HEADER RNA 03-JAN-22 7WIF TITLE THE THF-II RIBOSWITCH BOUND TO H4B 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 3 29-MAY-24 7WIF 1 REMARK REVDAT 2 08-FEB-23 7WIF 1 JRNL REVDAT 1 18-JAN-23 7WIF 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. 2.86 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) : 2.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 5731 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.880 REMARK 3 FREE R VALUE TEST SET COUNT : 566 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 28.6800 - 4.5300 1.00 1368 148 0.1502 0.1615 REMARK 3 2 4.5300 - 3.6000 1.00 1288 140 0.2220 0.2477 REMARK 3 3 3.6000 - 3.1400 1.00 1265 146 0.2147 0.2744 REMARK 3 4 3.1400 - 2.8600 0.97 1244 132 0.3371 0.4190 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) : 0.292 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.666 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 80.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 86.64 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 1223 REMARK 3 ANGLE : 0.595 1906 REMARK 3 CHIRALITY : 0.027 255 REMARK 3 PLANARITY : 0.003 51 REMARK 3 DIHEDRAL : 10.955 628 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 7WIF 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_1300026764. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-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 : 5787 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 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) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 0.55900 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 REMARK 200 STARTING MODEL: 7WI9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.62 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 30.93100 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 61.86200 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 61.86200 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 30.93100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 KCAL/MOL 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 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 H4B V 101 DBREF 7WIF V 6 56 PDB 7WIF 7WIF 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 H4B V 101 32 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM H4B 5,6,7,8-TETRAHYDROBIOPTERIN FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 H4B C9 H15 N5 O3 LINK O3' GTP V 6 P G V 7 1555 1555 1.60 CRYST1 66.226 66.226 92.793 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 0.015100 0.008718 0.000000 0.00000 SCALE2 0.000000 0.017436 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010777 0.00000 HETATM 1 PG GTP V 6 9.168 55.461 26.224 1.00179.79 P HETATM 2 O1G GTP V 6 9.831 55.623 27.578 1.00167.21 O HETATM 3 O2G GTP V 6 8.743 56.783 25.615 1.00175.05 O HETATM 4 O3G GTP V 6 8.057 54.430 26.224 1.00177.96 O HETATM 5 O3B GTP V 6 10.320 54.874 25.251 1.00158.56 O HETATM 6 PB GTP V 6 11.647 55.512 24.624 1.00149.63 P HETATM 7 O1B GTP V 6 11.269 56.324 23.449 1.00139.24 O HETATM 8 O2B GTP V 6 12.418 56.130 25.723 1.00142.72 O HETATM 9 O3A GTP V 6 12.383 54.165 24.174 1.00136.78 O HETATM 10 PA GTP V 6 12.882 52.922 25.046 1.00144.82 P HETATM 11 O1A GTP V 6 13.244 51.809 24.132 1.00152.48 O HETATM 12 O2A GTP V 6 11.900 52.676 26.132 1.00133.63 O HETATM 13 O5' GTP V 6 14.219 53.532 25.673 1.00109.15 O HETATM 14 C5' GTP V 6 15.280 53.837 24.741 1.00112.55 C HETATM 15 C4' GTP V 6 16.458 54.422 25.482 1.00119.18 C HETATM 16 O4' GTP V 6 16.047 55.593 26.218 1.00121.26 O HETATM 17 C3' GTP V 6 17.107 53.539 26.548 1.00116.47 C HETATM 18 O3' GTP V 6 17.911 52.496 26.012 1.00125.52 O HETATM 19 C2' GTP V 6 17.916 54.596 27.303 1.00109.35 C HETATM 20 O2' GTP V 6 19.026 55.000 26.531 1.00110.46 O HETATM 21 C1' GTP V 6 16.894 55.734 27.358 1.00109.12 C HETATM 22 N9 GTP V 6 16.072 55.703 28.566 1.00100.84 N HETATM 23 C8 GTP V 6 14.704 55.654 28.658 1.00 98.58 C HETATM 24 N7 GTP V 6 14.261 55.638 29.892 1.00 80.59 N HETATM 25 C5 GTP V 6 15.417 55.683 30.664 1.00 92.03 C HETATM 26 C6 GTP V 6 15.569 55.692 32.074 1.00 95.88 C HETATM 27 O6 GTP V 6 14.685 55.659 32.942 1.00 95.55 O HETATM 28 N1 GTP V 6 16.914 55.745 32.440 1.00101.34 N HETATM 29 C2 GTP V 6 17.976 55.786 31.568 1.00107.80 C HETATM 30 N2 GTP V 6 19.203 55.832 32.111 1.00 88.05 N HETATM 31 N3 GTP V 6 17.840 55.776 30.243 1.00101.03 N HETATM 32 C4 GTP V 6 16.538 55.725 29.866 1.00 96.54 C