HEADER RNA 24-MAY-25 9V4Y TITLE CRYSTAL STRUCTURE OF GUANINE-II RIBOSWITCH IN COMPLEX WITH 8- TITLE 2 AMINOGUANINE 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 9V4Y 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. 2.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 2.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 5513 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.960 REMARK 3 FREE R VALUE TEST SET COUNT : 549 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 55.3800 - 4.4200 0.99 1376 152 0.1823 0.2474 REMARK 3 2 4.4200 - 3.5100 0.85 1104 123 0.2319 0.2687 REMARK 3 3 3.5100 - 3.0700 0.92 1204 134 0.2728 0.3412 REMARK 3 4 3.0700 - 2.7900 1.00 1280 140 0.3150 0.3598 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.630 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 : 0.002 1715 REMARK 3 ANGLE : 0.517 2667 REMARK 3 CHIRALITY : 0.026 355 REMARK 3 PLANARITY : 0.002 73 REMARK 3 DIHEDRAL : 19.938 849 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): -7.3561 -8.4185 -26.3179 REMARK 3 T TENSOR REMARK 3 T11: 0.4412 T22: 0.7541 REMARK 3 T33: 0.4085 T12: 0.0528 REMARK 3 T13: -0.0696 T23: 0.0689 REMARK 3 L TENSOR REMARK 3 L11: 1.4182 L22: 0.9754 REMARK 3 L33: 2.1609 L12: 1.0581 REMARK 3 L13: 0.5253 L23: -0.0905 REMARK 3 S TENSOR REMARK 3 S11: -0.2107 S12: 0.9356 S13: 0.0974 REMARK 3 S21: -0.4809 S22: 0.2373 S23: 0.1905 REMARK 3 S31: -0.0876 S32: -0.0627 S33: -0.0397 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 9V4Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 27-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300059809. 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 : 5601 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.790 REMARK 200 RESOLUTION RANGE LOW (A) : 55.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.19500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.94 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 (%): 48.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 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 110.76150 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 110.76150 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 19.06150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.93500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.06150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.93500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 110.76150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.06150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 25.93500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 110.76150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.06150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 25.93500 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 232 DISTANCE = 6.97 ANGSTROMS 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 C A 71 O3' REMARK 620 2 C A 71 O2' 92.4 REMARK 620 3 HOH A 207 O 91.0 94.3 REMARK 620 4 HOH A 217 O 161.5 96.6 104.4 REMARK 620 N 1 2 3 DBREF 9V4Y A 1 71 PDB 9V4Y 9V4Y 1 71 SEQRES 1 A 71 G 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 ANG A 101 12 HET ANG A 102 12 HET MG A 103 1 HETNAM ANG 8-AMINOGUANINE HETNAM MG MAGNESIUM ION FORMUL 2 ANG 2(C5 H6 N6 O) FORMUL 4 MG MG 2+ FORMUL 5 HOH *32(H2 O) LINK O3' C A 71 MG MG A 103 1555 1555 1.98 LINK O2' C A 71 MG MG A 103 1555 1555 1.87 LINK MG MG A 103 O HOH A 207 1555 1555 1.98 LINK MG MG A 103 O HOH A 217 1555 1555 2.14 CRYST1 38.123 51.870 221.523 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 0.026231 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019279 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004514 0.00000 CONECT 1500 1537 CONECT 1502 1537 CONECT 1513 1514 1523 CONECT 1514 1513 1515 1521 CONECT 1515 1514 1516 CONECT 1516 1515 1517 1518 CONECT 1517 1516 CONECT 1518 1516 1519 CONECT 1519 1518 1520 1521 CONECT 1520 1519 CONECT 1521 1514 1519 1522 CONECT 1522 1521 1523 CONECT 1523 1513 1522 1524 CONECT 1524 1523 CONECT 1525 1526 1535 CONECT 1526 1525 1527 1533 CONECT 1527 1526 1528 CONECT 1528 1527 1529 1530 CONECT 1529 1528 CONECT 1530 1528 1531 CONECT 1531 1530 1532 1533 CONECT 1532 1531 CONECT 1533 1526 1531 1534 CONECT 1534 1533 1535 CONECT 1535 1525 1534 1536 CONECT 1536 1535 CONECT 1537 1500 1502 1544 1554 CONECT 1544 1537 CONECT 1554 1537 MASTER 249 0 3 0 0 0 0 6 1568 1 29 6 END