10 20 30 40 50 60 70 80 1V3N - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 03-NOV-03 1V3N
TITLE CRYSTAL STRUCTURE OF D(GCGAGAGC): THE DNA QUADRUPLEX TITLE 2 STRUCTURE SPLIT FROM THE OCTAPLEX
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*(CBR)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, KEYWDS 2 BASE-INTERCALATED MOTIF, SHEARED G:A PAIR, DNA, KEYWDS 3 DEOXYRIBONUCLEIC ACID, X-RAY ANALYSIS, CRYSTAL STRUTURE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.KONDO,S.UMEDA,T.SUNAMI,A.TAKENAKA
REVDAT 2 24-FEB-09 1V3N 1 VERSN REVDAT 1 08-JUN-04 1V3N 0
JRNL AUTH J.KONDO,W.ADACHI,S.UMEDA,T.SUNAMI,A.TAKENAKA JRNL TITL CRYSTAL STRUCTURES OF A DNA OCTAPLEX WITH I-MOTIF JRNL TITL 2 OF G-QUARTETS AND ITS SPLITTING INTO TWO JRNL TITL 3 QUADRUPLEXES SUGGEST A FOLDING MECHANISM OF EIGHT JRNL TITL 4 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 1
REMARK 2 REMARK 2 RESOLUTION. 1.80 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. REMARK 3 D52, 57-64 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 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) (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 4227 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) : 0.225 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 436 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3350 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 35 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 : 110 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) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.32 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) : 0.90 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.80 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 1V3N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-NOV-03. REMARK 100 THE RCSB ID CODE IS RCSB006164.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0, 0.91961, 0.92020 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4543 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 32.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : 0.05000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.26500 REMARK 200 R SYM FOR SHELL (I) : 0.26500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-METHYL-2,4-PENTANEDIOL, SPERMINE REMARK 280 TETRAHYDROCHLORIDE, SODIUM CHLORIDE, POTASSIUM CHLORIDE, REMARK 280 SODIUM CACODYLATE , PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 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 16.90500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.73500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.10000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 16.90500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.73500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.10000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 16.90500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 21.73500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.10000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 16.90500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 21.73500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 32.10000 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 REMARK 300 THE DUPLEX IN THE ASYMMETRIC UNIT BY THE OPERATIONS: X, Y, Z AND REMARK 300 -X, Y, -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 127 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 89 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 55 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 66 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 84 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 118 LIES ON A SPECIAL POSITION.
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 31 DISTANCE = 7.51 ANGSTROMS REMARK 525 HOH A 49 DISTANCE = 5.73 ANGSTROMS REMARK 525 HOH B 66 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH B 85 DISTANCE = 7.66 ANGSTROMS REMARK 525 HOH A 86 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH A 89 DISTANCE = 7.17 ANGSTROMS REMARK 525 HOH B 106 DISTANCE = 11.06 ANGSTROMS REMARK 525 HOH A 103 DISTANCE = 8.51 ANGSTROMS REMARK 525 HOH A 113 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH A 117 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A 123 DISTANCE = 5.58 ANGSTROMS
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 127 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 13 O6 REMARK 620 2 HOH A 21 O 63.8 REMARK 620 3 HOH B 59 O 70.7 88.1 REMARK 620 4 DG A 5 O6 84.4 75.4 154.4 REMARK 620 5 DG A 5 O6 71.3 123.8 107.4 68.1 REMARK 620 6 HOH A 21 O 122.3 158.8 76.4 123.8 75.4 REMARK 620 7 HOH B 59 O 134.2 76.4 87.0 107.4 154.4 88.1 REMARK 620 8 DG B 13 O6 150.7 122.3 134.2 71.3 84.4 63.8 70.7 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 127
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1V3O RELATED DB: PDB REMARK 900 THE SAME STRUCTURE, I-DERIVATIVE REMARK 900 RELATED ID: 1V3P RELATED DB: PDB REMARK 900 THE SAME STRUCTURE, I-DERIVATIVE, WITH I-MOTIF OF G-QUARTET
DBREF 1V3N A 1 8 PDB 1V3N 1V3N 1 8 DBREF 1V3N B 9 16 PDB 1V3N 1V3N 9 16
SEQRES 1 A 8 DG CBR DG DA DG DA DG DC SEQRES 1 B 8 DG CBR DG DA DG DA DG DC
MODRES 1V3N CBR A 2 DC MODRES 1V3N CBR B 10 DC
HET CBR A 2 20 HET CBR B 10 20 HET K A 127 1
HETNAM CBR 5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM K POTASSIUM ION
FORMUL 1 CBR 2(C9 H13 BR N3 O7 P) FORMUL 3 K K 1+ FORMUL 4 HOH *110(H2 O)
LINK O3' DG A 1 P CBR A 2 1555 1555 1.60 LINK O3' CBR A 2 P DG A 3 1555 1555 1.61 LINK K K A 127 O6 DG B 13 1555 1555 2.90 LINK K K A 127 O HOH A 21 1555 1555 3.09 LINK K K A 127 O HOH B 59 1555 1555 2.85 LINK K K A 127 O6 DG A 5 1555 1555 2.78 LINK O3' DG B 9 P CBR B 10 1555 1555 1.61 LINK O3' CBR B 10 P DG B 11 1555 1555 1.61 LINK K K A 127 O6 DG A 5 1555 3555 2.78 LINK K K A 127 O HOH A 21 1555 3555 3.09 LINK K K A 127 O HOH B 59 1555 3555 2.85 LINK K K A 127 O6 DG B 13 1555 3555 2.90
SITE 1 AC1 4 DG A 5 HOH A 21 DG B 13 HOH B 59
CRYST1 33.810 43.470 64.200 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 0.029577 0.000000 0.000000 0.00000
SCALE2 0.000000 0.023004 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015576 0.00000