HEADER RNA 21-JAN-24 8XZW TITLE CRYSTAL STRUCTURE OF THF-II RIBOSWITCH WITH THF AND SOAKED WITH IR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (53-MER); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ENV6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNIDENTIFIED EUBACTERIUM CLONE A70; SOURCE 3 ORGANISM_TAXID: 41312; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS RIBOSWITCH, THF, RNA EXPDTA X-RAY DIFFRACTION AUTHOR C.Y.LI,A.M.REN REVDAT 1 24-JUL-24 8XZW 0 JRNL AUTH C.LI,X.XU,Z.GENG,L.ZHENG,Q.SONG,X.SHEN,J.WU,J.ZHAO,H.LI, JRNL AUTH 2 M.HE,X.TAI,L.ZHANG,J.MA,Y.DONG,A.REN JRNL TITL STRUCTURE-BASED CHARACTERIZATION AND COMPOUND IDENTIFICATION JRNL TITL 2 OF THE WILD-TYPE THF CLASS-II RIBOSWITCH. JRNL REF NUCLEIC ACIDS RES. 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38769061 JRNL DOI 10.1093/NAR/GKAE377 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 26146 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2619 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 19.5000 - 5.0600 1.00 1264 142 0.1324 0.1642 REMARK 3 2 5.0500 - 4.0300 1.00 1249 141 0.1442 0.1611 REMARK 3 3 4.0200 - 3.5200 1.00 1261 134 0.1648 0.1801 REMARK 3 4 3.5200 - 3.2000 1.00 1243 164 0.2128 0.2702 REMARK 3 5 3.2000 - 2.9700 1.00 1259 123 0.2353 0.2914 REMARK 3 6 2.9700 - 2.8000 1.00 1263 145 0.3317 0.4225 REMARK 3 7 2.8000 - 2.6600 1.00 1254 143 0.3127 0.3970 REMARK 3 8 2.6600 - 2.5400 1.00 1268 140 0.2953 0.3507 REMARK 3 9 2.5400 - 2.4400 1.00 1242 130 0.3057 0.3216 REMARK 3 10 2.4400 - 2.3600 1.00 1251 156 0.3063 0.3528 REMARK 3 11 2.3600 - 2.2900 1.00 1249 138 0.3027 0.3348 REMARK 3 12 2.2900 - 2.2200 1.00 1276 112 0.3529 0.3929 REMARK 3 13 2.2200 - 2.1600 1.00 1241 149 0.3717 0.3826 REMARK 3 14 2.1600 - 2.1100 1.00 1265 156 0.3751 0.3947 REMARK 3 15 2.1100 - 2.0600 1.00 1278 141 0.4112 0.4290 REMARK 3 16 2.0600 - 2.0200 1.00 1249 136 0.4241 0.4043 REMARK 3 17 2.0200 - 1.9800 1.00 1262 131 0.4403 0.4744 REMARK 3 18 1.9800 - 1.9400 1.00 1241 143 0.4989 0.5556 REMARK 3 19 1.9400 - 1.9100 0.71 912 95 0.5456 0.5211 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) : 0.520 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 40.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.005 1312 REMARK 3 ANGLE : 1.097 2029 REMARK 3 CHIRALITY : 0.041 266 REMARK 3 PLANARITY : 0.006 58 REMARK 3 DIHEDRAL : 17.915 660 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 8XZW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300044548. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-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) : 1.102 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-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26146 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.20200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.30 REMARK 200 R MERGE FOR SHELL (I) : 1.54100 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08 M SODIUM CHLORIDE, 0.04 M SODIUM REMARK 280 CACODYLATE TRIHYDRATE PH 7.0, 30% V/V MPD, 0.012 M SPERMINE REMARK 280 TETRAHYDROCHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 24.55250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.09250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.09250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.55250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.75000 REMARK 290 SMTRY3 4 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: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N7 A A 33 O HOH A 201 2.02 REMARK 500 O HOH A 214 O HOH A 219 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 G A 2 O3' - P - OP1 ANGL. DEV. = 7.