HEADER RNA 24-MAY-25 9V4Z TITLE CRYSTAL STRUCTURE OF GUANINE-II RIBOSWITCH IN COMPLEX WITH 8- TITLE 2 OXOGUANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (71-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS GUANINE RIBOSWITCH, RNA EXPDTA X-RAY DIFFRACTION AUTHOR H.C.LI,A.M.REN REVDAT 1 26-NOV-25 9V4Z 0 JRNL AUTH H.LI,X.SHEN,X.XU,X.TAI,M.HE,J.ZHANG,A.REN JRNL TITL LIGAND SPECIFICITY AND ADAPTABILITY REVEALED BY THE FIRST JRNL TITL 2 GUANINE-II RIBOSWITCH TERTIARY STRUCTURE. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 40966503 JRNL DOI 10.1093/NAR/GKAF884 REMARK 2 REMARK 2 RESOLUTION. 2.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 5805 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) : 0.206 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.960 REMARK 3 FREE R VALUE TEST SET COUNT : 578 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 54.9400 - 4.3600 1.00 1382 154 0.1525 0.1962 REMARK 3 2 4.3600 - 3.4600 0.99 1280 142 0.1979 0.2537 REMARK 3 3 3.4600 - 3.0200 0.98 1293 143 0.2531 0.3168 REMARK 3 4 3.0200 - 2.7400 0.99 1272 139 0.3596 0.4067 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) : 0.480 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.010 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 1710 REMARK 3 ANGLE : 1.208 2661 REMARK 3 CHIRALITY : 0.056 354 REMARK 3 PLANARITY : 0.007 72 REMARK 3 DIHEDRAL : 21.105 851 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -7.0734 -8.6812 -26.3015 REMARK 3 T TENSOR REMARK 3 T11: 0.4477 T22: 0.6003 REMARK 3 T33: 0.4167 T12: 0.0108 REMARK 3 T13: -0.0955 T23: 0.0557 REMARK 3 L TENSOR REMARK 3 L11: 2.3009 L22: 1.3181 REMARK 3 L33: 5.8221 L12: 0.2799 REMARK 3 L13: 0.8747 L23: 0.6303 REMARK 3 S TENSOR REMARK 3 S11: -0.1916 S12: 0.6223 S13: -0.0863 REMARK 3 S21: -0.4276 S22: 0.0747 S23: 0.1185 REMARK 3 S31: -0.3869 S32: 0.0414 S33: 0.0742 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 9V4Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 28-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300059810. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-24 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) : 1.10213 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 : 5897 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.740 REMARK 200 RESOLUTION RANGE LOW (A) : 109.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : 0.14900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 (%): 46.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 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 (+/-)-2-METHYL-2,4- REMARK 280 PENTANEDIOL, AND 0.012 M SPERMINE TETRAHYDROCHLORIDE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 109.87900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 109.87900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 18.91000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.20400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 18.91000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.20400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 109.87900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 18.91000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 25.20400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 109.87900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 18.91000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 25.20400 REMARK 290 SMTRY3 8 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 O3' C A 71 MG MG A 103 1.56 REMARK 500 MG MG A 103 O HOH A 207 1.69 REMARK 500 O HOH A 216 O HOH A 219 2.09 REMARK 500 O HOH A 214 O HOH A 217 2.13 REMARK 500 O2 U A 23 O HOH A 201 2.16 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 - OP2 ANGL. DEV. = 11.0 DEGREES REMARK 500 U A 22 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 A A 35 C3' - O3' - P ANGL. DEV. = 7.7 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 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 7 O2' REMARK 620 2 A A 8 O4' 84.0 REMARK 620 3 U A 36 O4 160.1 88.9 REMARK 620 4 HOH A 211 O 87.0 143.2 87.6 REMARK 620 5 HOH A 215 O 99.0 160.4 93.9 56.4 REMARK 620 N 1 2 3 4 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 C A 71 O2' REMARK 620 2 HOH A 204 O 95.7 REMARK 620 3 HOH A 215 O 129.0 73.7 REMARK 620 N 1 2 DBREF 9V4Z A 1 71 PDB 9V4Z 9V4Z 1 71 SEQRES 1 A 71 GTP G G U U G U A U A A G C SEQRES 2 A 71 U C G U U A A U U U G G A SEQRES 3 A 71 A U G A G C G U A U C U A SEQRES 4 A 71 C A G G C A A C C G U A A SEQRES 5 A 71 A U U G C C C C A G G C U SEQRES 6 A 71 A C A A U C HET GTP A 1 32 HET OXG A 101 12 HET MG A 102 1 HET MG A 103 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM OXG 8-OXOGUANINE HETNAM MG MAGNESIUM ION FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 OXG C5 H3 N5 O2 FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *19(H2 O) LINK O3' GTP A 1 P G A 2 1555 1555 1.56 LINK O2' U A 7 MG MG A 102 1555 1555 2.77 LINK O4' A A 8 MG MG A 102 1555 1555 2.66 LINK O4 U A 36 MG MG A 102 1555 1555 2.11 LINK O2' C A 71 MG MG A 103 1555 1555 1.99 LINK MG MG A 102 O HOH A 211 1555 1555 2.80 LINK MG MG A 102 O HOH A 215 1555 8545 2.93 LINK MG MG A 103 O HOH A 204 1555 1555 2.52 LINK MG MG A 103 O HOH A 215 1555 1555 1.82 CRYST1 37.820 50.408 219.758 90.00 90.00 90.00 C 2 2 21 8 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 0.026441 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019838 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004550 0.00000 CONECT 1 2 3 4 5 CONECT 2 1 CONECT 3 1 CONECT 4 1 CONECT 5 1 6 CONECT 6 5 7 8 9 CONECT 7 6 CONECT 8 6 CONECT 9 6 10 CONECT 10 9 11 12 13 CONECT 11 10 CONECT 12 10 CONECT 13 10 14 CONECT 14 13 15 CONECT 15 14 16 17 CONECT 16 15 21 CONECT 17 15 18 19 CONECT 18 17 33 CONECT 19 17 20 21 CONECT 20 19 CONECT 21 16 19 22 CONECT 22 21 23 32 CONECT 23 22 24 CONECT 24 23 25 CONECT 25 24 26 32 CONECT 26 25 27 28 CONECT 27 26 CONECT 28 26 29 CONECT 29 28 30 31 CONECT 30 29 CONECT 31 29 32 CONECT 32 22 25 31 CONECT 33 18 CONECT 152 1534 CONECT 168 1534 CONECT 778 1534 CONECT 1511 1535 CONECT 1522 1523 1532 CONECT 1523 1522 1524 1533 CONECT 1524 1523 1525 CONECT 1525 1524 1526 1532 CONECT 1526 1525 1527 1528 CONECT 1527 1526 CONECT 1528 1526 1529 CONECT 1529 1528 1530 1531 CONECT 1530 1529 CONECT 1531 1529 1532 CONECT 1532 1522 1525 1531 CONECT 1533 1523 CONECT 1534 152 168 778 1546 CONECT 1535 1511 1539 1550 CONECT 1539 1535 CONECT 1546 1534 CONECT 1550 1535 MASTER 280 0 4 0 0 0 0 6 1553 1 54 6 END