HEADER RNA 21-JAN-24 8XZR TITLE CRYSTAL STRUCTURE OF FOLE RIBOSWITCH WITH 8-NH2 GUANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (53-MER); COMPND 3 CHAIN: A; COMPND 4 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, 8-NH2 GUANINE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR C.Y.LI,A.M.REN REVDAT 2 21-AUG-24 8XZR 1 JRNL REVDAT 1 24-JUL-24 8XZR 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. V. 52 8454 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38769061 JRNL DOI 10.1093/NAR/GKAE377 REMARK 2 REMARK 2 RESOLUTION. 1.83 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) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.7 REMARK 3 NUMBER OF REFLECTIONS : 13551 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1342 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 25.1500 - 3.9300 1.00 1597 176 0.1490 0.1845 REMARK 3 2 3.9300 - 3.1200 0.91 1379 156 0.2041 0.2271 REMARK 3 3 3.1200 - 2.7300 1.00 1494 163 0.2754 0.3108 REMARK 3 4 2.7300 - 2.4800 0.84 1243 145 0.3131 0.3294 REMARK 3 5 2.4800 - 2.3000 1.00 1494 156 0.3073 0.3337 REMARK 3 6 2.3000 - 2.1700 0.48 694 82 0.3252 0.3426 REMARK 3 7 2.1700 - 2.1000 1.00 881 95 0.2963 0.3636 REMARK 3 8 2.0500 - 1.9700 1.00 1371 152 0.2949 0.4037 REMARK 3 9 1.9700 - 1.9000 0.70 984 103 0.3201 0.3899 REMARK 3 10 1.8700 - 1.8300 1.00 1072 114 0.2902 0.3160 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.870 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 1291 REMARK 3 ANGLE : 1.217 2001 REMARK 3 CHIRALITY : 0.044 264 REMARK 3 PLANARITY : 0.006 54 REMARK 3 DIHEDRAL : 17.591 646 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 8XZR 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_1300044564. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-22 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) : 0.97853 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 : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33977 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.260 REMARK 200 RESOLUTION RANGE LOW (A) : 32.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 67.5 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 3.18300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 54.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 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 25.14950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.55950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.55950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.14950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.29500 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: 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 - OP2 ANGL. DEV. = 15.6 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 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 5 O6 REMARK 620 2 HOH A 233 O 79.6 REMARK 620 3 HOH A 238 O 91.8 96.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 107 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 14 O2' REMARK 620 2 C A 15 OP2 98.1 REMARK 620 3 HOH A 237 O 112.5 76.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 106 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 29 O2' REMARK 620 2 HOH A 212 O 75.4 REMARK 620 N 1 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' 75.