HEADER DNA 22-DEC-22 8HU5 TITLE CRYSTAL STRUCTURE OF DNA OCTAMER CONTAINING GUNA[ME,TBU] COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*(LR6)P*GP*(BRU)P*AP*CP*AP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DNA, OLIGONUCLEOTIDE, MODIFIED BASE, ARTIFICIAL NUCLEIC ACID EXPDTA X-RAY DIFFRACTION AUTHOR H.AOYAMA,H.OBIKA,T.YAMAGUCHI REVDAT 2 06-SEP-23 8HU5 1 JRNL REVDAT 1 09-AUG-23 8HU5 0 JRNL AUTH T.YAMAGUCHI,N.HORIE,H.AOYAMA,S.KUMAGAI,S.OBIKA JRNL TITL MECHANISM OF THE EXTREMELY HIGH DUPLEX-FORMING ABILITY OF JRNL TITL 2 OLIGONUCLEOTIDES MODIFIED WITH N-TERT-BUTYLGUANIDINE- OR JRNL TITL 3 N-TERT-BUTYL-N'- METHYLGUANIDINE-BRIDGED NUCLEIC ACIDS. JRNL REF NUCLEIC ACIDS RES. V. 51 7749 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 37462081 JRNL DOI 10.1093/NAR/GKAD608 REMARK 2 REMARK 2 RESOLUTION. 0.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20-1-4487 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 27813 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2778 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 10.0000 - 2.5300 0.98 1260 145 0.1846 0.1995 REMARK 3 2 2.5300 - 2.0100 1.00 1276 136 0.1814 0.2162 REMARK 3 3 2.0100 - 1.7500 1.00 1275 144 0.1712 0.1896 REMARK 3 4 1.7500 - 1.5900 1.00 1291 146 0.1556 0.1800 REMARK 3 5 1.5900 - 1.4800 1.00 1283 140 0.1851 0.2032 REMARK 3 6 1.4800 - 1.3900 1.00 1285 143 0.1981 0.2298 REMARK 3 7 1.3900 - 1.3200 1.00 1262 142 0.2036 0.2211 REMARK 3 8 1.3200 - 1.2600 1.00 1287 148 0.1988 0.1972 REMARK 3 9 1.2600 - 1.2200 1.00 1274 137 0.1945 0.1970 REMARK 3 10 1.2200 - 1.1700 1.00 1290 140 0.2044 0.2337 REMARK 3 11 1.1700 - 1.1400 1.00 1265 145 0.2084 0.2211 REMARK 3 12 1.1400 - 1.1000 1.00 1299 141 0.2141 0.2669 REMARK 3 13 1.1000 - 1.0800 1.00 1275 143 0.2303 0.2418 REMARK 3 14 1.0800 - 1.0500 1.00 1278 142 0.2342 0.2676 REMARK 3 15 1.0500 - 1.0300 1.00 1293 138 0.2468 0.3015 REMARK 3 16 1.0300 - 1.0000 1.00 1272 144 0.2422 0.2460 REMARK 3 17 1.0000 - 0.9800 1.00 1263 144 0.2508 0.2956 REMARK 3 18 0.9800 - 0.9600 0.99 1272 135 0.2793 0.2963 REMARK 3 19 0.9600 - 0.9500 0.95 1241 138 0.2928 0.3228 REMARK 3 20 0.9500 - 0.9300 0.62 794 87 0.3031 0.2761 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.270 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 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 : 0.008 191 REMARK 3 ANGLE : 2.399 296 REMARK 3 CHIRALITY : 0.088 31 REMARK 3 PLANARITY : 0.017 10 REMARK 3 DIHEDRAL : 23.321 85 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.3033 8.7428 3.6578 REMARK 3 T TENSOR REMARK 3 T11: 0.0966 T22: 0.0867 REMARK 3 T33: 0.0760 T12: 0.0064 REMARK 3 T13: 0.0010 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 1.3772 L22: 2.3202 REMARK 3 L33: 0.6077 L12: 0.8143 REMARK 3 L13: 0.2878 L23: -0.0906 REMARK 3 S TENSOR REMARK 3 S11: -0.0083 S12: 0.1349 S13: 0.0310 REMARK 3 S21: -0.1852 S22: 0.0768 S23: 0.0455 REMARK 3 S31: 0.0354 S32: 0.0713 S33: -0.0560 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 8HU5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300033721. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9199 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27813 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.930 REMARK 200 RESOLUTION RANGE LOW (A) : 21.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 6.560 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.99 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23700 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: SAD 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 (%): 41.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% V/V (+/-)-2-METHYL-2,4 REMARK 280 -PENTANEDIOL, 0.040M SODIUM CACODYLATE TRIHYDRATE PH 6.0, 0.012M REMARK 280 SPERMINE TETRAHYDROCHLORIDE, 0.012M SODIUM CHLORIDE, 0.080M REMARK 280 POTASSIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+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 12.15750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.24700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.24700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.23625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.24700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.24700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 6.07875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.24700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.24700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 18.23625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.24700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.24700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 6.07875 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 12.15750 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 TOTAL BURIED SURFACE AREA: 2030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 42.49400 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 42.49400 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 12.15750 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8HIS RELATED DB: PDB REMARK 900 8HIS CONTAINS THE SAME LIGAND AND WILL BE SUBMITTED TO THE SAME REMARK 900 PAPER. DBREF 8HU5 A 1 8 PDB 8HU5 8HU5 1 8 SEQRES 1 A 8 DG LR6 DG BRU DA DC DA DC HET LR6 A 2 30 HET BRU A 4 20 HETNAM LR6 [(1R,3R,4R,7S)-5-(N'-TERT-BUTYL-N-METHYL- HETNAM 2 LR6 CARBAMIMIDOYL)-3-[5-METHYL-2,4-BIS(OXIDANYLIDENE) HETNAM 3 LR6 PYRIMIDIN-1-YL]-7-OXIDANYL-2-OXA-5- HETNAM 4 LR6 AZABICYCLO[2.2.1]HEPTAN-1-YL]METHYL DIHYDROGEN HETNAM 5 LR6 PHOSPHATE HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE FORMUL 1 LR6 C17 H28 N5 O8 P FORMUL 1 BRU C9 H12 BR N2 O8 P FORMUL 2 HOH *50(H2 O) LINK O3' DG A 1 P LR6 A 2 1555 1555 1.60 LINK O3' LR6 A 2 P DG A 3 1555 1555 1.60 LINK O3' DG A 3 P BRU A 4 1555 1555 1.60 LINK O3' BRU A 4 P DA A 5 1555 1555 1.60 CRYST1 42.494 42.494 24.315 90.00 90.00 90.00 P 43 21 2 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 0.023533 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023533 0.000000 0.00000 SCALE3 0.000000 0.000000 0.041127 0.00000