HEADER DNA 23-JUN-23 8PJL TITLE DNA DUPLEX FORMING BASE TRIPLETS IN MINOR GROOVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*AP*CP*GP*TP*CP*TP*CP*TP*CP*AP*GP*TP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*AP*CP*TP*GP*AP*GP*AP*GP*AP*CP*GP*TP*A)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS DNA, TRIPLETS, DUPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.ABDULLRAHMAN,C.J.CARDIN,J.P.HALL REVDAT 1 10-JUL-24 8PJL 0 JRNL AUTH A.ABDULLRAHMAN,C.J.CARDIN,J.P.HALL JRNL TITL DNA DUPLEX WITH TRIPLETS BASES IN MINOR GROOVE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 6244 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.220 REMARK 3 FREE R VALUE TEST SET COUNT : 326 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 18.8700 - 2.5200 0.99 2993 141 0.1667 0.2170 REMARK 3 2 2.5200 - 2.0000 1.00 2925 185 0.2558 0.2710 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.164 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.22 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 665 REMARK 3 ANGLE : 0.632 1026 REMARK 3 CHIRALITY : 0.040 115 REMARK 3 PLANARITY : 0.003 29 REMARK 3 DIHEDRAL : 33.028 287 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.8220 1.5190 -7.2345 REMARK 3 T TENSOR REMARK 3 T11: 0.1382 T22: 0.1972 REMARK 3 T33: 0.1393 T12: 0.0213 REMARK 3 T13: 0.0162 T23: 0.0193 REMARK 3 L TENSOR REMARK 3 L11: 4.0343 L22: 1.4001 REMARK 3 L33: 0.2965 L12: -0.3623 REMARK 3 L13: 0.3828 L23: 0.3968 REMARK 3 S TENSOR REMARK 3 S11: -0.0825 S12: 0.0816 S13: -0.1024 REMARK 3 S21: 0.0077 S22: 0.0023 S23: 0.2234 REMARK 3 S31: 0.0003 S32: -0.2595 S33: 0.0780 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.6202 2.9344 -5.8256 REMARK 3 T TENSOR REMARK 3 T11: 0.1726 T22: 0.2399 REMARK 3 T33: 0.1462 T12: 0.0021 REMARK 3 T13: 0.0184 T23: 0.0374 REMARK 3 L TENSOR REMARK 3 L11: 7.6617 L22: 2.6975 REMARK 3 L33: 1.2546 L12: 0.2585 REMARK 3 L13: -1.0632 L23: 0.7988 REMARK 3 S TENSOR REMARK 3 S11: -0.1767 S12: -0.3190 S13: -0.5944 REMARK 3 S21: 0.0513 S22: -0.0241 S23: 0.2000 REMARK 3 S31: 0.0258 S32: -0.2768 S33: 0.1459 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8PJL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131440. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU PHOTONJET-S REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6283 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 19.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.10000 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: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: A SOLUTION CONTAINING 20MM NA REMARK 280 -CACODYLATE, 10 MM MGCL2, 0.6MM DNA WAS MIXED IN A 1:1 RATIO REMARK 280 WITH A SOLUTION CONTAINING 56.25% V/V (+/-)-2-METHYL-2,4- REMARK 280 PENTANEDIOL, 30 MM NA-CACODYLATE PH 6.0, 30 MM NA-CACODYLATE REMARK 280 3H2O, 12MM SRCL2 6H2O. TOTAL DROP VOLUME WAS 400NL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 29.48200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 14.74100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.22300 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DG B 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DG B 1 N9 C8 N7 C5 C6 O6 N1 REMARK 470 DG B 1 C2 N2 N3 C4 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 A 253 DISTANCE = 8.83 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 MG A 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 1 O2 REMARK 620 2 DT A 5 O2 101.0 REMARK 620 3 HOH A 214 O 91.9 26.3 REMARK 620 4 DC B 11 O2 87.7 13.3 24.3 REMARK 620 5 HOH B 211 O 106.5 104.7 83.9 108.