HEADER DNA 03-NOV-03 1V3O TITLE CRYSTAL STRUCTURE OF D(GCGAGAGC): THE DNA QUADRUPLEX STRUCTURE SPLIT TITLE 2 FROM THE OCTAPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS OCTAPLEX, QUADRUPLEX, G-DUET, BASE-INTERCALATED DUPLEX, BASE- KEYWDS 2 INTERCALATED MOTIF, SHEARED G:A PAIR, DNA, DEOXYRIBONUCLEIC ACID, X- KEYWDS 3 RAY ANALYSIS EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,S.UMEDA,T.SUNAMI,A.TAKENAKA REVDAT 5 25-OCT-23 1V3O 1 REMARK LINK REVDAT 4 16-APR-14 1V3O 1 REMARK VERSN REVDAT 3 15-SEP-09 1V3O 1 HET HETATM REVDAT 2 24-FEB-09 1V3O 1 VERSN REVDAT 1 08-JUN-04 1V3O 0 JRNL AUTH J.KONDO,W.ADACHI,S.UMEDA,T.SUNAMI,A.TAKENAKA JRNL TITL CRYSTAL STRUCTURES OF A DNA OCTAPLEX WITH I-MOTIF OF JRNL TITL 2 G-QUARTETS AND ITS SPLITTING INTO TWO QUADRUPLEXES SUGGEST A JRNL TITL 3 FOLDING MECHANISM OF EIGHT TANDEM REPEATS JRNL REF NUCLEIC ACIDS RES. V. 32 2541 2004 JRNL REFN ISSN 0305-1048 JRNL PMID 15133122 JRNL DOI 10.1093/NAR/GKH575 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : G. PARKINSON ET AL., (1996) ACTACRYST. D52, REMARK 3 57-64 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 5063 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.262 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 528 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.5554 REMARK 3 BIN FREE R VALUE : 0.6045 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 50 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 332 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : 0.60 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1V3O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-NOV-03. REMARK 100 THE DEPOSITION ID IS D_1000006165. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD PX210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK, SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5269 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.13700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1V3N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-METHYL-2,4-PENTANEDIOL, SPERMINE REMARK 280 TETRAHYDROCHLORIDE, SODIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM REMARK 280 CACODYLATE , PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 17.32500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.24500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.04000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 17.32500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.24500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.04000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 17.32500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 21.24500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.04000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 17.32500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 21.24500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 32.04000 REMARK 290 REMARK 290 REMARK: NULL 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A QUADRUPLEX GENERATED FROM THE REMARK 300 DUPLEX IN THE ASYMMETRIC UNIT BY THE OPERATIONS: X, Y, Z AND -X, Y, REMARK 300 -Z. 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: TETRAMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 K K A 104 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 29 LIES ON A SPECIAL POSITION. REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 104 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 5 O6 REMARK 620 2 DG A 5 O6 62.6 REMARK 620 3 HOH A 25 O 78.1 123.0 REMARK 620 4 HOH A 25 O 123.0 78.1 157.1 REMARK 620 5 DG B 13 O6 85.0 72.7 63.8 122.0 REMARK 620 6 DG B 13 O6 72.7 85.0 122.0 63.8 154.0 REMARK 620 7 HOH B 97 O 109.7 148.1 81.7 82.5 139.2 63.6 REMARK 620 8 HOH B 97 O 148.1 109.7 82.5 81.7 63.6 139.2 92.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 104 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1V3N RELATED DB: PDB REMARK 900 THE SAME STRUCTURE, BR-DERIVATIVE REMARK 900 RELATED ID: 1V3P RELATED DB: PDB REMARK 900 THE SAME STRUCTURE, I-DERIVATIVE, WITH I-MOTIF OF G-QUARTET DBREF 1V3O A 1 8 PDB 1V3O 1V3O 1 8 DBREF 1V3O B 9 16 PDB 1V3O 1V3O 9 16 SEQRES 1 A 8 DG C38 DG DA DG DA DG DC SEQRES 1 B 8 DG C38 DG DA DG DA DG DC MODRES 1V3O C38 A 2 DC MODRES 1V3O C38 B 10 DC HET C38 A 2 20 HET C38 B 10 20 HET K A 104 1 HETNAM C38 5-IODO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM K POTASSIUM ION FORMUL 1 C38 2(C9 H13 I N3 O7 P) FORMUL 3 K K 1+ FORMUL 4 HOH *87(H2 O) LINK O3' DG A 1 P C38 A 2 1555 1555 1.61 LINK O3' C38 A 2 P DG A 3 1555 1555 1.60 LINK O3' DG B 9 P C38 B 10 1555 1555 1.61 LINK O3' C38 B 10 P DG B 11 1555 1555 1.60 LINK O6 DG A 5 K K A 104 1555 1555 2.67 LINK O6 DG A 5 K K A 104 3555 1555 2.67 LINK O HOH A 25 K K A 104 1555 1555 3.03 LINK O HOH A 25 K K A 104 3555 1555 3.03 LINK K K A 104 O6 DG B 13 1555 1555 2.89 LINK K K A 104 O6 DG B 13 1555 3555 2.89 LINK K K A 104 O HOH B 97 1555 1555 3.17 LINK K K A 104 O HOH B 97 1555 3555 3.17 SITE 1 AC1 3 DG A 5 HOH A 25 DG B 13 CRYST1 34.650 42.490 64.080 90.00 90.00 90.00 I 2 2 2 16 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 0.028860 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023535 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015605 0.00000 CONECT 6 20 CONECT 20 6 21 22 23 CONECT 21 20 CONECT 22 20 CONECT 23 20 24 CONECT 24 23 25 CONECT 25 24 26 27 CONECT 26 25 30 CONECT 27 25 28 29 CONECT 28 27 40 CONECT 29 27 30 CONECT 30 26 29 31 CONECT 31 30 32 38 CONECT 32 31 33 34 CONECT 33 32 CONECT 34 32 35 CONECT 35 34 36 37 CONECT 36 35 CONECT 37 35 38 39 CONECT 38 31 37 CONECT 39 37 CONECT 40 28 CONECT 99 335 CONECT 173 187 CONECT 187 173 188 189 190 CONECT 188 187 CONECT 189 187 CONECT 190 187 191 CONECT 191 190 192 CONECT 192 191 193 194 CONECT 193 192 197 CONECT 194 192 195 196 CONECT 195 194 207 CONECT 196 194 197 CONECT 197 193 196 198 CONECT 198 197 199 205 CONECT 199 198 200 201 CONECT 200 199 CONECT 201 199 202 CONECT 202 201 203 204 CONECT 203 202 CONECT 204 202 205 206 CONECT 205 198 204 CONECT 206 204 CONECT 207 195 CONECT 266 335 CONECT 335 99 266 340 416 CONECT 340 335 CONECT 416 335 MASTER 270 0 3 0 0 0 1 6 420 2 49 2 END