HEADER RNA 03-JAN-22 7WI9 TITLE THE THF-II RIBOSWITCH BOUND TO THF AND SOAKING WITH SEUREA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (50-MER); COMPND 3 CHAIN: V; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MESORHIZOBIUM LOTI; SOURCE 3 ORGANISM_TAXID: 381; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS HOLO FORM, RNA EXPDTA X-RAY DIFFRACTION AUTHOR L.XU,X.FANG,Y.XIAO REVDAT 2 08-FEB-23 7WI9 1 JRNL REVDAT 1 18-JAN-23 7WI9 0 JRNL AUTH L.XU,Y.XIAO,J.ZHANG,X.FANG JRNL TITL STRUCTURAL INSIGHTS INTO TRANSLATION REGULATION BY THE JRNL TITL 2 THF-II RIBOSWITCH. JRNL REF NUCLEIC ACIDS RES. V. 51 952 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 36620887 JRNL DOI 10.1093/NAR/GKAC1257 REMARK 2 REMARK 2 RESOLUTION. 2.98 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) : 2.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9345 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 466 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 48.9600 - 4.3100 1.00 2966 161 0.1852 0.1927 REMARK 3 2 4.3000 - 3.4200 1.00 2976 153 0.2344 0.2867 REMARK 3 3 3.4100 - 2.9800 1.00 2937 152 0.2811 0.3063 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) : 0.191 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 83.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 101.2 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 : 0.002 1227 REMARK 3 ANGLE : 0.511 1905 REMARK 3 CHIRALITY : 0.022 252 REMARK 3 PLANARITY : 0.002 55 REMARK 3 DIHEDRAL : 11.331 612 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 7WI9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300026765. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-21 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 : SSRF REMARK 200 BEAMLINE : BL18U1 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9359 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.980 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 18.90 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.16 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.04400 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM CITRATE, PH6.5, 1.5-2.5M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-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 30.82667 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 61.65333 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 61.65333 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 30.82667 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: V 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GTP V 6 PG O1G O2G O3G 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 THG V 101 DBREF 7WI9 V 6 56 PDB 7WI9 7WI9 6 56 SEQRES 1 V 50 GTP G C G U G G U C C G U U SEQRES 2 V 50 C A A C U C G U U C C U C SEQRES 3 V 50 G A A A G A G G A A C U A SEQRES 4 V 50 C G G G A G A C G C C HET GTP V 6 28 HET THG V 101 13 HET SEY V 102 4 HET SEY V 103 4 HET SEY V 104 4 HET SEY V 105 4 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM THG (6S)-5,6,7,8-TETRAHYDROFOLATE HETNAM SEY SELENOUREA FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 THG C19 H23 N7 O6 FORMUL 3 SEY 4(C H4 N2 SE) LINK O3' GTP V 6 P G V 7 1555 1555 1.60 CRYST1 66.647 66.647 92.480 90.00 90.00 120.00 P 31 2 1 6 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 0.015004 0.008663 0.000000 0.00000 SCALE2 0.000000 0.017326 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010813 0.00000 HETATM 1 O3B GTP V 6 12.477 56.868 24.666 1.00156.99 O HETATM 2 PB GTP V 6 11.305 55.778 24.635 1.00171.29 P HETATM 3 O1B GTP V 6 11.142 55.310 23.243 1.00157.67 O HETATM 4 O2B GTP V 6 10.136 56.306 25.372 1.00140.90 O HETATM 5 O3A GTP V 6 11.965 54.594 25.489 1.00148.35 O HETATM 6 PA GTP V 6 13.208 53.621 25.215 1.00148.09 P HETATM 7 O1A GTP V 6 13.110 53.095 23.828 1.00146.42 O HETATM 8 O2A GTP V 6 13.297 52.653 26.337 1.00148.74 O HETATM 9 O5' GTP V 6 14.448 54.625 25.309 1.00136.73 O HETATM 10 C5' GTP V 6 15.580 54.318 24.463 1.00134.20 C HETATM 11 C4' GTP V 6 16.860 54.755 25.132 1.00134.24 C HETATM 12 O4' GTP V 6 16.688 56.038 25.775 1.00135.89 O HETATM 13 C3' GTP V 6 17.402 53.841 26.235 1.00140.98 C HETATM 14 O3' GTP V 6 18.041 52.675 25.729 1.00140.53 O HETATM 15 C2' GTP V 6 18.353 54.815 26.932 1.00126.58 C HETATM 16 O2' GTP V 6 19.478 55.079 26.121 1.00124.60 O HETATM 17 C1' GTP V 6 17.456 56.052 26.977 1.00122.00 C HETATM 18 N9 GTP V 6 16.549 56.052 28.122 1.00118.68 N HETATM 19 C8 GTP V 6 15.178 56.024 28.100 1.00123.03 C HETATM 20 N7 GTP V 6 14.632 56.030 29.291 1.00113.42 N HETATM 21 C5 GTP V 6 15.719 56.062 30.159 1.00104.85 C HETATM 22 C6 GTP V 6 15.750 56.082 31.576 1.00114.06 C HETATM 23 O6 GTP V 6 14.794 56.075 32.366 1.00120.78 O HETATM 24 N1 GTP V 6 17.058 56.115 32.057 1.00111.39 N HETATM 25 C2 GTP V 6 18.190 56.126 31.279 1.00114.32 C HETATM 26 N2 GTP V 6 19.365 56.159 31.926 1.00 98.79 N HETATM 27 N3 GTP V 6 18.169 56.108 29.949 1.00111.39 N HETATM 28 C4 GTP V 6 16.903 56.076 29.459 1.00108.04 C