HEADER RNA 27-JUL-18 6E81 TITLE CRYSTAL STRUCTURE OF THE CORN APTAMER IN COMPLEX WITH THT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (36-MER); 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 POLYRIBONUCLEOTIDE, FLUORIGENIC APTAMER, G-QUADRUPLEX, THIOFLAVIN T, KEYWDS 2 RNA EXPDTA X-RAY DIFFRACTION AUTHOR L.SJEKLOCA,A.R.FERRE-D'AMARE REVDAT 3 11-OCT-23 6E81 1 REMARK REVDAT 2 28-AUG-19 6E81 1 JRNL REVDAT 1 31-JUL-19 6E81 0 JRNL AUTH L.SJEKLOCA,A.R.FERRE-D'AMARE JRNL TITL BINDING BETWEEN G QUADRUPLEXES AT THE HOMODIMER INTERFACE OF JRNL TITL 2 THE CORN RNA APTAMER STRONGLY ACTIVATES THIOFLAVIN T JRNL TITL 3 FLUORESCENCE. JRNL REF CELL CHEM BIOL V. 26 1159 2019 JRNL REFN ESSN 2451-9456 JRNL PMID 31178406 JRNL DOI 10.1016/J.CHEMBIOL.2019.04.012 REMARK 2 REMARK 2 RESOLUTION. 2.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 3629 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.170 REMARK 3 FREE R VALUE TEST SET COUNT : 369 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 38.2697 - 3.9231 0.99 1120 123 0.2260 0.2196 REMARK 3 2 3.9231 - 3.1143 0.98 1059 129 0.2750 0.3393 REMARK 3 3 3.1143 - 2.7208 0.99 1081 117 0.3375 0.3798 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 85.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 111.8 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 : 0.006 924 REMARK 3 ANGLE : 1.224 1438 REMARK 3 CHIRALITY : 0.055 180 REMARK 3 PLANARITY : 0.007 42 REMARK 3 DIHEDRAL : 21.100 433 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 1.9361 50.9448 20.1079 REMARK 3 T TENSOR REMARK 3 T11: 0.4202 T22: 2.1706 REMARK 3 T33: 0.9266 T12: 0.7988 REMARK 3 T13: -0.0171 T23: -0.1022 REMARK 3 L TENSOR REMARK 3 L11: 0.2479 L22: 0.0047 REMARK 3 L33: 0.0839 L12: 0.0454 REMARK 3 L13: 0.0931 L23: 0.0561 REMARK 3 S TENSOR REMARK 3 S11: -0.1008 S12: 0.5513 S13: 0.1966 REMARK 3 S21: -0.0584 S22: 0.4011 S23: 0.1721 REMARK 3 S31: -0.6301 S32: -2.1287 S33: -0.0534 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 6E81 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000235869. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-17 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 : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00003 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3756 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.720 REMARK 200 RESOLUTION RANGE LOW (A) : 66.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 38.50 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 40.80 REMARK 200 R MERGE FOR SHELL (I) : 0.02300 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 2.7.16 REMARK 200 STARTING MODEL: 5BJP REMARK 200 REMARK 200 REMARK: RECTANGULAR PLATE-SHAPED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 5% PEG400, 0.2M AMMONIUM REMARK 280 ACETATE PH 6.7, 0.1 M SODIUM CITRATE PH 5.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 65.70200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.93307 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 13.54400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 65.70200 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 37.93307 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 13.54400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 65.70200 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 37.93307 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 13.54400 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 65.70200 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 37.93307 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 13.54400 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 65.70200 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 37.93307 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 13.54400 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 65.70200 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 37.93307 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 13.54400 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 75.86613 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 27.08800 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 75.86613 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 27.08800 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 75.86613 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 27.08800 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 75.86613 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 27.08800 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 75.86613 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 27.08800 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 75.86613 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 27.08800 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 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 -0.500000 -0.866025 0.000000 65.70200 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 37.93307 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 54.17600 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 K A 102 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 12 O6 REMARK 620 2 G A 13 O6 77.4 REMARK 620 3 G A 15 O6 78.4 91.3 REMARK 620 4 G A 16 O6 138.6 82.1 66.4 REMARK 620 5 G A 22 O6 106.7 153.6 64.9 78.0 REMARK 620 6 G A 23 O6 146.2 118.4 127.1 75.2 72.9 REMARK 620 7 G A 25 O6 63.9 120.0 120.9 154.6 83.7 82.7 REMARK 620 8 G A 26 O6 91.2 61.3 152.4 109.9 142.6 74.1 75.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TFX A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5BJP RELATED DB: PDB DBREF 6E81 A 1 36 PDB 6E81 6E81 1 36 SEQRES 1 A 36 G G C G C G A G G A A G G SEQRES 2 A 36 A G G U C U G A G G A G G SEQRES 3 A 36 U C A C U G C G C C HET TFX A 101 40 HET K A 102 1 HETNAM TFX 2-[4-(DIMETHYLAMINO)PHENYL]-3,6-DIMETHYL-1,3- HETNAM 2 TFX BENZOTHIAZOL-3-IUM HETNAM K POTASSIUM ION HETSYN TFX THIOFLAVIN T FORMUL 2 TFX C17 H19 N2 S 1+ FORMUL 3 K K 1+ LINK O6 G A 12 K K A 102 1555 1555 2.75 LINK O6 G A 13 K K A 102 1555 1555 2.99 LINK O6 G A 15 K K A 102 1555 1555 2.72 LINK O6 G A 16 K K A 102 1555 1555 2.61 LINK O6 G A 22 K K A 102 1555 1555 2.81 LINK O6 G A 23 K K A 102 1555 1555 2.79 LINK O6 G A 25 K K A 102 1555 1555 2.62 LINK O6 G A 26 K K A 102 1555 1555 2.81 SITE 1 AC1 4 G A 12 G A 15 G A 22 G A 25 SITE 1 AC2 8 G A 12 G A 13 G A 15 G A 16 SITE 2 AC2 8 G A 22 G A 23 G A 25 G A 26 CRYST1 131.404 131.404 40.632 90.00 90.00 120.00 H 3 2 18 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 0.007610 0.004394 0.000000 0.00000 SCALE2 0.000000 0.008787 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024611 0.00000