HEADER DNA 29-JAN-01 1I0P TITLE 1.3 A STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-METHYL- TITLE 2 [TRI(OXYETHYL)], MEDIUM K-SALT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*TP*AP*(126)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-FORM DOUBLE HELIX, MODIFIED SUGAR, DNA EXPDTA X-RAY DIFFRACTION AUTHOR V.TERESHKO,C.J.WILDS,G.MINASOV,T.P.PRAKASH,M.A.MAIER,A.HOWARD, AUTHOR 2 Z.WAWRZAK,M.MANOHARAN,M.EGLI REVDAT 3 07-FEB-24 1I0P 1 REMARK LINK REVDAT 2 24-FEB-09 1I0P 1 VERSN REVDAT 1 04-APR-01 1I0P 0 JRNL AUTH V.TERESHKO,C.J.WILDS,G.MINASOV,T.P.PRAKASH,M.A.MAIER, JRNL AUTH 2 A.HOWARD,Z.WAWRZAK,M.MANOHARAN,M.EGLI JRNL TITL DETECTION OF ALKALI METAL IONS IN DNA CRYSTALS USING JRNL TITL 2 STATE-OF-THE-ART X-RAY DIFFRACTION EXPERIMENTS. JRNL REF NUCLEIC ACIDS RES. V. 29 1208 2001 JRNL REFN ISSN 0305-1048 JRNL PMID 11222771 JRNL DOI 10.1093/NAR/29.5.1208 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.161 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 12024 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 426 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 134 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1I0P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1000012760. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8151 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12024 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: K SALT, PH 6.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP AT 298 K 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 12.59000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.40500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.42000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.40500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.59000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.42000 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 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 167 O HOH B 218 1.40 REMARK 500 O HOH B 196 O HOH B 204 1.42 REMARK 500 O HOH A 142 O HOH A 149 1.44 REMARK 500 O HOH B 172 O HOH B 189 1.45 REMARK 500 O HOH B 195 O HOH B 206 1.55 REMARK 500 O HOH B 214 O HOH B 228 1.60 REMARK 500 O HOH B 194 O HOH B 215 1.60 REMARK 500 OP2 DC A 10 O HOH A 217 1.65 REMARK 500 O4 DT B 14 O HOH B 215 1.65 REMARK 500 O4' DG B 19 O HOH B 224 1.66 REMARK 500 N2 DG B 13 O HOH B 193 1.66 REMARK 500 OP1 126 B 16 O HOH B 204 1.68 REMARK 500 OP2 DC A 2 O HOH A 208 1.68 REMARK 500 O4' DC B 18 O HOH B 181 1.68 REMARK 500 O HOH A 121 O HOH A 208 1.70 REMARK 500 O5' DG B 11 O HOH B 195 1.77 REMARK 500 OP1 DG B 13 O HOH B 235 1.83 REMARK 500 O HOH B 135 O HOH B 139 1.90 REMARK 500 O4' DG B 13 O HOH B 236 1.94 REMARK 500 O HOH B 162 O HOH B 188 2.05 REMARK 500 O4' DG B 11 O HOH B 180 2.07 REMARK 500 C4' DA A 7 O HOH A 164 2.09 REMARK 500 O HOH B 159 O HOH B 167 2.10 REMARK 500 C7 DT A 4 O HOH A 185 2.10 REMARK 500 O HOH A 125 O HOH A 197 2.12 REMARK 500 O HOH B 127 O HOH B 193 2.12 REMARK 500 O HOH A 145 O HOH A 174 2.12 REMARK 500 OP1 DA B 17 O HOH B 165 2.14 REMARK 500 CK' 126 A 6 O HOH A 230 2.15 REMARK 500 O HOH B 117 O HOH B 182 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 166 O HOH A 178 3545 1.29 REMARK 500 O HOH A 153 O HOH A 178 3545 1.45 REMARK 500 