HEADER DNA-RNA HYBRID 23-JUN-21 7OXS TITLE 1.91 A CRYSTAL STRUCTURE OF DNA/2'-O-METHYL-RNA HETERODUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*TP*CP*TP*CP*CP*TP*AP*G)-3'); COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'-R(*(OMC)P*(OMU)P*(A2M)P*(OMG)P*(OMG)P*(A2M)P*(OMG) COMPND 7 P*(A2M)P*(OMC))-3'); COMPND 8 CHAIN: B, D; COMPND 9 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, 2'-O-METHYL-RNA, HETERODUPLEX, OLIGONUCLEOTIDES, DNA-RNA HYBRID EXPDTA X-RAY DIFFRACTION AUTHOR R.M.DOLOT,A.MACIASZEK,B.C.NAWROT REVDAT 3 31-JAN-24 7OXS 1 REMARK REVDAT 2 08-JUN-22 7OXS 1 JRNL REVDAT 1 14-JUL-21 7OXS 0 JRNL AUTH R.DOLOT,A.MACIASZEK,B.MIKOLAJCZYK,B.NAWROT JRNL TITL FIRST HIGH-RESOLUTION CRYSTAL STRUCTURES OF JRNL TITL 2 DNA:2'-O-METHYL-RNA HETERODUPLEXES JRNL REF CRYSTALS 2022 JRNL REFN ESSN 2073-4352 JRNL DOI 10.3390/CRYST12060760 REMARK 2 REMARK 2 RESOLUTION. 1.91 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 20911 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.860 REMARK 3 FREE R VALUE TEST SET COUNT : 1852 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 25.4200 - 4.4800 1.00 1482 142 0.1381 0.1499 REMARK 3 2 4.4700 - 3.5600 1.00 1455 146 0.1495 0.1625 REMARK 3 3 3.5500 - 3.1100 0.99 1477 141 0.1752 0.1770 REMARK 3 4 3.1000 - 2.8200 1.00 1462 145 0.2273 0.2229 REMARK 3 5 2.8200 - 2.6200 1.00 1471 138 0.2870 0.3151 REMARK 3 6 2.6200 - 2.4700 1.00 1477 145 0.2640 0.2800 REMARK 3 7 2.4600 - 2.3400 1.00 1477 144 0.2321 0.2964 REMARK 3 8 2.3400 - 2.2400 1.00 1465 142 0.2284 0.2477 REMARK 3 9 2.2400 - 2.1500 1.00 1450 141 0.2447 0.2801 REMARK 3 10 2.1500 - 2.0800 1.00 1484 144 0.2479 0.2910 REMARK 3 11 2.0800 - 2.0100 1.00 1478 145 0.2399 0.3350 REMARK 3 12 2.0100 - 1.9600 1.00 1466 140 0.2623 0.2945 REMARK 3 13 1.9600 - 1.9100 0.96 1415 139 0.2864 0.2780 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) : 0.264 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.268 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.51 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 : 0.008 854 REMARK 3 ANGLE : 1.109 1308 REMARK 3 CHIRALITY : 0.046 142 REMARK 3 PLANARITY : 0.004 258 REMARK 3 DIHEDRAL : 10.994 546 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7OXS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1292116439. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91840 REMARK 200 MONOCHROMATOR : DCM SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20931 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 48.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.01 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: 7OW0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M LI2SO4, 50 MM SODIUM CACODYLATE REMARK 280 PH 6.5, 10 MM SPERMINE, 15 MM MGCL2, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.84000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.42000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.42000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.84000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 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 B 130 DISTANCE = 5.82 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7OW0 RELATED DB: PDB REMARK 900 7OW0 CONTAINS DNA/2'OMERNA HETERODUPLEX WITH OVERHANGS DBREF 7OXS A 1 9 PDB 7OXS 7OXS 1 9 DBREF 7OXS B 1 9 PDB 7OXS 7OXS 1 9 DBREF 7OXS C 1 9 PDB 7OXS 7OXS 1 9 DBREF 7OXS D 1 9 PDB 7OXS 7OXS 1 9 SEQRES 1 A 9 DG DT DC DT DC DC DT DA DG SEQRES 1 B 9 OMC OMU A2M OMG OMG A2M OMG A2M OMC SEQRES 1 C 9 DG DT DC DT DC DC DT DA DG SEQRES 1 D 9 OMC OMU A2M OMG OMG A2M OMG A2M OMC HET OMC B 1 18 HET OMU B 2 21 HET A2M B 3 23 HET OMG B 4 24 HET OMG B 5 24 HET A2M B 6 23 HET OMG B 7 24 HET A2M B 8 23 HET OMC B 9 21 HET OMC D 1 18 HET OMU D 2 21 HET A2M D 3 23 HET OMG D 4 24 HET OMG D 5 24 HET A2M D 6 23 HET OMG D 7 24 HET A2M D 8 23 HET OMC D 9 21 HET SO4 A 101 5 HET SO4 C 101 5 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM OMU O2'-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM A2M 2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM OMG O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 2 OMC 4(C10 H16 N3 O8 P) FORMUL 2 OMU 2(C10 H15 N2 O9 P) FORMUL 2 A2M 6(C11 H16 N5 O7 P) FORMUL 2 OMG 6(C11 H16 N5 O8 P) FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 HOH *77(H2 O) LINK O3' OMC B 1 P OMU B 2 1555 1555 1.60 LINK O3' OMU B 2 P A2M B 3 1555 1555 1.60 LINK O3' A2M B 3 P OMG B 4 1555 1555 1.60 LINK O3' OMG B 4 P OMG B 5 1555 1555 1.60 LINK O3' OMG B 5 P A2M B 6 1555 1555 1.60 LINK O3' A2M B 6 P OMG B 7 1555 1555 1.61 LINK O3' OMG B 7 P A2M B 8 1555 1555 1.60 LINK O3' A2M B 8 P OMC B 9 1555 1555 1.60 LINK O3' OMC D 1 P OMU D 2 1555 1555 1.62 LINK O3' OMU D 2 P A2M D 3 1555 1555 1.61 LINK O3' A2M D 3 P OMG D 4 1555 1555 1.60 LINK O3' OMG D 4 P OMG D 5 1555 1555 1.60 LINK O3' OMG D 5 P A2M D 6 1555 1555 1.61 LINK O3' A2M D 6 P OMG D 7 1555 1555 1.60 LINK O3' OMG D 7 P A2M D 8 1555 1555 1.60 LINK O3' A2M D 8 P OMC D 9 1555 1555 1.60 CRYST1 56.130 56.130 76.260 90.00 90.00 120.00 P 32 2 1 12 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 0.017816 0.010286 0.000000 0.00000 SCALE2 0.000000 0.020572 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013113 0.00000