HEADER DNA 08-JUN-99 1K4X TITLE POTASSIUM FORM OF OXY-1.5 QUADRUPLEX DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE FROM OXYTRICHA NOVA KEYWDS DEOXYRIBONUCLEIC ACID, QUADRUPLEX, POTASSIUM ION, DNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR P.SCHULTZE,N.V.HUD,F.W.SMITH,J.FEIGON REVDAT 6 27-DEC-23 1K4X 1 REMARK REVDAT 5 23-FEB-22 1K4X 1 REMARK REVDAT 4 24-FEB-09 1K4X 1 VERSN REVDAT 3 01-APR-03 1K4X 1 JRNL REVDAT 2 15-DEC-99 1K4X 1 JRNL REVDAT 1 23-JUN-99 1K4X 0 JRNL AUTH P.SCHULTZE,N.V.HUD,F.W.SMITH,J.FEIGON JRNL TITL THE EFFECT OF SODIUM, POTASSIUM AND AMMONIUM IONS ON THE JRNL TITL 2 CONFORMATION OF THE DIMERIC QUADRUPLEX FORMED BY THE JRNL TITL 3 OXYTRICHA NOVA TELOMERE REPEAT OLIGONUCLEOTIDE JRNL TITL 4 D(G(4)T(4)G(4)). JRNL REF NUCLEIC ACIDS RES. V. 27 3018 1999 JRNL REFN ISSN 0305-1048 JRNL PMID 10454595 JRNL DOI 10.1093/NAR/27.15.3018 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.W.SMITH,J.FEIGON REMARK 1 TITL QUADRUPLEX STRUCTURE OF OXYTRICHA TELOMERIC DNA REMARK 1 TITL 2 OLIGONUCLEOTIDES REMARK 1 REF NATURE V. 356 164 1992 REMARK 1 REFN ISSN 0028-0836 REMARK 1 DOI 10.1038/356164A0 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DETAILS GIVEN IN PUBLICATION REMARK 4 REMARK 4 1K4X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUN-99. REMARK 100 THE DEPOSITION ID IS D_1000001166. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; P.COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AURELIA, X-PLOR 3.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY/ SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST OVERALL ENERGY 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: 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 H2'' DT B 5 H72 DT B 7 1.15 REMARK 500 H2'' DT A 5 H72 DT A 7 1.15 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 2 C2' DG A 2 C1' 0.082 REMARK 500 1 DG A 4 C5' DG A 4 C4' 0.103 REMARK 500 1 DG A 4 C4' DG A 4 C3' 0.097 REMARK 500 1 DT A 5 C2' DT A 5 C1' 0.126 REMARK 500 1 DT A 5 C5 DT A 5 C7 0.039 REMARK 500 1 DT A 6 C5' DT A 6 C4' 0.067 REMARK 500 1 DT A 6 C5 DT A 6 C7 0.041 REMARK 500 1 DT A 7 C5 DT A 7 C6 0.043 REMARK 500 1 DT A 7 C5 DT A 7 C7 0.058 REMARK 500 1 DT A 8 C5' DT A 8 C4' 0.044 REMARK 500 1 DG A 9 C5' DG A 9 C4' 0.069 REMARK 500 1 DG A 9 C2' DG A 9 C1' 0.081 REMARK 500 1 DG A 10 C2' DG A 10 C1' 0.082 REMARK 500 1 DG A 11 C5' DG A 11 C4' 0.050 REMARK 500 1 DG B 2 C2' DG B 2 C1' 0.082 REMARK 500 1 DG B 4 C5' DG B 4 C4' 0.104 REMARK 500 1 DG B 4 C4' DG B 4 C3' 0.096 REMARK 500 1 DT B 5 C2' DT B 5 C1' 0.121 REMARK 500 1 DT B 5 C5 DT B 5 C7 0.038 REMARK 500 1 DT B 6 C5' DT B 6 C4' 0.069 REMARK 500 1 DT B 6 C5 DT B 6 C7 0.040 REMARK 500 1 DT B 7 C5 DT B 7 C6 0.043 REMARK 500 1 DT B 7 C5 DT B 7 C7 0.057 REMARK 500 1 DT B 8 C5' DT B 8 C4' 0.042 REMARK 500 1 DG B 9 C5' DG B 9 C4' 0.065 REMARK 500 1 DG B 9 C2' DG B 9 C1' 0.072 REMARK 500 1 DG B 10 C2' DG B 10 C1' 0.061 REMARK 500 1 DG B 11 C5' DG B 11 C4' 0.050 REMARK 500 2 DG A 1 C5' DG A 1 C4' 0.053 REMARK 500 2 DG A 2 C3' DG A 2 C2' -0.057 REMARK 500 2 DG A 2 C2' DG A 2 C1' 0.076 REMARK 500 2 DG A 3 C5' DG A 3 C4' 0.048 REMARK 500 2 DG A 4 C5' DG A 4 C4' 0.100 REMARK 500 2 DG A 4 C4' DG A 4 C3' 0.102 REMARK 500 2 DT A 5 C2' DT A 5 C1' 0.124 REMARK 500 2 DT A 5 C5 DT A 5 C7 0.047 REMARK 500 2 DT A 6 C5' DT A 6 C4' 0.081 REMARK 500 2 DT A 6 C5 DT A 6 C7 0.045 REMARK 500 2 DT A 7 C2' DT A 7 C1' 0.071 REMARK 500 2 DG A 9 C2' DG A 9 C1' 0.077 REMARK 500 2 DG A 10 C2' DG A 10 C1' 0.071 REMARK 500 2 DG B 1 C5' DG B 1 C4' 0.052 REMARK 500 2 DG B 2 C3' DG B 2 C2' -0.056 REMARK 500 2 DG B 2 C2' DG B 2 C1' 0.076 REMARK 500 2 DG B 3 C5' DG B 3 C4' 0.048 REMARK 500 2 DG B 4 C5' DG B 4 C4' 0.101 REMARK 500 2 DG B 4 C4' DG B 4 C3' 0.102 REMARK 500 2 DT B 5 C2' DT B 5 C1' 0.121 REMARK 500 2 DT B 5 C5 DT B 5 C7 0.046 REMARK 500 2 DT B 6 C5' DT B 6 C4' 0.082 REMARK 500 REMARK 500 THIS ENTRY HAS 232 BOND DEVIATIONS. 