HEADER RNA 28-NOV-20 7KVV TITLE CRYSTAL STRUCTURE OF SQUASH RNA APTAMER IN COMPLEX WITH DFHBI-1T COMPND MOL_ID: 1; COMPND 2 MOLECULE: SQUASH RNA APTAMER BOUND TO DFHO; COMPND 3 CHAIN: D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FLUOROGENIC APTAMER, ADENINE RIBOSWITCH, RNA EXPDTA X-RAY DIFFRACTION AUTHOR L.TRUONG,A.R.FERRE-D'AMARE REVDAT 3 18-OCT-23 7KVV 1 REMARK REVDAT 2 16-FEB-22 7KVV 1 JRNL REVDAT 1 19-JAN-22 7KVV 0 JRNL AUTH L.TRUONG,H.KOOSHAPUR,S.K.DEY,X.LI,N.TJANDRA,S.R.JAFFREY, JRNL AUTH 2 A.R.FERRE-D'AMARE JRNL TITL THE FLUORESCENT APTAMER SQUASH EXTENSIVELY REPURPOSES THE JRNL TITL 2 ADENINE RIBOSWITCH FOLD. JRNL REF NAT.CHEM.BIOL. V. 18 191 2022 JRNL REFN ESSN 1552-4469 JRNL PMID 34937911 JRNL DOI 10.1038/S41589-021-00931-2 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 7090 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 710 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 52.1400 - 4.8800 1.00 1365 153 0.1848 0.2042 REMARK 3 2 4.8700 - 3.8700 1.00 1287 143 0.2388 0.2774 REMARK 3 3 3.8700 - 3.3800 1.00 1257 140 0.2547 0.2788 REMARK 3 4 3.3800 - 3.0700 1.00 1223 135 0.2632 0.2936 REMARK 3 5 3.0700 - 2.8500 0.99 1248 139 0.4476 0.5428 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) : 0.577 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 109.7 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 95.80 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 : 0.001 2020 REMARK 3 ANGLE : 0.398 3146 REMARK 3 CHIRALITY : 0.018 414 REMARK 3 PLANARITY : 0.002 85 REMARK 3 DIHEDRAL : 14.258 998 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 7KVV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000253154. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-20 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7090 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 52.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 31.40 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 93.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 3.45800 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: NULL REMARK 200 STARTING MODEL: 7KVT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 MM NA CACODYLATE PH 7.0, 80 MM REMARK 280 NACL, 12 MM SPERMINE HYDROCHLORIDE, 36% (V/V) MPD, AND 40 MM NAI, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.13550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.13550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.05350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.13550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.13550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.05350 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.13550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.13550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 26.05350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.13550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.13550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.05350 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: 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 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 747 D 302 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 MG D 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G D 41 O6 REMARK 620 2 G D 46 O2' 85.