HEADER RNA 24-MAY-25 9V4U TITLE CRYSTAL STRUCTURE OF GUANINE-II RIBOSWITCH IN COMPLEX WITH 7,8- TITLE 2 DIHYDRONEOPTERIN 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 9V4U 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. 2.54 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) : 2.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 7479 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 359 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 36.4200 - 3.6600 1.00 2490 122 0.1811 0.2097 REMARK 3 2 3.6600 - 2.9100 0.99 2332 126 0.2474 0.2732 REMARK 3 3 2.9100 - 2.5400 0.97 2298 111 0.3789 0.4428 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) : 0.500 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.590 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 : 0.006 1708 REMARK 3 ANGLE : 1.166 2656 REMARK 3 CHIRALITY : 0.046 357 REMARK 3 PLANARITY : 0.006 72 REMARK 3 DIHEDRAL : 17.348 854 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): -7.1419 -8.0137 -25.9581 REMARK 3 T TENSOR REMARK 3 T11: 0.5510 T22: 0.6472 REMARK 3 T33: 0.4154 T12: 0.0131 REMARK 3 T13: -0.0992 T23: 0.0473 REMARK 3 L TENSOR REMARK 3 L11: 3.9113 L22: 0.5772 REMARK 3 L33: 3.4350 L12: 0.5369 REMARK 3 L13: 0.6197 L23: 0.2150 REMARK 3 S TENSOR REMARK 3 S11: -0.2427 S12: 1.3064 S13: -0.0307 REMARK 3 S21: -0.4107 S22: 0.0830 S23: 0.1383 REMARK 3 S31: -0.4167 S32: 0.2479 S33: 0.1029 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 9V4U 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_1300059802. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-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) : 1.10221 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7622 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.540 REMARK 200 RESOLUTION RANGE LOW (A) : 109.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.16100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.68 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 (%): 50.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 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 109.26200 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 109.26200 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 18.96650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.21550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 18.96650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.21550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 109.26200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 18.96650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 26.21550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 109.26200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 18.96650 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 26.21550 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 MG MG A 102 O HOH A 201 1.60 REMARK 500 MG MG A 102 O HOH A 220 1.68 REMARK 500 O2' C A 71 O HOH A 201 2.10 REMARK 500 O2' U A 21 N6 A A 51 2.15 REMARK 500 O HOH A 229 O HOH A 235 2.18 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 C A 71 O3' REMARK 620 2 C A 71 O2' 93.0 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 HOH A 215 O REMARK 620 2 HOH A 229 O 130.5 REMARK 620 3 HOH A 232 O 66.5 161.1 REMARK 620 4 HOH A 235 O 66.7 66.2 132.4 REMARK 620 N 1 2 3 DBREF 9V4U A 1 71 PDB 9V4U 9V4U 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 NPR A 101 18 HET MG A 102 1 HET MG A 103 1 HETNAM NPR 2-AMINO-7,8-DIHYDRO-6-(1,2,3-TRIHYDROXYPROPYL)-4(1H)- HETNAM 2 NPR PTERIDINONE HETNAM MG MAGNESIUM ION HETSYN NPR 7,8-DIHYDRONEOPTERIN FORMUL 2 NPR C9 H13 N5 O4 FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *36(H2 O) LINK O3' C A 71 MG MG A 102 1555 1555 1.96 LINK O2' C A 71 MG MG A 102 1555 1555 1.71 LINK MG MG A 103 O HOH A 215 1555 1555 2.10 LINK MG MG A 103 O HOH A 229 1555 1555 1.94 LINK MG MG A 103 O HOH A 232 1555 1555 2.07 LINK MG MG A 103 O HOH A 235 1555 1555 2.05 CRYST1 37.933 52.431 218.524 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 0.026362 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019073 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004576 0.00000 CONECT 1500 1531 CONECT 1502 1531 CONECT 1513 1514 CONECT 1514 1513 1515 1524 CONECT 1515 1514 1516 CONECT 1516 1515 1517 1518 CONECT 1517 1516 CONECT 1518 1516 1519 1523 CONECT 1519 1518 1520 CONECT 1520 1519 1521 1525 CONECT 1521 1520 1522 CONECT 1522 1521 1523 CONECT 1523 1518 1522 1524 CONECT 1524 1514 1523 CONECT 1525 1520 1526 1527 CONECT 1526 1525 CONECT 1527 1525 1528 1529 CONECT 1528 1527 CONECT 1529 1527 1530 CONECT 1530 1529 CONECT 1531 1500 1502 CONECT 1532 1547 1561 1564 1567 CONECT 1547 1532 CONECT 1561 1532 CONECT 1564 1532 CONECT 1567 1532 MASTER 256 0 3 0 0 0 0 6 1567 1 26 6 END