HEADER DNA 09-JUL-01 1JJP TITLE A(GGGG) PENTAD-CONTAINING DIMERIC DNA QUADRUPLEX INVOLVING STACKED TITLE 2 G(ANTI)G(ANTI)G(ANTI)G(SYN) TETRADS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*AP*GP*GP*TP*TP*TP*GP*GP*GP*AP*T)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED ON AN APPLIED BIOSYSTEMS 392 DNA SOURCE 4 SYNTHESIZER KEYWDS A(GGGG) PENTAD, DIMERIC QUADRUPLEX, DOUBLE CHAIN REVERSAL LOOP, KEYWDS 2 G(ANTI)G(ANTI)G(ANTI)G(SYN) TETRADS, V-SHAPED LOOP AND SCAFFOLD, DNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR N.ZHANG,A.GORIN,A.MAJUMDAR,A.KETTANI,N.CHERNICHENKO,E.SKRIPKIN, AUTHOR 2 D.J.PATEL REVDAT 4 23-FEB-22 1JJP 1 REMARK REVDAT 3 24-FEB-09 1JJP 1 VERSN REVDAT 2 01-APR-03 1JJP 1 JRNL REVDAT 1 19-SEP-01 1JJP 0 JRNL AUTH N.ZHANG,A.GORIN,A.MAJUMDAR,A.KETTANI,N.CHERNICHENKO, JRNL AUTH 2 E.SKRIPKIN,D.J.PATEL JRNL TITL V-SHAPED SCAFFOLD: A NEW ARCHITECTURAL MOTIF IDENTIFIED IN JRNL TITL 2 AN A X (G X G X G X G) PENTAD-CONTAINING DIMERIC DNA JRNL TITL 3 QUADRUPLEX INVOLVING STACKED G(ANTI) X G(ANTI) X G(ANTI) X JRNL TITL 4 G(SYN) TETRADS. JRNL REF J.MOL.BIOL. V. 311 1063 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11531340 JRNL DOI 10.1006/JMBI.2001.4916 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.91 REMARK 3 AUTHORS : A. BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DESCRIBED IN THE PRIMARY CITATION REMARK 4 REMARK 4 1JJP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1000013852. 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 : 100MM NACL, 2MM PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 100MM 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 : FELIX 2000 REMARK 210 METHOD USED : SIMULATED ANNEALING IN TORSIONAL REMARK 210 ANGLE SPACE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 8 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: 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: 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 O2 DT A 8 H61 DA A 13 1.42 REMARK 500 O2 DT B 8 H61 DA B 13 1.42 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 DG A 1 C3' DG A 1 C2' 0.085 REMARK 500 1 DT A 8 C3' DT A 8 C2' -0.074 REMARK 500 1 DT A 14 C5 DT A 14 C7 0.061 REMARK 500 1 DG B 1 C3' DG B 1 C2' 0.086 REMARK 500 1 DT B 8 C3' DT B 8 C2' -0.074 REMARK 500 1 DT B 14 C5 DT B 14 C7 0.060 REMARK 500 2 DG A 1 C3' DG A 1 C2' 0.089 REMARK 500 2 DT A 8 C3' DT A 8 C2' -0.049 REMARK 500 2 DT A 14 C5 DT A 14 C7 0.041 REMARK 500 2 DG B 1 C3' DG B 1 C2' 0.089 REMARK 500 2 DT B 8 C3' DT B 8 C2' -0.048 REMARK 500 2 DT B 14 C5 DT B 14 C7 0.040 REMARK 500 3 DG A 1 C3' DG A 1 C2' 0.094 REMARK 500 3 DT A 7 C5 DT A 7 C7 0.049 REMARK 500 3 DG B 1 C3' DG B 1 C2' 0.093 REMARK 500 3 DT B 7 C5 DT B 7 C7 0.050 REMARK 500 4 DG A 1 C3' DG A 1 C2' 0.089 REMARK 500 4 DT A 8 C3' DT A 8 C2' -0.050 REMARK 500 4 DT A 14 C5 DT A 14 C7 0.036 REMARK 500 4 DG B 1 C3' DG B 1 C2' 0.090 REMARK 500 4 DT B 8 C3' DT B 8 C2' -0.051 REMARK 500 4 DT B 14 C5 DT B 14 C7 0.037 REMARK 500 5 DG A 1 C3' DG A 1 C2' 0.104 REMARK 500 5 DA A 4 C5' DA A 4 C4' 0.046 REMARK 500 5 DT A 8 C3' DT A 8 C2' -0.048 REMARK 500 5 DG B 1 C3' DG B 1 C2' 0.103 REMARK 500 5 DA B 4 C5' DA B 4 C4' 0.045 REMARK 500 5 DT B 8 C3' DT B 8 C2' -0.049 REMARK 500 6 DG A 1 C3' DG A 1 C2' 0.088 REMARK 500 6 DT A 14 C5 DT A 14 C7 0.042 REMARK 500 6 DG B 1 C3' DG B 1 C2' 0.088 REMARK 500 6 DT B 14 C5 DT B 14 C7 0.042 REMARK 500 7 DG A 1 C3' DG A 1 C2' 0.099 REMARK 500 7 DT A 8 C3' DT A 8 C2' -0.062 REMARK 500 