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 7 OP2 REMARK 620 2 HOH A 224 O 81.3 REMARK 620 3 HOH A 230 O 92.2 90.8 REMARK 620 4 HOH B 201 O 84.2 163.5 81.9 REMARK 620 5 HOH B 206 O 90.0 88.6 177.5 99.3 REMARK 620 6 HOH B 209 O 176.1 95.9 85.1 98.1 92.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 104 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 14 O2 REMARK 620 2 HOH A 205 O 10.5 REMARK 620 3 HOH A 208 O 7.8 3.3 REMARK 620 4 HOH A 234 O 7.8 5.4 5.6 REMARK 620 5 HOH A 249 O 12.1 5.8 7.9 4.4 REMARK 620 6 HOH B 217 O 12.9 2.5 5.3 7.7 6.9 REMARK 620 7 HOH B 231 O 14.4 4.3 7.5 7.8 5.3 3.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 204 O REMARK 620 2 HOH A 206 O 96.8 REMARK 620 3 HOH A 210 O 86.8 175.8 REMARK 620 4 HOH A 213 O 83.0 84.6 97.9 REMARK 620 5 HOH A 216 O 92.7 95.5 82.2 175.6 REMARK 620 6 HOH A 245 O 175.2 84.1 92.5 92.4 91.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 105 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 201 O REMARK 620 2 HOH A 203 O 51.9 REMARK 620 3 HOH A 229 O 67.4 67.3 REMARK 620 4 HOH A 239 O 103.9 61.0 56.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA B 10 OP1 REMARK 620 2 HOH B 229 O 98.6 REMARK 620 N 1 DBREF 8PJL A 1 14 PDB 8PJL 8PJL 1 14 DBREF 8PJL B 1 14 PDB 8PJL 8PJL 1 14 SEQRES 1 A 14 DT DA DC DG DT DC DT DC DT DC DA DG DT SEQRES 2 A 14 DC SEQRES 1 B 14 DG DA DC DT DG DA DG DA DG DA DC DG DT SEQRES 2 B 14 DA HET MG A 101 1 HET MG A 102 1 HET MG A 103 1 HET K A 104 1 HET K A 105 1 HET MG B 101 1 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION FORMUL 3 MG 4(MG 2+) FORMUL 6 K 2(K 1+) FORMUL 9 HOH *92(H2 O) LINK O2 DT A 1 MG MG A 103 1555 1555 2.46 LINK O2 DT A 5 MG MG A 103 1555 3555 2.37 LINK OP2 DT A 7 MG MG A 102 1555 1555 2.11 LINK O2 DC A 14 K K A 104 1555 1455 2.65 LINK MG MG A 101 O HOH A 204 1555 4554 2.28 LINK MG MG A 101 O HOH A 206 1555 1555 2.24 LINK MG MG A 101 O HOH A 210 1555 4554 2.21 LINK MG MG A 101 O HOH A 213 1555 4554 1.98 LINK MG MG A 101 O HOH A 216 1555 1555 2.11 LINK MG MG A 101 O HOH A 245 1555 4554 2.28 LINK MG MG A 102 O HOH A 224 1555 1555 2.27 LINK MG MG A 102 O HOH A 230 1555 1555 2.05 LINK MG MG A 102 O HOH B 201 1555 3555 2.31 LINK MG MG A 102 O HOH B 206 1555 3555 2.22 LINK MG MG A 102 O HOH B 209 1555 3555 2.03 LINK MG MG A 103 O HOH A 214 1555 4554 2.36 LINK MG MG A 103 O2 DC B 11 3555 1555 2.34 LINK MG MG A 103 O HOH B 211 1555 4554 2.45 LINK K K A 104 O HOH A 205 1555 1555 2.70 LINK K K A 104 O HOH A 208 1555 1555 2.87 LINK K K A 104 O HOH A 234 1555 1555 2.69 LINK K K A 104 O HOH A 249 1555 1655 2.80 LINK K K A 104 O HOH B 217 1555 1555 2.82 LINK K K A 104 O HOH B 231 1555 1555 3.06 LINK K K A 105 O HOH A 201 1555 1555 2.98 LINK K K A 105 O HOH A 203 1555 1555 2.89 LINK K K A 105 O HOH A 229 1555 1555 2.86 LINK K K A 105 O HOH A 239 1555 1555 2.79 LINK OP1 DA B 10 MG MG B 101 1555 1555 2.28 LINK MG MG B 101 O HOH B 229 1555 1555 2.95 CRYST1 39.833 39.833 58.964 90.00 90.00 90.00 P 41 4 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 0.025105 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025105 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016960 0.00000