O HOH B 137 O HOH B 200 2454 1.70 REMARK 500 O HOH A 131 O HOH B 177 3655 2.04 REMARK 500 O HOH A 220 O HOH B 184 2455 2.05 REMARK 500 O HOH A 229 O HOH B 176 2554 2.08 REMARK 500 O HOH A 179 O HOH B 160 2554 2.10 REMARK 500 O HOH A 175 O HOH B 188 4555 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 22 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 O6 REMARK 620 2 DT A 4 O4 66.5 REMARK 620 3 DA A 5 N6 107.6 65.6 REMARK 620 4 HOH A 128 O 143.8 78.8 64.4 REMARK 620 5 HOH A 161 O 73.0 128.9 160.5 126.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 21 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 9 O3' REMARK 620 2 DC A 10 OP1 48.5 REMARK 620 3 HOH A 148 O 65.7 65.3 REMARK 620 4 DT B 14 O3' 128.4 82.3 81.6 REMARK 620 5 DA B 15 OP1 172.8 124.3 111.3 44.5 REMARK 620 6 HOH B 202 O 119.6 122.1 61.4 69.5 61.6 REMARK 620 7 HOH B 210 O 67.4 101.5 125.4 151.9 118.2 126.9 REMARK 620 8 HOH B 222 O 116.6 130.8 161.9 106.8 68.5 105.9 49.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 23 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 10 OP2 REMARK 620 2 DC A 10 OP1 45.7 REMARK 620 3 HOH A 114 O 101.7 76.7 REMARK 620 4 DT B 14 O4' 118.7 97.2 115.8 REMARK 620 5 DC B 20 O3' 101.9 147.5 115.4 103.0 REMARK 620 6 HOH B 193 O 125.5 153.5 127.2 63.7 39.8 REMARK 620 N 1 2 3 4 5 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 21 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 22 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 23 DBREF 1I0P A 1 10 PDB 1I0P 1I0P 1 10 DBREF 1I0P B 11 20 PDB 1I0P 1I0P 11 20 SEQRES 1 A 10 DG DC DG DT DA 126 DA DC DG DC SEQRES 1 B 10 DG DC DG DT DA 126 DA DC DG DC MODRES 1I0P 126 A 6 U MODRES 1I0P 126 B 16 U HET 126 A 6 31 HET 126 B 16 31 HET K A 21 1 HET K A 22 1 HET K B 23 1 HETNAM 126 2'-O-METHYL-[TRI(OXYETHYL)]-5-METHYL-URIDINE-5'- HETNAM 2 126 MONOPHOSPHATE HETNAM K POTASSIUM ION FORMUL 1 126 2(C17 H29 N2 O12 P) FORMUL 3 K 3(K 1+) FORMUL 6 HOH *134(H2 O) LINK O3' DA A 5 P 126 A 6 1555 1555 1.60 LINK O3' 126 A 6 P DA A 7 1555 1555 1.61 LINK O3' DA B 15 P 126 B 16 1555 1555 1.60 LINK O3' 126 B 16 P DA B 17 1555 1555 1.61 LINK O6 DG A 3 K K A 22 1555 1555 3.50 LINK O4 DT A 4 K K A 22 1555 1555 2.57 LINK N6 DA A 5 K K A 22 1555 1555 3.34 LINK O3' DG A 9 K K A 21 1555 1555 3.22 LINK OP1 DC A 10 K K A 21 1555 1555 2.62 LINK OP2 DC A 10 K K B 23 4456 1555 3.49 LINK OP1 DC A 10 K K B 23 4456 1555 2.90 LINK K K A 21 O HOH A 148 1555 1555 3.28 LINK K K A 21 O3' DT B 14 1555 4556 3.17 LINK K K A 21 OP1 DA B 15 1555 4556 3.35 LINK K K A 21 O HOH B 202 1555 3555 3.07 LINK K K A 21 O HOH B 210 1555 3555 3.15 LINK K K A 21 O HOH B 222 1555 3555 3.35 LINK K K A 22 O HOH A 128 1555 1555 3.71 LINK K K A 22 O HOH A 161 1555 1555 3.19 LINK O HOH A 114 K K B 23 4456 1555 2.84 LINK O4' DT B 14 K K B 23 1555 1555 2.97 LINK O3' DC B 20 K K B 23 3555 1555 3.17 LINK K K B 23 O HOH B 193 1555 1555 3.70 SITE 1 AC1 5 DG A 9 DC A 10 DT B 14 DA B 15 SITE 2 AC1 5 HOH B 202 SITE 1 AC2 3 DG A 3 DT A 4 DA A 5 SITE 1 AC3 4 DC A 10 HOH A 114 DT B 14 DC B 20 CRYST1 25.180 44.840 44.810 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 0.039714 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022302 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022316 0.00000