HEADER RNA 09-FEB-26 23KA TITLE PRE-MIR-6074 INTERNAL LOOP IN COMPLEX WITH AMILORIDE (FORM 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (35-MER); COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS PRE-MIR-6074, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,M.OKADA,K.TSUZUKI,K.ONIZUKA,R.NAGASAWA,E.MIYASHITA, AUTHOR 2 K.R.KOMATSU,H.SAITO,F.NAGATSUGI REVDAT 1 06-MAY-26 23KA 0 JRNL AUTH K.TSUZUKI,K.ONIZUKA,M.OKADA,R.NAGASAWA,E.MIYASHITA, JRNL AUTH 2 K.R.KOMATSU,H.SAITO,J.KONDO,F.NAGATSUGI JRNL TITL RNA-BINDING LANDSCAPE OF AMILORIDE: LARGE-SCALE PROFILING JRNL TITL 2 AND STRUCTURAL BASIS OF U-U MISMATCH RECOGNITION JRNL REF RSC CHEM BIOL 2025 JRNL REFN ESSN 2633-0679 JRNL DOI 10.1039/D6CB00055J REMARK 2 REMARK 2 RESOLUTION. 2.59 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) : 2.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 13903 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1413 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 37.6000 - 5.5800 1.00 1217 152 0.1335 0.1649 REMARK 3 2 5.5800 - 4.4300 1.00 1265 139 0.1246 0.1393 REMARK 3 3 4.4300 - 3.8700 1.00 1256 136 0.1522 0.1716 REMARK 3 4 3.8700 - 3.5200 1.00 1263 144 0.1623 0.2153 REMARK 3 5 3.5200 - 3.2700 1.00 1254 136 0.2023 0.2454 REMARK 3 6 3.2700 - 3.0700 1.00 1215 142 0.2029 0.2562 REMARK 3 7 3.0700 - 2.9200 1.00 1266 146 0.2588 0.3517 REMARK 3 8 2.9200 - 2.7900 1.00 1244 140 0.3234 0.3948 REMARK 3 9 2.7900 - 2.6900 1.00 1282 150 0.3730 0.4398 REMARK 3 10 2.6900 - 2.5900 0.99 1228 128 0.3324 0.3130 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.600 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 : 0.009 2557 REMARK 3 ANGLE : 1.591 3975 REMARK 3 CHIRALITY : 0.089 522 REMARK 3 PLANARITY : 0.011 111 REMARK 3 DIHEDRAL : 14.402 1251 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 23KA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1300070025. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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 : 13907 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.590 REMARK 200 RESOLUTION RANGE LOW (A) : 37.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.34300 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE TRIBASIC DIHYDRATE, REMARK 280 SODIUM CACODYLATE TRIHYDRATE, 2-PROPANOL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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 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 70.77200 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 35.38600 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 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 G B 28 O3' - P - OP1 ANGL. DEV. = 7.8 DEGREES 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 NA A 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 13 O6 REMARK 620 2 HOH A 205 O 65.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 103 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 10 O3' REMARK 620 2 A B 10 O2' 63.0 REMARK 620 3 G B 12 O6 132.1 76.