HEADER DNA 15-DEC-04 1Y9F TITLE CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-ALLYL THYMIDINE TITLE 2 (T*) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*TP*AP*(2AT)P*AP*CP*GP*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS A-DNA, O2'-MODIFICATION, DECAMER, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.EGLI,G.MINASOV,V.TERESHKO,P.S.PALLAN,M.TEPLOVA,G.B.INAMATI, AUTHOR 2 E.A.LESNIK,S.R.OWENS,B.S.ROSS,T.P.PRAKASH,M.MANOHARAN REVDAT 3 23-AUG-23 1Y9F 1 LINK REVDAT 2 24-FEB-09 1Y9F 1 VERSN REVDAT 1 28-JUN-05 1Y9F 0 JRNL AUTH M.EGLI,G.MINASOV,V.TERESHKO,P.S.PALLAN,M.TEPLOVA, JRNL AUTH 2 G.B.INAMATI,E.A.LESNIK,S.R.OWENS,B.S.ROSS,T.P.PRAKASH, JRNL AUTH 3 M.MANOHARAN JRNL TITL PROBING THE INFLUENCE OF STEREOELECTRONIC EFFECTS ON THE JRNL TITL 2 BIOPHYSICAL PROPERTIES OF OLIGONUCLEOTIDES: COMPREHENSIVE JRNL TITL 3 ANALYSIS OF THE RNA AFFINITY, NUCLEASE RESISTANCE, AND JRNL TITL 4 CRYSTAL STRUCTURE OF TEN 2'-O-RIBONUCLEIC ACID JRNL TITL 5 MODIFICATIONS. JRNL REF BIOCHEMISTRY V. 44 9045 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15966728 JRNL DOI 10.1021/BI050574M REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 6528 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) : 0.158 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 712 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 55.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2449 REMARK 3 BIN FREE R VALUE : 0.2706 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 39 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 : 412 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.58600 REMARK 3 B22 (A**2) : -4.72100 REMARK 3 B33 (A**2) : 3.13500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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) : NULL 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.320 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 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: CONJUGATE GRADIENT REFINEMENT USING REMARK 3 MAXIMUM LIKELIHOOD TARGET FOR AMPLITUDES REMARK 4 REMARK 4 1Y9F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031282. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-98 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 : NULL REMARK 200 OPTICS : MIRRORS 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 : 6760 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.22200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 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 410D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10%MPD, 40MM NA-CACODILATE, 12 MM REMARK 280 SPERMINE, 80MM KCL, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 12.34800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.82000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.53500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.82000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.34800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.53500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: CHAINS A AND B FORM DUPLEX 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: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG B 19 0.07 SIDE CHAIN REMARK 500 DC B 20 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y7F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2- REMARK 900 [HYDROXY(METHYLENEAMINO)OXY]ETHYL] THYMIDINE (T*) REMARK 900 RELATED ID: 1Y84 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2- REMARK 900 (IMIDAZOLYL)ETHYL] THYMIDINE (T*) REMARK 900 RELATED ID: 1Y86 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2-(FLUORO) REMARK 900 ETHYL] THYMIDINE (T*) REMARK 900 RELATED ID: 1Y8L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2-(TRIFLUORO) REMARK 900 ETHYL] THYMIDINE (T*) REMARK 900 RELATED ID: 1Y8V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-PROPYL REMARK 900 THYMIDINE (T*) REMARK 900 RELATED ID: 1Y9S RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-PROPARGYL REMARK 900 THYMIDINE (T*) REMARK 900 RELATED ID: 1WV5 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O- REMARK 900 BUTYL THYMINE IN PLACE OF T6, MG-FORM REMARK 900 RELATED ID: 1WV6 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O- REMARK 900 BUTYL THYMINE IN PLACE OF T6, SR-FORM DBREF 1Y9F A 1 10 PDB 1Y9F 1Y9F 1 10 DBREF 1Y9F B 11 20 PDB 1Y9F 1Y9F 11 20 SEQRES 1 A 10 DG DC DG DT DA 2AT DA DC DG DC SEQRES 1 B 10 DG DC DG DT DA 2AT DA DC DG DC MODRES 1Y9F 2AT A 6 DT 2'-O-ALLYL THYMIDINE-5'-MONOPHOSPHATE MODRES 1Y9F 2AT B 16 DT 2'-O-ALLYL THYMIDINE-5'-MONOPHOSPHATE HET 2AT A 6 24 HET 2AT B 16 24 HETNAM 2AT 2'-O-ALLYL THYMIDINE-5'-MONOPHOSPHATE FORMUL 1 2AT 2(C13 H19 N2 O9 P) FORMUL 3 HOH *127(H2 O) LINK O3' DA A 5 P 2AT A 6 1555 1555 1.60 LINK O3' 2AT A 6 P DA A 7 1555 1555 1.61 LINK O3' DA B 15 P 2AT B 16 1555 1555 1.60 LINK O3' 2AT B 16 P DA B 17 1555 1555 1.59 CRYST1 24.696 45.070 45.640 90.00 90.00 90.00 P 21 21 21 8 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 0.040492 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022188 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021911 0.00000 CONECT 89 102 CONECT 102 89 103 104 105 CONECT 103 102 CONECT 104 102 CONECT 105 102 106 CONECT 106 105 107 CONECT 107 106 108 124 CONECT 108 107 109 CONECT 109 108 110 119 CONECT 110 109 111 112 CONECT 111 110 117 CONECT 112 110 113 114 CONECT 113 112 CONECT 114 112 115 CONECT 115 114 116 117 CONECT 116 115 CONECT 117 111 115 118 CONECT 118 117 CONECT 119 109 120 124 CONECT 120 119 121 CONECT 121 120 122 CONECT 122 121 123 CONECT 123 122 CONECT 124 107 119 125 CONECT 125 124 126 CONECT 126 125 CONECT 296 309 CONECT 309 296 310 311 312 CONECT 310 309 CONECT 311 309 CONECT 312 309 313 CONECT 313 312 314 CONECT 314 313 315 331 CONECT 315 314 316 CONECT 316 315 317 326 CONECT 317 316 318 319 CONECT 318 317 324 CONECT 319 317 320 321 CONECT 320 319 CONECT 321 319 322 CONECT 322 321 323 324 CONECT 323 322 CONECT 324 318 322 325 CONECT 325 324 CONECT 326 316 327 331 CONECT 327 326 328 CONECT 328 327 329 CONECT 329 328 330 CONECT 330 329 CONECT 331 314 326 332 CONECT 332 331 333 CONECT 333 332 MASTER 254 0 2 0 0 0 0 6 539 2 52 2 END