10 20 30 40 50 60 70 80 1XCE - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 01-SEP-04 1XCE
TITLE HELICA STRUCTURE OF DNA BY DESIGN: THE T(GGGG)T HEXAD TITLE 2 ALIGNMENT
CAVEAT 1XCE CHIRALITY ERROR AT G4
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*GP*TP*TP*GP*GP*AP*T)-3'; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HOMO SOURCE 4 SAPIENS (HUMANS)
KEYWDS DNA QUADRUPLEX, HEXAD
EXPDTA SOLUTION NMR
AUTHOR M.WEBBA DA SILVA
REVDAT 3 24-FEB-09 1XCE 1 VERSN REVDAT 2 15-MAR-05 1XCE 1 JRNL REVDAT 1 08-FEB-05 1XCE 0
JRNL AUTH M.WEBBA DA SILVA JRNL TITL EXPERIMENTAL DEMONSTRATION OF T:(G:G:G):T HEXAD JRNL TITL 2 AND T:A:A:T TETRAD ALIGNMENTS WITHIN A DNA JRNL TITL 3 QUADRUPLEX STEM JRNL REF BIOCHEMISTRY V. 44 3754 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15751952 JRNL DOI 10.1021/BI0478190
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 2.1, XPLOR-NIH 2.9.7 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER/SCHWIETERS (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1XCE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-SEP-04. REMARK 100 THE RCSB ID CODE IS RCSB030199.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 20; 0 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 100 MM NACL; 100 MM NACL REMARK 210 PRESSURE : NORMAL; NORMAL REMARK 210 SAMPLE CONTENTS : SYNTHESIZED BY SOLID PHASE REMARK 210 PHOSPHORAMIDITE METHODS, REMARK 210 PHOSPHATE BUFFER PH 6.8, H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY, 2D TOCSY, 2D NOESY, REMARK 210 1H,15N HSQC, 31P,1H HETCOR, JR REMARK 210 -NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 15 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINE USING STANDARD AND NON- REMARK 210 STANDARD HOMO- AND HETERONUCLEAR NMR TECHNIQUES
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: 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 O3' DT A 6 C5' DG A 7 2.11 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 DG A 1 C2' DG A 1 C1' -0.087 REMARK 500 DG A 1 C8 DG A 1 N9 -0.061 REMARK 500 DC A 2 N1 DC A 2 C6 -0.039 REMARK 500 DG A 3 C8 DG A 3 N9 -0.045 REMARK 500 DG A 4 C4' DG A 4 C3' -0.080 REMARK 500 DG A 4 C3' DG A 4 C2' -0.054 REMARK 500 DG A 4 N9 DG A 4 C4 0.053 REMARK 500 DT A 5 C4' DT A 5 C3' -0.062 REMARK 500 DT A 6 C2 DT A 6 N3 0.054 REMARK 500 DT A 6 C5 DT A 6 C6 -0.081 REMARK 500 DT A 6 C6 DT A 6 N1 -0.131 REMARK 500 DT A 6 C5 DT A 6 C7 -0.094 REMARK 500 DG A 7 C8 DG A 7 N9 -0.067 REMARK 500 DG A 8 C2' DG A 8 C1' -0.068 REMARK 500 DG A 8 C8 DG A 8 N9 -0.067 REMARK 500 DA A 9 C3' DA A 9 C2' -0.057 REMARK 500 DT A 10 C4' DT A 10 C3' -0.080 REMARK 500 DT A 10 C5 DT A 10 C6 -0.074 REMARK 500 DT A 10 C6 DT A 10 N1 -0.052 REMARK 500 DT B 5 C5 DT B 5 C7 0.049 REMARK 500 DT B 6 C6 DT B 6 N1 -0.056 REMARK 500 DT C 6 C2' DT C 6 C1' -0.061 REMARK 500 DT C 6 C6 DT C 6 N1 -0.083 REMARK 500 DT D 6 C6 DT D 6 N1 -0.054 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 DG A 1 C4' - C3' - C2' ANGL. DEV. = -10.5 DEGREES REMARK 500 DG A 1 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG A 1 C5 - N7 - C8 ANGL. DEV. = -4.6 DEGREES REMARK 500 DC A 2 O4' - C4' - C3' ANGL. DEV. = -5.1 DEGREES