HEADER RNA 03-JAN-22 7WIE TITLE THE THF-II RIBOSWITCH BOUND TO 7DG 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 7WIE 1 JRNL REVDAT 1 18-JAN-23 7WIE 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. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 5708 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 288 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 28.9900 - 3.6500 1.00 2776 152 0.1556 0.1854 REMARK 3 2 3.6500 - 2.9000 0.99 2644 136 0.2500 0.2860 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) : 0.111 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.205 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 93.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 108.2 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 1217 REMARK 3 ANGLE : 0.644 1897 REMARK 3 CHIRALITY : 0.031 252 REMARK 3 PLANARITY : 0.003 51 REMARK 3 DIHEDRAL : 11.242 621 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 7WIE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300026766. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-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 : BL19U1 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5770 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.30 REMARK 200 R MERGE FOR SHELL (I) : 1.13200 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: AUTOSOL REMARK 200 STARTING MODEL: 7WI9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.77 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 31.52400 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 63.04800 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 63.04800 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 31.52400 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 DBREF 7WIE V 6 56 PDB 7WIE 7WIE 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 32 HET 7DG V 101 17 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM 7DG 7-DEAZAGUANINE FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 7DG C6 H6 N4 O LINK O3' GTP V 6 P G V 7 1555 1555 1.60 CRYST1 66.944 66.944 94.572 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 0.014938 0.008624 0.000000 0.00000 SCALE2 0.000000 0.017249 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010574 0.00000 HETATM 1 PG GTP V 6 -53.877 -20.009 9.836 1.00172.03 P HETATM 2 O1G GTP V 6 -54.596 -20.976 10.757 1.00170.44 O HETATM 3 O2G GTP V 6 -52.925 -20.698 8.876 1.00150.95 O HETATM 4 O3G GTP V 6 -54.852 -19.083 9.137 1.00145.22 O HETATM 5 O3B GTP V 6 -52.949 -19.081 10.788 1.00167.74 O HETATM 6 PB GTP V 6 -53.226 -17.837 11.759 1.00174.21 P HETATM 7 O1B GTP V 6 -52.281 -17.891 12.895 1.00165.66 O HETATM 8 O2B GTP V 6 -54.679 -17.735 12.009 1.00150.01 O HETATM 9 O3A GTP V 6 -52.761 -16.609 10.839 1.00156.94 O HETATM 10 PA GTP V 6 -53.332 -15.871 9.537 1.00158.97 P HETATM 11 O1A GTP V 6 -52.277 -14.968 9.009 1.00167.16 O HETATM 12 O2A GTP V 6 -53.944 -16.860 8.615 1.00135.35 O HETATM 13 O5' GTP V 6 -54.479 -14.985 10.209 1.00121.09 O HETATM 14 C5' GTP V 6 -55.231 -14.133 9.318 1.00129.59 C HETATM 15 C4' GTP V 6 -56.182 -13.279 10.120 1.00142.12 C HETATM 16 O4' GTP V 6 -57.058 -14.113 10.906 1.00139.31 O HETATM 17 C3' GTP V 6 -55.553 -12.343 11.154 1.00138.68 C HETATM 18 O3' GTP V 6 -54.899 -11.213 10.590 1.00131.48 O HETATM 19 C2' GTP V 6 -56.801 -12.008 11.971 1.00126.77 C HETATM 20 O2' GTP V 6 -57.677 -11.199 11.215 1.00134.09 O HETATM 21 C1' GTP V 6 -57.410 -13.404 12.096 1.00124.48 C HETATM 22 N9 GTP V 6 -56.917 -14.150 13.248 1.00114.58 N HETATM 23 C8 GTP V 6 -56.187 -15.310 13.258 1.00115.70 C HETATM 24 N7 GTP V 6 -55.892 -15.738 14.461 1.00108.73 N HETATM 25 C5 GTP V 6 -56.466 -14.790 15.304 1.00107.88 C HETATM 26 C6 GTP V 6 -56.477 -14.720 16.720 1.00115.28 C HETATM 27 O6 GTP V 6 -55.968 -15.505 17.534 1.00126.41 O HETATM 28 N1 GTP V 6 -57.172 -13.597 17.169 1.00120.50 N HETATM 29 C2 GTP V 6 -57.777 -12.662 16.364 1.00127.20 C HETATM 30 N2 GTP V 6 -58.399 -11.645 16.981 1.00114.83 N HETATM 31 N3 GTP V 6 -57.768 -12.723 15.033 1.00120.90 N HETATM 32 C4 GTP V 6 -57.099 -13.808 14.579 1.00113.09 C