HEADER DNA 29-JAN-01 1I0J TITLE 1.06 A STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O- TITLE 2 METHYL-3'-METHYLENEPHOSPHONATE (T23) THYMINE IN PLACE OF T6, HIGH CS- TITLE 3 SALT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*TP*AP*(T23)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 4 07-FEB-24 1I0J 1 REMARK REVDAT 3 22-JUN-22 1I0J 1 REMARK SEQRES LINK REVDAT 2 24-FEB-09 1I0J 1 VERSN REVDAT 1 04-APR-01 1I0J 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. 1.06 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 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.06 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) : 0.150 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.169 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) : 6913 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 : 408 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 92 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 1I0J 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_1000012754. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-99 REMARK 200 TEMPERATURE (KELVIN) : NULL 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 : 6913 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.060 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 (%) : 97.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05700 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: SAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CS, PH 6.0, VAPOR DIFFUSION, HANGING REMARK 280 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 12.41000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.41000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.16500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.41000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.41000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.16500 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 A 133 O HOH A 173 1.09 REMARK 500 O HOH B 174 O HOH B 182 1.39 REMARK 500 OP1 DG B 13 O HOH B 148 1.59 REMARK 500 N3 DA B 17 O HOH B 189 1.59 REMARK 500 O HOH A 113 O HOH A 146 1.66 REMARK 500 O HOH A 110 O HOH A 172 1.67 REMARK 500 O HOH B 143 O HOH B 188 1.72 REMARK 500 OP2 DC B 20 O HOH B 179 1.74 REMARK 500 O HOH B 178 O HOH B 189 1.77 REMARK 500 O HOH A 119 O HOH A 176 1.82 REMARK 500 N6 DA B 15 O HOH B 164 1.89 REMARK 500 C1' DG B 13 O HOH B 135 1.90 REMARK 500 C2 DA A 5 O HOH B 158 1.96 REMARK 500 O HOH B 141 O HOH B 162 1.97 REMARK 500 C5' DG A 3 O HOH A 176 2.02 REMARK 500 C5' DT A 4 O HOH A 175 2.04 REMARK 500 O HOH B 125 O HOH B 135 2.10 REMARK 500 OP1 DT B 14 O HOH B 140 2.15 REMARK 500 O HOH B 164 O HOH B 192 2.16 REMARK 500 C5' T23 B 16 O HOH B 154 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 130 O HOH B 136 3545 1.65 REMARK 500 O HOH A 133 O HOH A 138 2555 1.90 REMARK 500 O HOH A 126 O HOH A 172 2554 1.93 REMARK 500 O HOH A 133 O HOH A 175 2555 2.16 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 CS A 22 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 O6 REMARK 620 2 DG A 3 N7 52.2 REMARK 620 3 DT A 4 O4 61.7 82.9 REMARK 620 4 DA A 5 N6 96.7 137.3 54.9 REMARK 620 5 HOH A 153 O 73.1 52.1 130.3 155.7 REMARK 620 6 HOH A 159 O 110.3 61.9 92.4 119.9 84.4 REMARK 620 7 HOH A 191 O 127.9 128.3 66.7 44.4 156.4 78.1 REMARK 620 8 HOH B 164 O 145.0 162.8 105.0 54.4 124.2 