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 A 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 53 O3' REMARK 620 2 U A 53 O2' 89.8 REMARK 620 3 HOH A 202 O 63.7 113.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 203 O REMARK 620 2 HOH A 204 O 70.2 REMARK 620 3 HOH A 207 O 94.5 163.0 REMARK 620 N 1 2 DBREF 8XZW A 1 53 PDB 8XZW 8XZW 1 53 SEQRES 1 A 53 GTP G G U G U G U A C C G U SEQRES 2 A 53 U C A A C U C G U C C C A SEQRES 3 A 53 G C U U C G A C U G G G A SEQRES 4 A 53 C U A C G G G A G C G C C SEQRES 5 A 53 U HET GTP A 1 32 HET THG A 101 32 HET SPM A 102 14 HET MG A 103 1 HET MG A 104 1 HET MG A 105 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM THG (6S)-5,6,7,8-TETRAHYDROFOLATE HETNAM SPM SPERMINE HETNAM MG MAGNESIUM ION FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 THG C19 H23 N7 O6 FORMUL 3 SPM C10 H26 N4 FORMUL 4 MG 3(MG 2+) FORMUL 7 HOH *20(H2 O) LINK O3' GTP A 1 P G A 2 1555 1555 1.67 LINK O3' U A 53 MG MG A 103 1555 1555 1.83 LINK O2' U A 53 MG MG A 103 1555 1555 1.97 LINK MG MG A 103 O HOH A 202 1555 1555 2.41 LINK MG MG A 104 O HOH A 208 1555 1555 1.98 LINK MG MG A 105 O HOH A 203 1555 1555 2.35 LINK MG MG A 105 O HOH A 204 1555 1555 2.45 LINK MG MG A 105 O HOH A 207 1555 1555 2.13 CRYST1 49.105 57.500 62.185 90.00 90.00 90.00 P 21 21 21 4 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 0.020365 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017391 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016081 0.00000 HETATM 1 PG GTP A 1 14.648 34.735 52.803 1.00139.03 P HETATM 2 O1G GTP A 1 15.409 34.655 51.497 1.00130.60 O HETATM 3 O2G GTP A 1 14.669 33.390 53.497 1.00134.23 O HETATM 4 O3G GTP A 1 13.207 35.076 52.491 1.00132.72 O HETATM 5 O3B GTP A 1 15.260 35.885 53.786 1.00136.16 O HETATM 6 PB GTP A 1 16.821 36.309 53.990 1.00130.74 P HETATM 7 O1B GTP A 1 16.894 37.758 54.435 1.00121.72 O HETATM 8 O2B GTP A 1 17.498 35.437 55.028 1.00114.58 O HETATM 9 O3A GTP A 1 17.527 36.174 52.536 1.00125.18 O HETATM 10 PA GTP A 1 18.479 34.934 52.105 1.00121.21 P HETATM 11 O1A GTP A 1 17.965 33.628 52.674 1.00118.00 O HETATM 12 O2A GTP A 1 18.563 34.842 50.594 1.00116.68 O HETATM 13 O5' GTP A 1 19.920 35.283 52.754 1.00106.44 O HETATM 14 C5' GTP A 1 20.221 36.567 53.259 1.00 97.72 C HETATM 15 C4' GTP A 1 21.585 36.551 53.936 1.00 93.52 C HETATM 16 O4' GTP A 1 21.383 36.275 55.308 1.00 94.13 O HETATM 17 C3' GTP A 1 22.503 35.448 53.438 1.00 89.63 C HETATM 18 O3' GTP A 1 23.336 35.851 52.373 1.00 89.66 O HETATM 19 C2' GTP A 1 23.304 35.085 54.673 1.00 85.22 C HETATM 20 O2' GTP A 1 24.456 35.888 54.768 1.00 80.88 O HETATM 21 C1' GTP A 1 22.349 35.374 55.819 1.00 87.18 C HETATM 22 N9 GTP A 1 21.685 34.099 56.180 1.00 86.47 N HETATM 23 C8 GTP A 1 20.367 33.770 55.968 1.00 86.88 C HETATM 24 N7 GTP A 1 20.146 32.515 56.427 1.00 78.48 N HETATM 25 C5 GTP A 1 21.301 32.031 56.941 1.00 78.48 C HETATM 26 C6 GTP A 1 21.638 30.813 57.537 1.00 74.49 C HETATM 27 O6 GTP A 1 20.805 29.912 57.689 1.00 72.55 O HETATM 28 N1 GTP A 1 22.933 30.613 57.964 1.00 74.95 N HETATM 29 C2 GTP A 1 23.880 31.603 57.806 1.00 77.12 C HETATM 30 N2 GTP A 1 25.124 31.398 58.220 1.00 77.40 N HETATM 31 N3 GTP A 1 23.543 32.803 57.218 1.00 79.38 N HETATM 32 C4 GTP A 1 22.275 33.017 56.791 1.00 81.41 C