HEADER DNA 17-AUG-98 1BQJ TITLE CRYSTAL STRUCTURE OF D(ACCCT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*CP*CP*CP*T)-3'); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS HUMAN TELOMERIC FRAGMENT, DNA EXPDTA X-RAY DIFFRACTION AUTHOR J.WEIL,T.MIN,C.YANG,S.WANG,C.SUTHERLAND,N.SINHA,C.H.KANG REVDAT 4 02-AUG-23 1BQJ 1 REMARK REVDAT 3 24-FEB-09 1BQJ 1 VERSN REVDAT 2 01-APR-03 1BQJ 1 JRNL REVDAT 1 18-MAR-99 1BQJ 0 JRNL AUTH J.WEIL,T.MIN,C.YANG,S.WANG,C.SUTHERLAND,N.SINHA,C.KANG JRNL TITL STABILIZATION OF THE I-MOTIF BY INTRAMOLECULAR JRNL TITL 2 ADENINE-ADENINE-THYMINE BASE TRIPLE IN THE STRUCTURE OF JRNL TITL 3 D(ACCCT). JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 55 422 1999 JRNL REFN ISSN 0907-4449 JRNL PMID 10089350 JRNL DOI 10.1107/S0907444998012529 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 6914 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 689 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 360 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 51 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 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) : 0.570 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.070 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 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 1BQJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000172003. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-97 REMARK 200 TEMPERATURE (KELVIN) : 103.15 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 12 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7136 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: 191D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 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 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+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 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 46.90500 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 46.90500 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 46.90500 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 46.90500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 46.90500 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 46.90500 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 46.90500 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 46.90500 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 46.90500 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 46.90500 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 46.90500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 46.90500 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 46.90500 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 46.90500 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 46.90500 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 46.90500 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 46.90500 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 46.90500 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 46.90500 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 46.90500 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 46.90500 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 46.90500 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 46.90500 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 46.90500 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 46.90500 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 46.90500 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 46.90500 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 46.90500 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 46.90500 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 46.90500 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 46.90500 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 46.90500 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 46.90500 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 46.90500 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 46.90500 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 46.90500 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 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, C, D 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 DT A 5 DBREF 1BQJ A 1 5 PDB 1BQJ 1BQJ 1 5 DBREF 1BQJ B 6 10 PDB 1BQJ 1BQJ 6 10 DBREF 1BQJ C 11 15 PDB 1BQJ 1BQJ 11 15 DBREF 1BQJ D 16 20 PDB 1BQJ 1BQJ 16 20 SEQRES 1 A 5 DA DC DC DC DT SEQRES 1 B 5 DA DC DC DC DT SEQRES 1 C 5 DA DC DC DC DT SEQRES 1 D 5 DA DC DC DC DT FORMUL 5 HOH *51(H2 O) CRYST1 93.810 93.810 93.810 90.00 90.00 90.00 I 2 3 96 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 0.010660 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010660 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010660 0.00000