7 DT A 14 C5 DT A 14 C7 0.057 REMARK 500 7 DG B 1 C3' DG B 1 C2' 0.098 REMARK 500 7 DT B 8 C3' DT B 8 C2' -0.063 REMARK 500 7 DT B 14 C5 DT B 14 C7 0.056 REMARK 500 8 DG A 1 C3' DG A 1 C2' 0.105 REMARK 500 8 DT A 9 C5 DT A 9 C7 0.037 REMARK 500 8 DT A 14 C5 DT A 14 C7 0.050 REMARK 500 8 DG B 1 C3' DG B 1 C2' 0.105 REMARK 500 8 DT B 9 C5 DT B 9 C7 0.036 REMARK 500 8 DT B 14 C5 DT B 14 C7 0.048 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 C5' - C4' - C3' ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DG A 1 C1' - O4' - C4' ANGL. DEV. = -8.4 DEGREES REMARK 500 1 DG A 1 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA A 4 C1' - O4' - C4' ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DA A 4 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 5 C5' - C4' - O4' ANGL. DEV. = 8.8 DEGREES REMARK 500 1 DG A 5 O4' - C1' - C2' ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DG A 5 N3 - C2 - N2 ANGL. DEV. = -6.8 DEGREES REMARK 500 1 DG A 6 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DT A 7 C4 - C5 - C7 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 9.2 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 8 C3' - O3' - P ANGL. DEV. = 12.1 DEGREES REMARK 500 1 DT A 9 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 11 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 11 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DA A 13 O4' - C4' - C3' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DA A 13 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 1 DT A 14 O4' - C4' - C3' ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG B 1 C5' - C4' - C3' ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DG B 1 C1' - O4' - C4' ANGL. DEV. = -8.4 DEGREES REMARK 500 1 DG B 1 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA B 4 C1' - O4' - C4' ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DA B 4 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG B 5 C5' - C4' - O4' ANGL. DEV. = 8.8 DEGREES REMARK 500 1 DG B 5 O4' - C1' - C2' ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DG B 5 N3 - C2 - N2 ANGL. DEV. = -6.8 DEGREES REMARK 500 1 DG B 6 C1' - O4' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 1 DG B 6 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DT B 7 C4 - C5 - C7 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT B 7 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DT B 8 O4' - C1' - N1 ANGL. DEV. = 9.2 DEGREES REMARK 500 1 DT B 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT B 8 C3' - O3' - P ANGL. DEV. = 12.1 DEGREES REMARK 500 1 DT B 9 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG B 11 C3' - C2' - C1' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 11 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 1 DA B 13 O4' - C4' - C3' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DA B 13 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DT B 14 O4' - C4' - C3' ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DG A 1 O4' - C4' - C3' ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DG A 1 C1' - O4' - C4' ANGL. DEV. = -10.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 447 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1JJP A 1 14 PDB 1JJP 1JJP 1 14 DBREF 1JJP B 1 14 PDB 1JJP 1JJP 1 14 SEQRES 1 A 14 DG DG DG DA DG DG DT DT DT DG DG DG DA SEQRES 2 A 14 DT SEQRES 1 B 14 DG DG DG DA DG DG DT DT DT DG DG DG DA SEQRES 2 B 14 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