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G D 42 OP2 REMARK 620 2 A D 45 OP2 116.9 REMARK 620 3 G D 46 O6 75.0 82.6 REMARK 620 4 HOH D2301 O 54.1 64.2 56.6 REMARK 620 N 1 2 3 DBREF 7KVV D 1 83 PDB 7KVV 7KVV 1 83 SEQRES 1 D 83 GTP G G A A G A U A C A A G SEQRES 2 D 83 G U G A G C C C A A U A A SEQRES 3 D 83 U A U G G U U U G G G U U SEQRES 4 D 83 A G G A U A G G A A G U A SEQRES 5 D 83 G A G C C U U A A A C U C SEQRES 6 D 83 U C U A A G C G G U A U C SEQRES 7 D 83 U U C C C HET GTP D 1 32 HET MG D 301 1 HET 747 D 302 19 HET MG D 303 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM 747 (5Z)-5-[(3,5-DIFLUORO-4-HYDROXYPHENYL)METHYLIDENE]-2- HETNAM 2 747 [(E)-(HYDROXYIMINO)METHYL]-3-METHYL-3,5-DIHYDRO-4H- HETNAM 3 747 IMIDAZOL-4-ONE FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 MG 2(MG 2+) FORMUL 3 747 C12 H9 F2 N3 O3 FORMUL 5 HOH *2(H2 O) LINK C3' GTP D 1 OP1 G D 2 1555 1555 1.37 LINK O6 G D 41 MG MG D 303 1555 1555 2.51 LINK OP2 G D 42 MG MG D 301 1555 1555 2.39 LINK OP2 A D 45 MG MG D 301 1555 1555 2.08 LINK O6 G D 46 MG MG D 301 1555 1555 2.25 LINK O2' G D 46 MG MG D 303 1555 1555 2.39 LINK MG MG D 301 O HOH D2301 1555 1555 2.74 CRYST1 104.271 104.271 52.107 90.00 90.00 90.00 P 42 21 2 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 0.009590 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009590 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019191 0.00000 HETATM 1 PG GTP D 1 101.855 -1.217 -37.535 1.00186.53 P HETATM 2 O1G GTP D 1 103.287 -1.670 -37.382 1.00166.74 O HETATM 3 O2G GTP D 1 101.014 -1.864 -36.460 1.00167.70 O HETATM 4 O3G GTP D 1 101.339 -1.612 -38.898 1.00157.91 O HETATM 5 O3B GTP D 1 101.810 0.386 -37.366 1.00163.79 O HETATM 6 PB GTP D 1 102.051 1.363 -38.625 1.00167.79 P HETATM 7 O1B GTP D 1 102.038 2.801 -38.163 1.00157.71 O HETATM 8 O2B GTP D 1 103.337 1.033 -39.343 1.00150.89 O HETATM 9 O3A GTP D 1 100.782 1.084 -39.574 1.00144.25 O HETATM 10 PA GTP D 1 99.327 1.612 -39.136 1.00147.60 P HETATM 11 O1A GTP D 1 99.312 1.898 -37.654 1.00147.05 O HETATM 12 O2A GTP D 1 98.256 0.614 -39.509 1.00142.67 O HETATM 13 O5' GTP D 1 99.147 2.985 -39.957 1.00138.55 O HETATM 14 C5' GTP D 1 98.397 2.995 -41.150 1.00131.48 C HETATM 15 C4' GTP D 1 99.299 3.147 -42.371 1.00124.43 C HETATM 16 O4' GTP D 1 100.554 2.525 -42.184 1.00122.39 O HETATM 17 C3' GTP D 1 98.710 2.482 -43.603 1.00119.72 C HETATM 18 O3' GTP D 1 97.939 3.397 -44.347 1.00130.40 O HETATM 19 C2' GTP D 1 99.925 2.044 -44.396 1.00117.89 C HETATM 20 O2' GTP D 1 100.110 2.883 -45.512 1.00112.21 O HETATM 21 C1' GTP D 1 101.105 2.171 -43.441 1.00119.49 C HETATM 22 N9 GTP D 1 101.840 0.893 -43.341 1.00117.04 N HETATM 23 C8 GTP D 1 102.245 0.297 -42.176 1.00122.16 C HETATM 24 N7 GTP D 1 102.901 -0.846 -42.477 1.00113.82 N HETATM 25 C5 GTP D 1 102.937 -0.985 -43.819 1.00110.22 C HETATM 26 C6 GTP D 1 103.484 -1.965 -44.640 1.00106.86 C HETATM 27 O6 GTP D 1 104.067 -2.931 -44.150 1.00103.88 O HETATM 28 N1 GTP D 1 103.371 -1.850 -46.010 1.00105.12 N HETATM 29 C2 GTP D 1 102.716 -0.764 -46.554 1.00105.96 C HETATM 30 N2 GTP D 1 102.607 -0.652 -47.875 1.00102.90 N HETATM 31 N3 GTP D 1 102.177 0.205 -45.731 1.00108.46 N HETATM 32 C4 GTP D 1 102.280 0.103 -44.381 1.00111.09 C