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. = 9.2 DEGREES REMARK 500 1 DG A 1 C5' - C4' - O4' ANGL. DEV. = -13.0 DEGREES REMARK 500 1 DG A 1 C4' - C3' - C2' ANGL. DEV. = -8.0 DEGREES REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DG A 1 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 2 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG A 2 C5' - C4' - O4' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DG A 2 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 2 O4' - C1' - C2' ANGL. DEV. = -8.7 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG A 3 C5' - C4' - C3' ANGL. DEV. = 13.0 DEGREES REMARK 500 1 DG A 3 O4' - C1' - C2' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 8.2 DEGREES REMARK 500 1 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 4 O4' - C4' - C3' ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DG A 4 C4' - C3' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 1 DG A 4 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 4 N9 - C1' - C2' ANGL. DEV. = 11.3 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 6 C3' - C2' - C1' ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DT A 6 O4' - C1' - C2' ANGL. DEV. = -14.8 DEGREES REMARK 500 1 DT A 7 C1' - O4' - C4' ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 7 O4' - C1' - C2' ANGL. DEV. = -8.4 DEGREES REMARK 500 1 DT A 7 N1 - C1' - C2' ANGL. DEV. = -15.9 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 8.0 DEGREES REMARK 500 1 DT A 7 C4 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT A 8 O4' - C1' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 9 O4' - C4' - C3' ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DG A 9 C4' - C3' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG A 9 O4' - C1' - C2' ANGL. DEV. = -9.7 DEGREES REMARK 500 1 DG A 9 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 10 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DG A 10 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 10 C3' - O3' - P ANGL. DEV. = 11.0 DEGREES REMARK 500 1 DG A 11 C5' - C4' - C3' ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DG A 11 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 11 C3' - O3' - P ANGL. DEV. = 10.3 DEGREES REMARK 500 1 DG A 12 O4' - C4' - C3' ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DG A 12 C5' - C4' - C3' ANGL. DEV. = 8.9 DEGREES REMARK 500 1 DG A 12 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 12 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 12 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG B 1 C5' - C4' - C3' ANGL. DEV. = 9.2 DEGREES REMARK 500 1 DG B 1 C5' - C4' - O4' ANGL. DEV. = -13.0 DEGREES REMARK 500 1 DG B 1 C4' - C3' - C2' ANGL. DEV. = -8.0 DEGREES REMARK 500 1 DG B 1 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DG B 1 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 678 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1K4X A 1 12 PDB 1K4X 1K4X 1 12 DBREF 1K4X B 1 12 PDB 1K4X 1K4X 1 12 SEQRES 1 A 12 DG DG DG DG DT DT DT DT DG DG DG DG SEQRES 1 B 12 DG DG DG DG DT DT DT DT DG DG DG DG 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 MODEL 1