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