10 20 30 40 50 60 70 80 1JJP - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 09-JUL-01 1JJP
TITLE A(GGGG) PENTAD-CONTAINING DIMERIC DNA QUADRUPLEX INVOLVING TITLE 2 STACKED 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)- COMPND 3 3'; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED ON AN APPLIED BIOSYSTEMS 392 SOURCE 4 DNA SYNTHESIZER
KEYWDS A(GGGG) PENTAD, DIMERIC QUADRUPLEX, DOUBLE CHAIN REVERSAL KEYWDS 2 LOOP, G(ANTI)G(ANTI)G(ANTI)G(SYN) TETRADS, V-SHAPED LOOP KEYWDS 3 AND SCAFFOLD, DNA
EXPDTA SOLUTION NMR
NUMMDL 8
AUTHOR N.ZHANG,A.GORIN,A.MAJUMDAR,A.KETTANI,N.CHERNICHENKO, AUTHOR 2 E.SKRIPKIN,D.J.PATEL
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, JRNL AUTH 2 N.CHERNICHENKO,E.SKRIPKIN,D.J.PATEL JRNL TITL V-SHAPED SCAFFOLD: A NEW ARCHITECTURAL MOTIF JRNL TITL 2 IDENTIFIED IN AN A X (G X G X G X G) JRNL TITL 3 PENTAD-CONTAINING DIMERIC DNA QUADRUPLEX INVOLVING JRNL TITL 4 STACKED G(ANTI) X G(ANTI) X G(ANTI) X G(SYN) JRNL TITL 5 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 1
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 RCSB ID CODE IS RCSB013852.
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 REMARK 210 TORSIONAL 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 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. = -4.9 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 9 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT A 8 C3' - O3' - P ANGL. DEV. = 12.1 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. = -4.9 DEGREES REMARK 500 1 DG B 5 C5' - C4' - O4' ANGL. DEV. = 8.7 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 9 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT B 8 C3' - O3' - P ANGL. DEV. = 12.1 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. = 2.4 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 1.000 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