102.1 46.6 REMARK 620 9 HOH B 192 O 152.5 133.0 138.5 88.7 91.1 89.7 73.3 34.7 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CS A 21 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 9 O3' REMARK 620 2 DC A 10 OP1 46.7 REMARK 620 3 HOH A 123 O 99.7 88.8 REMARK 620 4 DT B 14 O3' 112.4 68.6 95.6 REMARK 620 5 DA B 15 OP1 153.6 107.1 72.8 45.6 REMARK 620 6 DC B 20 OP1 92.9 132.8 73.2 153.9 108.3 REMARK 620 7 DC B 20 OP2 82.4 127.3 116.9 142.1 123.7 43.8 REMARK 620 8 HOH B 120 O 69.9 93.8 47.2 140.4 115.9 42.3 77.0 REMARK 620 9 HOH B 161 O 155.8 147.3 100.1 79.3 48.0 79.7 76.3 115.3 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CS A 23 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 10 OP2 REMARK 620 2 DC A 10 OP1 41.8 REMARK 620 3 HOH A 131 O 142.6 132.4 REMARK 620 4 DT B 14 O4' 113.2 71.6 80.6 REMARK 620 5 DC B 20 O3' 97.8 101.4 117.2 91.0 REMARK 620 6 HOH B 125 O 161.7 139.9 54.1 71.6 64.1 REMARK 620 7 HOH B 128 O 106.2 135.9 91.7 123.6 44.2 59.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CS A 21 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CS A 22 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CS A 23 DBREF 1I0J A 1 10 PDB 1I0J 1I0J 1 10 DBREF 1I0J B 11 20 PDB 1I0J 1I0J 11 20 SEQRES 1 A 10 DG DC DG DT DA T23 DA DC DG DC SEQRES 1 B 10 DG DC DG DT DA T23 DA DC DG DC HET T23 A 6 22 HET T23 B 16 22 HET CS A 21 1 HET CS A 22 1 HET CS A 23 1 HETNAM T23 2'-O-METHYL-3'-METHYL-3'-DEOXY-ARABINOFURANOSYL- HETNAM 2 T23 THYMINE-5'-PHOSPHATE HETNAM CS CESIUM ION FORMUL 1 T23 2(C12 H19 N2 O8 P) FORMUL 3 CS 3(CS 1+) FORMUL 6 HOH *92(H2 O) LINK O3' DA A 5 P T23 A 6 1555 1555 1.61 LINK C3M T23 A 6 P DA A 7 1555 1555 1.62 LINK O3' DA B 15 P T23 B 16 1555 1555 1.60 LINK C3M T23 B 16 P DA B 17 1555 1555 1.62 LINK O6 DG A 3 CS CS A 22 1555 1555 3.56 LINK N7 DG A 3 CS CS A 22 1555 1555 3.50 LINK O4 DT A 4 CS CS A 22 1555 1555 3.08 LINK N6 DA A 5 CS CS A 22 1555 1555 3.89 LINK O3' DG A 9 CS CS A 21 1555 1555 3.17 LINK OP1 DC A 10 CS CS A 21 1555 1555 3.17 LINK OP2 DC A 10 CS CS A 23 1555 1555 2.89 LINK OP1 DC A 10 CS CS A 23 1555 1555 3.86 LINK CS CS A 21 O HOH A 123 1555 2555 3.34 LINK CS CS A 21 O3' DT B 14 1555 4556 3.18 LINK CS CS A 21 OP1 DA B 15 1555 4556 3.32 LINK CS CS A 21 OP1 DC B 20 1555 3555 3.61 LINK CS CS A 21 OP2 DC B 20 1555 3555 3.24 LINK CS CS A 21 O HOH B 120 1555 3555 3.44 LINK CS CS A 21 O HOH B 161 1555 4556 3.25 LINK CS CS A 21 O HOH B 179 1555 3555 2.64 LINK CS CS A 21 O HOH B 190 1555 3555 2.94 LINK CS CS A 22 O HOH A 153 1555 1555 3.35 LINK CS CS A 22 O HOH A 159 1555 1555 3.77 LINK CS CS A 22 O HOH A 191 1555 1555 2.91 LINK CS CS A 22 O HOH B 164 1555 1555 3.70 LINK CS CS A 22 O HOH B 192 1555 1555 2.58 LINK CS CS A 22 O HOH B 193 1555 1555 3.33 LINK CS CS A 23 O HOH A 131 1555 3655 3.04 LINK CS CS A 23 O4' DT B 14 1555 4556 3.27 LINK CS CS A 23 O3' DC B 20 1555 2555 3.42 LINK CS CS A 23 O HOH B 125 1555 4556 3.30 LINK CS CS A 23 O HOH B 128 1555 2555 3.28 SITE 1 AC1 7 DG A 9 DC A 10 DT B 14 DA B 15 SITE 2 AC1 7 DC B 20 HOH B 179 HOH B 190 SITE 1 AC2 4 DG A 3 DT A 4 HOH A 191 HOH B 192 SITE 1 AC3 4 DC A 10 HOH A 131 DT B 14 DC B 20 CRYST1 24.820 44.330 44.820 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 0.040290 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022558 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022311 0.00000