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 109 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 205 O REMARK 620 2 HOH A 209 O 97.4 REMARK 620 3 HOH A 214 O 100.1 97.5 REMARK 620 4 HOH A 215 O 94.9 165.4 87.9 REMARK 620 5 HOH A 250 O 84.8 92.7 167.9 80.6 REMARK 620 6 HOH A 251 O 176.1 86.3 80.4 81.3 94.0 REMARK 620 N 1 2 3 4 5 DBREF 8XZR A 1 53 PDB 8XZR 8XZR 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 ANG A 101 12 HET SPM A 102 14 HET MG A 103 1 HET MG A 104 1 HET MG A 105 1 HET MG A 106 1 HET MG A 107 1 HET MG A 108 1 HET MG A 109 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM ANG 8-AMINOGUANINE HETNAM SPM SPERMINE HETNAM MG MAGNESIUM ION FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 ANG C5 H6 N6 O FORMUL 3 SPM C10 H26 N4 FORMUL 4 MG 7(MG 2+) FORMUL 11 HOH *51(H2 O) LINK O3' GTP A 1 P G A 2 1555 1555 1.57 LINK O6 G A 5 MG MG A 104 1555 1555 2.84 LINK O2' U A 14 MG MG A 107 1555 1555 2.22 LINK OP2 C A 15 MG MG A 107 1555 1555 2.32 LINK O2' U A 29 MG MG A 106 1555 2664 2.73 LINK O3' U A 53 MG MG A 103 1555 1555 2.00 LINK O2' U A 53 MG MG A 103 1555 1555 2.46 LINK MG MG A 104 O HOH A 233 1555 1555 2.05 LINK MG MG A 104 O HOH A 238 1555 1555 2.37 LINK MG MG A 105 O HOH A 226 1555 1555 1.98 LINK MG MG A 106 O HOH A 212 1555 1555 2.89 LINK MG MG A 107 O HOH A 237 1555 1555 2.65 LINK MG MG A 108 O HOH A 235 1555 1555 2.81 LINK MG MG A 109 O HOH A 205 1555 1555 2.12 LINK MG MG A 109 O HOH A 209 1555 1555 2.20 LINK MG MG A 109 O HOH A 214 1555 1555 2.08 LINK MG MG A 109 O HOH A 215 1555 1555 2.22 LINK MG MG A 109 O HOH A 250 1555 1555 2.22 LINK MG MG A 109 O HOH A 251 1555 1555 2.23 CRYST1 50.299 58.590 61.119 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 0.019881 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017068 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016362 0.00000 HETATM 1 PG GTP A 1 15.517 35.235 52.294 1.00121.03 P HETATM 2 O1G GTP A 1 14.139 35.072 52.896 1.00116.13 O HETATM 3 O2G GTP A 1 15.372 35.856 50.920 1.00109.12 O HETATM 4 O3G GTP A 1 16.169 33.870 52.181 1.00111.76 O HETATM 5 O3B GTP A 1 16.352 36.215 53.284 1.00115.48 O HETATM 6 PB GTP A 1 17.489 37.267 52.795 1.00119.45 P HETATM 7 O1B GTP A 1 16.799 38.405 52.072 1.00113.39 O HETATM 8 O2B GTP A 1 18.271 37.829 53.967 1.00104.40 O HETATM 9 O3A GTP A 1 18.464 36.478 51.758 1.00109.15 O HETATM 10 PA GTP A 1 19.150 35.032 52.037 1.00 98.86 P HETATM 11 O1A GTP A 1 18.713 34.466 53.371 1.00 95.64 O HETATM 12 O2A GTP A 1 18.890 34.039 50.922 1.00 93.27 O HETATM 13 O5' GTP A 1 20.714 35.417 52.096 1.00 85.65 O HETATM 14 C5' GTP A 1 21.095 36.723 52.462 1.00 83.20 C HETATM 15 C4' GTP A 1 22.422 36.681 53.204 1.00 77.94 C HETATM 16 O4' GTP A 1 22.167 36.425 54.569 1.00 76.32 O HETATM 17 C3' GTP A 1 23.331 35.553 52.755 1.00 70.94 C HETATM 18 O3' GTP A 1 24.181 35.934 51.707 1.00 70.33 O HETATM 19 C2' GTP A 1 24.114 35.250 54.011 1.00 67.30 C HETATM 20 O2' GTP A 1 25.239 36.092 54.095 1.00 68.71 O HETATM 21 C1' GTP A 1 23.131 35.551 55.125 1.00 67.77 C HETATM 22 N9 GTP A 1 22.473 34.276 55.481 1.00 66.42 N HETATM 23 C8 GTP A 1 21.157 33.956 55.266 1.00 68.21 C HETATM 24 N7 GTP A 1 20.930 32.703 55.718 1.00 63.76 N HETATM 25 C5 GTP A 1 22.081 32.214 56.227 1.00 58.62 C HETATM 26 C6 GTP A 1 22.401 30.994 56.815 1.00 55.12 C HETATM 27 O6 GTP A 1 21.546 30.105 56.952 1.00 53.81 O HETATM 28 N1 GTP A 1 23.695 30.781 57.245 1.00 54.07 N HETATM 29 C2 GTP A 1 24.656 31.759 57.098 1.00 55.59 C HETATM 30 N2 GTP A 1 25.897 31.540 57.517 1.00 56.50 N HETATM 31 N3 GTP A 1 24.328 32.962 56.516 1.00 58.51 N HETATM 32 C4 GTP A 1 23.061 33.190 56.085 1.00 61.72 C