REMARK 500 DC A 2 C4' - C3' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 DC A 2 O4' - C1' - C2' ANGL. DEV. = -8.4 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 DC A 2 C2 - N3 - C4 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC A 2 N3 - C4 - C5 ANGL. DEV. = -5.3 DEGREES REMARK 500 DC A 2 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC A 2 C5 - C4 - N4 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG A 1 C3' - O3' - P ANGL. DEV. = 15.9 DEGREES REMARK 500 DG A 3 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES REMARK 500 DG A 3 C1' - O4' - C4' ANGL. DEV. = -8.3 DEGREES REMARK 500 DG A 3 O4' - C1' - C2' ANGL. DEV. = -8.4 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = -7.2 DEGREES REMARK 500 DG A 3 C2 - N3 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 DG A 3 C5 - N7 - C8 ANGL. DEV. = -3.3 DEGREES REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG A 3 C6 - C5 - N7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG A 4 C4' - C3' - C2' ANGL. DEV. = -8.4 DEGREES REMARK 500 DG A 4 O4' - C1' - C2' ANGL. DEV. = -12.8 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 DG A 4 N3 - C4 - C5 ANGL. DEV. = -3.5 DEGREES REMARK 500 DG A 4 N3 - C4 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG A 4 C4 - N9 - C1' ANGL. DEV. = 8.6 DEGREES REMARK 500 DT A 5 P - O5' - C5' ANGL. DEV. = -17.1 DEGREES REMARK 500 DT A 5 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DT A 5 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT A 5 C3' - C2' - C1' ANGL. DEV. = -9.6 DEGREES REMARK 500 DT A 5 O4' - C1' - C2' ANGL. DEV. = -8.1 DEGREES REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG A 4 C3' - O3' - P ANGL. DEV. = -10.4 DEGREES REMARK 500 DT A 6 O4' - C4' - C3' ANGL. DEV. = -10.5 DEGREES REMARK 500 DT A 6 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT A 6 C3' - C2' - C1' ANGL. DEV. = 8.6 DEGREES REMARK 500 DT A 6 O4' - C1' - C2' ANGL. DEV. = -28.5 DEGREES REMARK 500 DT A 6 N1 - C1' - C2' ANGL. DEV. = -17.6 DEGREES REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 13.1 DEGREES REMARK 500 DT A 6 C2 - N3 - C4 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT A 6 N3 - C4 - C5 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT A 6 C4 - C5 - C6 ANGL. DEV. = 7.7 DEGREES REMARK 500 DT A 6 N3 - C4 - O4 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 6 C4 - C5 - C7 ANGL. DEV. = 10.5 DEGREES REMARK 500 DT A 6 C6 - C5 - C7 ANGL. DEV. = -18.4 DEGREES REMARK 500 DT A 6 C6 - N1 - C1' ANGL. DEV. = -15.5 DEGREES REMARK 500 DT A 6 C2 - N1 - C1' ANGL. DEV. = 14.6 DEGREES REMARK 500 DG A 7 P - O5' - C5' ANGL. DEV. = -16.1 DEGREES REMARK 500 DG A 7 C4' - C3' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 183 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL
DBREF 1XCE A 1 10 PDB 1XCE 1XCE 1 10 DBREF 1XCE B 1 10 PDB 1XCE 1XCE 1 10 DBREF 1XCE C 1 10 PDB 1XCE 1XCE 1 10 DBREF 1XCE D 1 10 PDB 1XCE 1XCE 1 10
SEQRES 1 A 10 DG DC DG DG DT DT DG DG DA DT SEQRES 1 B 10 DG DC DG DG DT DT DG DG DA DT SEQRES 1 C 10 DG DC DG DG DT DT DG DG DA DT SEQRES 1 D 10 DG DC DG DG DT DT DG DG DA 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