HEADER DNA 29-AUG-01 1JVC TITLE DIMERIC DNA QUADRUPLEX CONTAINING MAJOR GROOVE-ALIGNED A.T.A.T AND TITLE 2 G.C.G.C TETRADS STABILIZED BY INTER-SUBUNIT WATSON-CRICK A:T AND G:C TITLE 3 PAIRS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*AP*GP*CP*AP*GP*GP*T)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS ATAT AND GCGC TETRADS, DIMERIC DNA QUADRUPLEX, HYDROGEN BOND KEYWDS 2 ALIGNMENTS, INTER-SUBUNIT WATSON-CRICK PAIRS, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR N.ZHANG,A.GORIN,A.MAJUMDAR,A.KETTANI,N.CHERNICHENKO,E.SKRIPKIN, AUTHOR 2 D.J.PATEL REVDAT 4 23-FEB-22 1JVC 1 REMARK REVDAT 3 24-FEB-09 1JVC 1 VERSN REVDAT 2 01-APR-03 1JVC 1 JRNL REVDAT 1 24-OCT-01 1JVC 0 JRNL AUTH N.ZHANG,A.GORIN,A.MAJUMDAR,A.KETTANI,N.CHERNICHENKO, JRNL AUTH 2 E.SKRIPKIN,D.J.PATEL JRNL TITL DIMERIC DNA QUADRUPLEX CONTAINING MAJOR GROOVE-ALIGNED JRNL TITL 2 A-T-A-T AND G-C-G-C TETRADS STABILIZED BY INTER-SUBUNIT JRNL TITL 3 WATSON-CRICK A-T AND G-C PAIRS. JRNL REF J.MOL.BIOL. V. 312 1073 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11580251 JRNL DOI 10.1006/JMBI.2001.5002 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.81 REMARK 3 AUTHORS : A. BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DESCRIBED IN THE PRIMARY CITATION REMARK 4 REMARK 4 1JVC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1000014225. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273 REMARK 210 PH : 6.6 REMARK 210 IONIC STRENGTH : 1M NACL, 2MM PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1M NACL, 2MM PHOSPHATE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, COSY, TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS WITH REMARK 210 SIMULATED ANNEALING METHOD IN REMARK 210 TORSIONAL SPACE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 9 DG A 1 C8 DG A 1 N9 -0.044 REMARK 500 9 DG B 1 C8 DG B 1 N9 -0.043 REMARK 500 10 DG A 1 C8 DG A 1 N9 -0.047 REMARK 500 10 DG B 1 C8 DG B 1 N9 -0.047 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 C4' - C3' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA A 2 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DA A 2 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DA A 2 O4' - C1' - N9 ANGL. DEV. = -9.0 DEGREES REMARK 500 1 DG A 3 O4' - C4' - C3' ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG A 3 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES REMARK 500 1 DC A 4 O4' - C4' - C3' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DC A 4 C5' - C4' - O4' ANGL. DEV. = 8.2 DEGREES REMARK 500 1 DC A 4 C4' - C3' - O3' ANGL. DEV. = 12.1 DEGREES REMARK 500 1 DC A 4 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DC A 4 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA A 5 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 11.1 DEGREES REMARK 500 1 DG A 6 O4' - C1' - C2' ANGL. DEV. = -12.2 DEGREES REMARK 500 1 DG A 6 C5 - C6 - O6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG A 7 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 7 O4' - C1' - C2' ANGL. DEV. = -12.5 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG B 1 C4' - C3' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA B 2 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DA B 2 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DA B 2 O4' - C1' - N9 ANGL. DEV. = -9.0 DEGREES REMARK 500 1 DG B 3 O4' - C4' - C3' ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DG B 3 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES REMARK 500 1 DC B 4 O4' - C4' - C3' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DC B 4 C5' - C4' - O4' ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DC B 4 C4' - C3' - O3' ANGL. DEV. = 12.1 DEGREES REMARK 500 1 DC B 4 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC B 4 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DC B 4 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA B 5 C1' - O4' - C4' ANGL. DEV. = -7.1 DEGREES REMARK 500 1 DA B 5 O4' - C1' - N9 ANGL. DEV. = 11.1 DEGREES REMARK 500 1 DG B 6 O4' - C1' - C2' ANGL. DEV. = -12.1 DEGREES REMARK 500 1 DG B 6 C5 - C6 - O6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG B 7 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG B 7 O4' - C1' - C2' ANGL. DEV. = -12.5 DEGREES REMARK 500 1 DG B 7 O4' - C1' - N9 ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DT B 8 C6 - C5 - C7 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 DG A 1 C4' - C3' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 2 DA A 2 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 2 DA A 2 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 2 DA A 2 O4' - C1' - N9 ANGL. DEV. = -8.9 DEGREES REMARK 500 2 DG A 3 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DG A 3 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 2 DC A 4 O4' - C4' - C3' ANGL. DEV. = -5.9 DEGREES REMARK 500 2 DC A 4 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 485 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1JVC A 1 8 PDB 1JVC 1JVC 1 8 DBREF 1JVC B 1 8 PDB 1JVC 1JVC 1 8 SEQRES 1 A 8 DG DA DG DC DA DG DG DT SEQRES 1 B 8 DG DA DG DC DA DG DG DT CRYST1 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