DT A 13 C5 DT A 13 C7 0.055 REMARK 500 1 DT A 22 C5 DT A 22 C7 0.056 REMARK 500 1 DT A 23 C5 DT A 23 C7 0.055 REMARK 500 1 DT A 25 C5 DT A 25 C7 0.055 REMARK 500 1 DT A 28 C5 DT A 28 C7 0.055 REMARK 500 1 DT A 29 C5 DT A 29 C7 0.049 REMARK 500 1 DT A 31 C5 DT A 31 C7 0.057 REMARK 500 2 DT A 3 C5 DT A 3 C7 0.056 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 DT A 22 C5 DT A 22 C7 0.056 REMARK 500 2 DT A 23 C5 DT A 23 C7 0.054 REMARK 500 2 DT A 25 C5 DT A 25 C7 0.056 REMARK 500 2 DT A 28 C5 DT A 28 C7 0.054 REMARK 500 2 DT A 29 C5 DT A 29 C7 0.050 REMARK 500 2 DT A 31 C5 DT A 31 C7 0.057 REMARK 500 3 DT A 3 C5 DT A 3 C7 0.056 REMARK 500 3 DT A 12 C5 DT A 12 C7 0.056 REMARK 500 3 DT A 13 C5 DT A 13 C7 0.054 REMARK 500 3 DT A 22 C5 DT A 22 C7 0.056 REMARK 500 3 DT A 23 C5 DT A 23 C7 0.055 REMARK 500 3 DT A 25 C5 DT A 25 C7 0.055 REMARK 500 3 DT A 28 C5 DT A 28 C7 0.056 REMARK 500 3 DT A 29 C5 DT A 29 C7 0.051 REMARK 500 3 DT A 31 C5 DT A 31 C7 0.056 REMARK 500 4 DT A 3 C5 DT A 3 C7 0.056 REMARK 500 4 DT A 12 C5 DT A 12 C7 0.056 REMARK 500 4 DT A 13 C5 DT A 13 C7 0.054 REMARK 500 4 DT A 22 C5 DT A 22 C7 0.057 REMARK 500 4 DT A 23 C5 DT A 23 C7 0.054 REMARK 500 4 DT A 25 C5 DT A 25 C7 0.055 REMARK 500 4 DT A 28 C5 DT A 28 C7 0.053 REMARK 500 4 DT A 29 C5 DT A 29 C7 0.050 REMARK 500 4 DT A 31 C5 DT A 31 C7 0.057 REMARK 500 5 DT A 3 C5 DT A 3 C7 0.056 REMARK 500 5 DT A 12 C5 DT A 12 C7 0.056 REMARK 500 5 DT A 13 C5 DT A 13 C7 0.055 REMARK 500 5 DT A 22 C5 DT A 22 C7 0.056 REMARK 500 5 DT A 23 C5 DT A 23 C7 0.054 REMARK 500 5 DT A 25 C5 DT A 25 C7 0.056 REMARK 500 5 DT A 28 C5 DT A 28 C7 0.054 REMARK 500 5 DT A 29 C5 DT A 29 C7 0.049 REMARK 500 5 DT A 31 C5 DT A 31 C7 0.056 REMARK 500 6 DT A 3 C5 DT A 3 C7 0.057 REMARK 500 6 DT A 12 C5 DT A 12 C7 0.055 REMARK 500 6 DT A 13 C5 DT A 13 C7 0.054 REMARK 500 6 DC A 18 C5' DC A 18 C4' 0.050 REMARK 500 6 DT A 22 C5 DT A 22 C7 0.057 REMARK 500 REMARK 500 THIS ENTRY HAS 242 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 6 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 6 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG A 10 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 10 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 14 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 14 C8 - N9 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DC A 15 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 16 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 17 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DC A 18 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 19 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 19 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA A 20 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA A 20 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 20 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DC A 21 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 22 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 23 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 24 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG A 24 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 24 C8 - N9 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 25 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DC A 26 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 27 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG A 27 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 27 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DT A 28 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 29 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1674 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1EZN A 1 36 PDB 1EZN 1EZN 1 36 SEQRES 1 A 36 DC DG DT DG DC DA DC DC DC DG DC DT DT SEQRES 2 A 36 DG DC DG DG DC DG DA DC DT DT DG DT DC SEQRES 3 A 36 DG DT DT DG DT DG DC DA DC DG 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