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A C 10 O2' REMARK 620 2 G C 12 O6 67.5 REMARK 620 3 HOH C 207 O 177.3 111.0 REMARK 620 N 1 2 DBREF 23KA A 1 35 PDB 23KA 23KA 1 35 DBREF 23KA B 1 35 PDB 23KA 23KA 1 35 DBREF 23KA C 1 35 PDB 23KA 23KA 1 35 SEQRES 1 A 35 G C U U G C U C U A A G G SEQRES 2 A 35 C A U G A A A G U G C U A SEQRES 3 A 35 U G A G A U A G C SEQRES 1 B 35 G C U U G C U C U A A G G SEQRES 2 B 35 C A U G A A A G U G C U A SEQRES 3 B 35 U G A G A U A G C SEQRES 1 C 35 G C U U G C U C U A A G G SEQRES 2 C 35 C A U G A A A G U G C U A SEQRES 3 C 35 U G A G A U A G C HET AMR A 101 15 HET NA A 102 1 HET AMR B 101 15 HET CAD B 102 5 HET NA B 103 1 HET AMR C 101 15 HET NA C 102 1 HETNAM AMR 3,5-DIAMINO-N-(AMINOIMINOMETHYL)-6- HETNAM 2 AMR CHLOROPYRAZINECARBOXAMIDE HETNAM NA SODIUM ION HETNAM CAD CACODYLIC ACID HETSYN AMR AMILORIDE HETSYN CAD HYDROXYDIMETHYLARSINE OXIDE FORMUL 4 AMR 3(C6 H8 CL N7 O) FORMUL 5 NA 3(NA 1+) FORMUL 7 CAD C2 H7 AS O2 FORMUL 11 HOH *39(H2 O) LINK O2' U A 3 N6 AMR A 101 1555 1555 1.31 LINK O6 G A 13 NA NA A 102 1555 1555 3.08 LINK NA NA A 102 O HOH A 205 1555 1555 2.96 LINK O3' A B 10 NA NA B 103 1555 1555 2.77 LINK O2' A B 10 NA NA B 103 1555 1555 2.47 LINK O6 G B 12 NA NA B 103 1555 1555 2.45 LINK O2' A C 10 NA NA C 102 1555 1555 2.81 LINK O6 G C 12 NA NA C 102 1555 1555 2.63 LINK NA NA C 102 O HOH C 207 1555 1555 2.62 CRYST1 61.511 61.511 106.158 90.00 90.00 120.00 P 32 9 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 0.016257 0.009386 0.000000 0.00000 SCALE2 0.000000 0.018772 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009420 0.00000 CONECT 51 2251 CONECT 268 2260 CONECT 940 2281 CONECT 942 2281 CONECT 993 2281 CONECT 1690 2297 CONECT 1741 2297 CONECT 2245 2246 2258 CONECT 2246 2245 2247 2253 CONECT 2247 2246 2248 2252 CONECT 2248 2247 2249 CONECT 2249 2248 2250 2251 CONECT 2250 2249 CONECT 2251 51 2249 CONECT 2252 2247 CONECT 2253 2246 2254 2255 CONECT 2254 2253 CONECT 2255 2253 2256 CONECT 2256 2255 2257 2258 CONECT 2257 2256 CONECT 2258 2245 2256 2259 CONECT 2259 2258 CONECT 2260 268 2302 CONECT 2261 2262 2274 CONECT 2262 2261 2263 2269 CONECT 2263 2262 2264 2268 CONECT 2264 2263 2265 CONECT 2265 2264 2266 2267 CONECT 2266 2265 CONECT 2267 2265 CONECT 2268 2263 CONECT 2269 2262 2270 2271 CONECT 2270 2269 CONECT 2271 2269 2272 CONECT 2272 2271 2273 2274 CONECT 2273 2272 CONECT 2274 2261 2272 2275 CONECT 2275 2274 CONECT 2276 2277 2278 2279 2280 CONECT 2277 2276 CONECT 2278 2276 CONECT 2279 2276 CONECT 2280 2276 CONECT 2281 940 942 993 CONECT 2282 2283 2295 CONECT 2283 2282 2284 2290 CONECT 2284 2283 2285 2289 CONECT 2285 2284 2286 CONECT 2286 2285 2287 2288 CONECT 2287 2286 CONECT 2288 2286 CONECT 2289 2284 CONECT 2290 2283 2291 2292 CONECT 2291 2290 CONECT 2292 2290 2293 CONECT 2293 2292 2294 2295 CONECT 2294 2293 CONECT 2295 2282 2293 2296 CONECT 2296 2295 CONECT 2297 1690 1741 2326 CONECT 2302 2260 CONECT 2326 2297 MASTER 253 0 7 0 0 0 0 6 2333 3 62 9 END