HEADER RNA 17-MAY-24 9BUN TITLE RHOBAST APTAMER RNA IN COMPLEX WITH 5(6)-CARBOXYTETRAMETHYLRHODAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (48-MER); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RNA, APTAMER, FLUOROPHORE, DYE, TAMRA EXPDTA X-RAY DIFFRACTION AUTHOR R.T.BATEY,S.H.SIWIK REVDAT 1 05-JUN-24 9BUN 0 JRNL AUTH R.T.BATEY,S.H.SIWIK JRNL TITL STRUCTURE OF RHOBAST RNA APTAMER IN COMPLEX WITH JRNL TITL 2 5(6)-CARBOXYTETRAMETHYLRHODAMINE (TAMRA) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14-3260-000 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 46132 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.430 REMARK 3 FREE R VALUE TEST SET COUNT : 3040 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 44.2360 - 5.8799 1.00 3883 142 0.1968 0.2095 REMARK 3 2 5.8799 - 4.6687 1.00 3895 138 0.1778 0.1774 REMARK 3 3 4.6687 - 4.0790 1.00 3888 130 0.1853 0.2007 REMARK 3 4 4.0790 - 3.7063 1.00 3905 144 0.1901 0.2119 REMARK 3 5 3.7063 - 3.4408 1.00 3880 139 0.1914 0.2144 REMARK 3 6 3.4408 - 3.2380 1.00 3890 139 0.2082 0.2363 REMARK 3 7 3.2380 - 3.0758 1.00 3893 137 0.2153 0.2395 REMARK 3 8 3.0758 - 2.9420 1.00 3884 131 0.2352 0.3691 REMARK 3 9 2.9420 - 2.8287 1.00 3876 147 0.2657 0.2360 REMARK 3 10 2.8287 - 2.7311 1.00 3889 134 0.2874 0.3080 REMARK 3 11 2.7311 - 2.6458 1.00 3915 141 0.2734 0.3077 REMARK 3 12 2.6458 - 2.5701 1.00 3843 139 0.2656 0.3221 REMARK 3 13 2.5701 - 2.5025 1.00 3911 135 0.2575 0.2997 REMARK 3 14 2.5025 - 2.4414 1.00 3892 132 0.2656 0.3534 REMARK 3 15 2.4414 - 2.3859 1.00 3901 142 0.2776 0.3287 REMARK 3 16 2.3859 - 2.3352 1.00 3893 143 0.2762 0.2898 REMARK 3 17 2.3352 - 2.2885 1.00 3889 139 0.2794 0.3168 REMARK 3 18 2.2885 - 2.2453 1.00 3862 128 0.3097 0.4159 REMARK 3 19 2.2453 - 2.2052 1.00 3885 136 0.3174 0.4045 REMARK 3 20 2.2052 - 2.1678 1.00 3913 135 0.3044 0.3223 REMARK 3 21 2.1678 - 2.1328 1.00 3907 144 0.3132 0.3360 REMARK 3 22 2.1328 - 2.1000 1.00 3802 145 0.3202 0.3707 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.260 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 : 0.003 4874 REMARK 3 ANGLE : 0.627 7673 REMARK 3 CHIRALITY : 0.031 960 REMARK 3 PLANARITY : 0.005 212 REMARK 3 DIHEDRAL : 13.441 2304 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 9BUN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1000284172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-24 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 : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.09720 REMARK 200 MONOCHROMATOR : NULL 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58528 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 44.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 64.10 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 46.30 REMARK 200 R MERGE FOR SHELL (I) : 8.15000 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: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: ELONGATED PRISM REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 MM SODIUM CACODYLATE, 12 MM SODIUM REMARK 280 CHLORIDE, 80 MM POTASSIUM CHLORIDE, 5% MPD, 20 MM SPERMINE REMARK 280 TETRAHYDROCHLORIDE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.89550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.89550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 51.21200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 87.12100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 51.21200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 87.12100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.89550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 51.21200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 87.12100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.89550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 51.21200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 87.12100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH D 285 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 302 LIES ON A SPECIAL POSITION. 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 HN62 IRI D 102 O HOH D 202 1.52 REMARK 500 O HOH B 206 O HOH B 222 2.07 REMARK 500 OP2 C C 36 O HOH C 201 2.11 REMARK 500 O HOH B 228 O HOH B 262 2.11 REMARK 500 OP1 G D 13 O HOH D 201 2.11 REMARK 500 OP1 G B 31 O HOH B 201 2.13 REMARK 500 O HOH D 216 O HOH D 233 2.14 REMARK 500 O6 G D 2 N4 C D 46 2.15 REMARK 500 O2' C A 46 O HOH A 201 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH D 241 O HOH D 241 3656 1.83 REMARK 500 O HOH B 228 O HOH C 229 6554 1.97 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 C 330 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH C 331 DISTANCE = 7.65 ANGSTROMS REMARK 525 HOH D 303 DISTANCE = 6.06 ANGSTROMS DBREF 9BUN A 1 48 PDB 9BUN 9BUN 1 48 DBREF 9BUN B 1 48 PDB 9BUN 9BUN 1 48 DBREF 9BUN C 1 48 PDB 9BUN 9BUN 1 48 DBREF 9BUN D 1 48 PDB 9BUN 9BUN 1 48 SEQRES 1 A 48 G G A C U C G G A A A C G SEQRES 2 A 48 U G A A G G A G A G G C G SEQRES 3 A 48 C A A G G U U A A C C G C SEQRES 4 A 48 C U C A G U C C A SEQRES 1 B 48 G G A C U C G G A A A C G SEQRES 2 B 48 U G A A G G A G A G G C G SEQRES 3 B 48 C A A G G U U A A C C G C SEQRES 4 B 48 C U C A G U C C A SEQRES 1 C 48 G G A C U C G G A A A C G SEQRES 2 C 48 U G A A G G A G A G G C G SEQRES 3 C 48 C A A G G U U A A C C G C SEQRES 4 C 48 C U C A G U C C A SEQRES 1 D 48 G G A C U C G G A A A C G SEQRES 2 D 48 U G A A G G A G A G G C G SEQRES 3 D 48 C A A G G U U A A C C G C SEQRES 4 D 48 C U C A G U C C A HET IRI A 101 25 HET IRI A 102 25 HET IRI A 103 25 HET FH8 A 104 53 HET IRI B 101 25 HET IRI B 102 25 HET IRI B 103 25 HET IRI B 104 25 HET FH8 B 105 53 HET IRI C 101 25 HET IRI C 102 25 HET IRI C 103 25 HET IRI C 104 25 HET IRI C 105 25 HET FH8 C 106 53 HET IRI D 101 25 HET IRI D 102 25 HET IRI D 103 25 HET FH8 D 104 53 HETNAM IRI IRIDIUM HEXAMMINE ION HETNAM FH8 5-CARBOXY METHYLRHODAMINE FORMUL 5 IRI 15(H18 IR N6 3+) FORMUL 8 FH8 4(C25 H23 N2 O5 1+) FORMUL 24 HOH *463(H2 O) CRYST1 102.424 174.242 87.791 90.00 90.00 90.00 C 2 2 21 32 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 0.009763 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005739 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011391 0.00000