HEADER DNA 09-MAR-00 1EKW TITLE NMR STRUCTURE OF A DNA THREE-WAY JUNCTION CAVEAT 1EKW CHIRALLY INCORRECT C4' OF G 31 CHAIN R COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*CP*CP*AP*CP*CP*G)-3'); COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*GP*GP*TP*GP*CP*GP*TP*CP*C)-3'); COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(*GP*GP*AP*CP*GP*TP*CP*GP*CP*AP*GP*C)-3'); COMPND 11 CHAIN: R; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES KEYWDS THREE-WAY-JUNCTION, UNPAIRED BASES, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR V.THIVIYANATHAN,B.A.LUXON,N.B.LEONTIS,D.DONNE,D.G.GORENSTEIN REVDAT 4 28-DEC-11 1EKW 1 CAVEAT VERSN REVDAT 3 24-FEB-09 1EKW 1 VERSN REVDAT 2 01-APR-03 1EKW 1 JRNL REVDAT 1 20-MAR-00 1EKW 0 JRNL AUTH V.THIVIYANATHAN,B.A.LUXON,N.B.LEONTIS,N.ILLANGASEKARE, JRNL AUTH 2 D.G.DONNE,D.G.GORENSTEIN JRNL TITL HYBRID-HYBRID MATRIX STRUCTURAL REFINEMENT OF A DNA JRNL TITL 2 THREE-WAY JUNCTION FROM 3D NOESY-NOESY. JRNL REF J.BIOMOL.NMR V. 14 209 1999 JRNL REFN ISSN 0925-2738 JRNL PMID 10481274 JRNL DOI 10.1023/A:1008330011425 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PARTICLE MESH EWALD METHODS WERE USED. REMARK 4 REMARK 4 1EKW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-00. REMARK 100 THE RCSB ID CODE IS RCSB010688. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 301 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 100 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2 MM DNA, 0.5MM EDTA, 100 MM REMARK 210 SODIUM PHOSPHATE, 10 MM MGCL2, REMARK 210 100MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D NOESY-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MORASS 2.5 REMARK 210 METHOD USED : COMPLETE RELAXATION MATRIX REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, H, R 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 DT X 3 C6 DT X 3 N1 -0.044 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 DC X 2 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT X 3 O4' - C4' - C3' ANGL. DEV. = 6.8 DEGREES REMARK 500 DT X 3 C4' - C3' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 DT X 3 C4 - C5 - C7 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT X 3 C6 - C5 - C7 ANGL. DEV. = -9.7 DEGREES REMARK 500 DT X 3 C6 - N1 - C1' ANGL. DEV. = -9.9 DEGREES REMARK 500 DG X 4 O4' - C1' - N9 ANGL. DEV. = 9.4 DEGREES REMARK 500 DC X 6 C4' - C3' - C2' ANGL. DEV. = -7.9 DEGREES REMARK 500 DC X 6 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DA X 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC X 8 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC X 9 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC X 9 C6 - N1 - C1' ANGL. DEV. = -7.5 DEGREES REMARK 500 DG X 10 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC H 11 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG H 12 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG H 13 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG H 13 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 DC H 16 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 DC H 16 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG H 17 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT H 18 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC H 19 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC H 20 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG R 22 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC R 24 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DC R 24 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC R 24 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG R 25 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 DG R 25 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT R 26 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 DC R 27 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG R 28 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DA R 30 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG R 31 C4' - C3' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 DC R 32 C5' - C4' - O4' ANGL. DEV. = 6.9 DEGREES REMARK 500 DC R 32 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC R 32 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES 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 DG X 1 0.09 SIDE CHAIN REMARK 500 DT X 3 0.20 SIDE CHAIN REMARK 500 DC X 5 0.12 SIDE CHAIN REMARK 500 DC X 6 0.13 SIDE CHAIN REMARK 500 DA X 7 0.10 SIDE CHAIN REMARK 500 DC X 9 0.11 SIDE CHAIN REMARK 500 DG X 10 0.12 SIDE CHAIN REMARK 500 DG H 13 0.09 SIDE CHAIN REMARK 500 DG H 15 0.14 SIDE CHAIN REMARK 500 DC H 16 0.13 SIDE CHAIN REMARK 500 DC H 19 0.09 SIDE CHAIN REMARK 500 DG R 22 0.09 SIDE CHAIN REMARK 500 DG R 25 0.12 SIDE CHAIN REMARK 500 DG R 28 0.07 SIDE CHAIN REMARK 500 DG R 31 0.20 SIDE CHAIN REMARK 500 DC R 32 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1EKW X 1 10 PDB 1EKW 1EKW 1 10 DBREF 1EKW H 11 20 PDB 1EKW 1EKW 11 20 DBREF 1EKW R 21 32 PDB 1EKW 1EKW 21 32 SEQRES 1 X 10 DG DC DT DG DC DC DA DC DC DG SEQRES 1 H 10 DC DG DG DT DG DC DG DT DC DC SEQRES 1 R 12 DG DG DA DC DG DT DC DG DC DA 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 MASTER 172 0 0 0 0 0 0 6 0 0 0 3 END