HEADER RNA 21-JAN-24 8XZQ TITLE CRYSTAL STRUCTURE OF FOLE RIBOSWITCH WITH 8-N GUANINE 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, 8-N GUANINE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR C.Y.LI,A.M.REN REVDAT 2 21-AUG-24 8XZQ 1 JRNL REVDAT 1 24-JUL-24 8XZQ 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) : 24.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16117 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 831 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 24.6300 - 3.3200 1.00 2671 147 0.1602 0.1790 REMARK 3 2 3.3200 - 2.6400 1.00 2570 144 0.2439 0.2650 REMARK 3 3 2.6300 - 2.3000 1.00 2547 134 0.2915 0.3348 REMARK 3 4 2.3000 - 2.0900 1.00 2497 142 0.2777 0.3219 REMARK 3 5 2.0900 - 1.9400 1.00 2530 127 0.2773 0.3199 REMARK 3 6 1.9400 - 1.8300 0.99 2471 137 0.2891 0.3522 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.070 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 1290 REMARK 3 ANGLE : 1.128 1999 REMARK 3 CHIRALITY : 0.043 264 REMARK 3 PLANARITY : 0.007 54 REMARK 3 DIHEDRAL : 16.902 646 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 8XZQ 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_1300044563. 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16181 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.70 REMARK 200 R MERGE FOR SHELL (I) : 1.38600 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 (%): 53.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 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 24.63400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.38900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.42150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.38900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.63400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.42150 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GTP A 1 O3' G A 2 P 0.095 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 106 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 4 O4 REMARK 620 2 G A 5 O6 101.8 REMARK 620 3 HOH A 224 O 160.2 77.6 REMARK 620 4 HOH A 226 O 89.6 92.3 110.2 REMARK 620 5 HOH A 234 O 75.3 102.2 85.4 160.9 REMARK 620 N 1 2 3 4 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 U A 22 O4 REMARK 620 2 HOH A 217 O 81.7 REMARK 620 3 HOH A 218 O 94.7 89.9 REMARK 620 4 HOH A 222 O 107.9 77.5 151.9 REMARK 620 N 1 2 3 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' 65.2 REMARK 620 3 HOH A 201 O 69.2 69.5 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 HOH A 211 O REMARK 620 2 HOH A 238 O 100.2 REMARK 620 N 1 DBREF 8XZQ A 1 53 PDB 8XZQ 8XZQ 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 AZG A 101 11 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 AZG 5-AMINO-1H-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-7-OL HETNAM SPM SPERMINE HETNAM MG MAGNESIUM ION HETSYN AZG 8-AZAGUANINE FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 AZG C4 H4 N6 O FORMUL 3 SPM C10 H26 N4 FORMUL 4 MG 7(MG 2+) FORMUL 11 HOH *40(H2 O) LINK O3' GTP A 1 P G A 2 1555 1555 1.70 LINK O6 G A 2 MG MG A 104 1555 1555 2.97 LINK O4 U A 4 MG MG A 106 1555 1555 2.76 LINK O6 G A 5 MG MG A 106 1555 1555 2.69 LINK O4 U A 22 MG MG A 109 1555 1555 2.55 LINK O3' U A 53 MG MG A 103 1555 1555 2.95 LINK O2' U A 53 MG MG A 103 1555 1555 1.93 LINK MG MG A 103 O HOH A 201 1555 1555 2.13 LINK MG MG A 105 O HOH A 223 1555 1555 2.68 LINK MG MG A 106 O HOH A 224 1555 1555 2.40 LINK MG MG A 106 O HOH A 226 1555 1555 2.61 LINK MG MG A 106 O HOH A 234 1555 1555 2.35 LINK MG MG A 107 O HOH A 211 1555 1555 2.05 LINK MG MG A 107 O HOH A 238 1555 1555 2.13 LINK MG MG A 109 O HOH A 217 1555 1555 2.75 LINK MG MG A 109 O HOH A 218 1555 1555 2.49 LINK MG MG A 109 O HOH A 222 1555 1555 2.69 CRYST1 49.268 56.843 62.778 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 0.020297 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017592 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015929 0.00000 HETATM 1 PG GTP A 1 14.630 34.831 53.379 1.00130.79 P HETATM 2 O1G GTP A 1 15.478 34.057 52.392 1.00121.76 O HETATM 3 O2G GTP A 1 13.517 33.945 53.892 1.00125.24 O HETATM 4 O3G GTP A 1 14.009 36.026 52.689 1.00127.24 O HETATM 5 O3B GTP A 1 15.520 35.354 54.629 1.00121.11 O HETATM 6 PB GTP A 1 17.135 35.298 54.690 1.00113.18 P HETATM 7 O1B GTP A 1 17.636 36.411 55.583 1.00107.77 O HETATM 8 O2B GTP A 1 17.587 33.951 55.216 1.00105.24 O HETATM 9 O3A GTP A 1 17.622 35.595 53.174 1.00108.34 O HETATM 10 PA GTP A 1 18.808 34.792 52.422 1.00102.90 P HETATM 11 O1A GTP A 1 19.015 33.408 53.000 1.00 99.17 O HETATM 12 O2A GTP A 1 18.507 34.687 50.942 1.00101.36 O HETATM 13 O5' GTP A 1 20.135 35.677 52.680 1.00 94.64 O HETATM 14 C5' GTP A 1 20.288 36.488 53.825 1.00 89.44 C HETATM 15 C4' GTP A 1 21.679 36.322 54.430 1.00 84.48 C HETATM 16 O4' GTP A 1 21.527 35.908 55.776 1.00 84.67 O HETATM 17 C3' GTP A 1 22.520 35.233 53.777 1.00 79.96 C HETATM 18 O3' GTP A 1 23.317 35.686 52.703 1.00 78.37 O HETATM 19 C2' GTP A 1 23.383 34.750 54.924 1.00 76.38 C HETATM 20 O2' GTP A 1 24.534 35.552 55.023 1.00 74.04 O HETATM 21 C1' GTP A 1 22.514 34.962 56.149 1.00 77.28 C HETATM 22 N9 GTP A 1 21.873 33.670 56.473 1.00 75.56 N HETATM 23 C8 GTP A 1 20.558 33.329 56.263 1.00 78.59 C HETATM 24 N7 GTP A 1 20.357 32.060 56.691 1.00 71.99 N HETATM 25 C5 GTP A 1 21.525 31.581 57.181 1.00 69.92 C HETATM 26 C6 GTP A 1 21.883 30.353 57.743 1.00 66.86 C HETATM 27 O6 GTP A 1 21.061 29.443 57.873 1.00 63.37 O HETATM 28 N1 GTP A 1 23.184 30.155 58.155 1.00 65.48 N HETATM 29 C2 GTP A 1 24.116 31.164 58.017 1.00 66.92 C HETATM 30 N2 GTP A 1 25.367 30.963 58.420 1.00 65.19 N HETATM 31 N3 GTP A 1 23.758 32.375 57.462 1.00 69.10 N HETATM 32 C4 GTP A 1 22.484 32.583 57.049 1.00 71.68 C