HEADER DNA 28-JUL-15 5AXE TITLE CRYSTAL STRUCTURE ANALYSIS OF DNA DUPLEXES CONTAINING SULFOAMIDE- TITLE 2 BRIDGED NUCLEIC ACID (SUNA-NH) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*GP*TP*AP*(LSH)P*AP*CP*GP*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS A-FORM DNA, SULFONAMIDE-BRIDGED NUCLEIC ACID, SUNA[NH], ANTISENSE, KEYWDS 2 DNA EXPDTA X-RAY DIFFRACTION AUTHOR Y.MITSUOKA,H.AOYAMA,A.KUGIMIYA,Y.FUJIMURA,T.YAMAMOTO,R.WAKI,F.WADA, AUTHOR 2 S.TAHARA,M.SAWAMURA,M.NODA,Y.HARI,S.OBIKA REVDAT 3 08-NOV-23 5AXE 1 REMARK REVDAT 2 26-FEB-20 5AXE 1 REMARK REVDAT 1 20-JUL-16 5AXE 0 JRNL AUTH Y.MITSUOKA,H.AOYAMA,A.KUGIMIYA,Y.FUJIMURA,T.YAMAMOTO,R.WAKI, JRNL AUTH 2 F.WADA,S.TAHARA,M.SAWAMURA,M.NODA,Y.HARI,S.OBIKA JRNL TITL EFFECT OF AN N-SUBSTITUENT IN SULFONAMIDE-BRIDGED NUCLEIC JRNL TITL 2 ACID (SUNA) ON HYBRIDIZATION ABILITY AND DUPLEX STRUCTURE. JRNL REF ORG.BIOMOL.CHEM. V. 14 6531 2016 JRNL REFN ESSN 1477-0539 JRNL PMID 27296230 JRNL DOI 10.1039/C6OB01051B REMARK 2 REMARK 2 RESOLUTION. 0.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 0.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 29154 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.126 REMARK 3 R VALUE (WORKING SET) : 0.125 REMARK 3 FREE R VALUE : 0.144 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2762 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 16.3540 - 2.5830 0.79 2084 118 0.1556 0.1842 REMARK 3 2 2.5830 - 2.0515 1.00 2616 164 0.1498 0.1525 REMARK 3 3 2.0515 - 1.7925 1.00 2657 125 0.1274 0.1391 REMARK 3 4 1.7925 - 1.6288 1.00 2657 126 0.1181 0.1270 REMARK 3 5 1.6288 - 1.5122 1.00 2627 152 0.1242 0.1561 REMARK 3 6 1.5122 - 1.4231 1.00 2648 118 0.1278 0.1465 REMARK 3 7 1.4231 - 1.3518 1.00 2635 152 0.1223 0.1430 REMARK 3 8 1.3518 - 1.2930 1.00 2629 151 0.1124 0.1417 REMARK 3 9 1.2930 - 1.2432 1.00 2667 105 0.1123 0.1249 REMARK 3 10 1.2432 - 1.2004 1.00 2703 100 0.1059 0.1346 REMARK 3 11 1.2004 - 1.1628 1.00 2628 152 0.1036 0.1226 REMARK 3 12 1.1628 - 1.1296 1.00 2585 158 0.1056 0.1149 REMARK 3 13 1.1296 - 1.0999 1.00 2692 128 0.1011 0.1164 REMARK 3 14 1.0999 - 1.0730 1.00 2625 127 0.1063 0.1273 REMARK 3 15 1.0730 - 1.0487 1.00 2636 154 0.1041 0.1324 REMARK 3 16 1.0487 - 1.0263 1.00 2605 165 0.1051 0.1236 REMARK 3 17 1.0263 - 1.0058 1.00 2657 147 0.1100 0.1259 REMARK 3 18 1.0058 - 0.9868 1.00 2622 140 0.1199 0.1695 REMARK 3 19 0.9868 - 0.9692 1.00 2672 122 0.1295 0.1656 REMARK 3 20 0.9692 - 0.9528 0.97 2521 158 0.1413 0.1379 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) : 0.050 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 10.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 4.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.50 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 : 0.010 734 REMARK 3 ANGLE : 1.600 1138 REMARK 3 CHIRALITY : 0.287 128 REMARK 3 PLANARITY : 0.017 32 REMARK 3 DIHEDRAL : 16.223 322 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: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 5AXE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1300000124. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29154 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 23.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 12.50 REMARK 200 R MERGE FOR SHELL (I) : 0.24100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 1I5W REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND REMARK 200 I_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, PH 7.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K 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 11.84250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.60250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.45250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.60250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 11.84250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.45250 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 170 O HOH B 160 2.04 REMARK 500 O HOH A 161 O HOH B 160 2.14 REMARK 500 O HOH A 147 O HOH A 170 2.15 REMARK 500 O HOH A 104 O HOH A 125 2.17 REMARK 500 O HOH A 134 O HOH A 147 2.18 REMARK 500 O HOH B 117 O HOH B 148 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 147 DISTANCE = 6.23 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AXF RELATED DB: PDB DBREF 5AXE A 1 10 PDB 5AXE 5AXE 1 10 DBREF 5AXE B 11 20 PDB 5AXE 5AXE 11 20 SEQRES 1 A 10 DG DC DG DT DA LSH DA DC DG DC SEQRES 1 B 10 DG DC DG DT DA LSH DA DC DG DC HET LSH A 6 25 HET LSH B 16 25 HETNAM LSH [(1R,5R,7R,8S)-7-[5-METHYL-2,4-BIS(OXIDANYLIDENE) HETNAM 2 LSH PYRIMIDIN-1-YL]-8-OXIDANYL-3,3-BIS(OXIDANYLIDENE)-6- HETNAM 3 LSH OXA-3$L^{6}-THIA-2-AZABICYCLO[3.2.1]OCTAN-5-YL]METHYL HETNAM 4 LSH DIHYDROGEN PHOSPHATE FORMUL 1 LSH 2(C11 H16 N3 O10 P S) FORMUL 3 HOH *140(H2 O) LINK O3' DA A 5 P LSH A 6 1555 1555 1.61 LINK O3' LSH A 6 P DA A 7 1555 1555 1.60 LINK O3' DA B 15 P LSH B 16 1555 1555 1.60 LINK O3' LSH B 16 P DA B 17 1555 1555 1.61 CRYST1 23.685 42.905 45.205 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 0.042221 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023307 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022121 0.00000