HEADER RNA 11-AUG-23 8KEB TITLE CRYSTAL STRUCTURE OF 2'-DG-III RIBOSWITCH WITH 2'-DG COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (72-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: BACILLUS SP.; SOURCE 4 ORGANISM_TAXID: 1409 KEYWDS RIBOSWITCH, 2'-DEOXYGUANOSINE, 2'-DG, APTAMER, RNA EXPDTA X-RAY DIFFRACTION AUTHOR W.LIAO,L.HUANG REVDAT 1 19-FEB-25 8KEB 0 JRNL AUTH W.LIAO,L.HUANG JRNL TITL CRYSTAL STRUCTURE OF 2'-DG-III RIBOSWITCH WITH 2'-DG JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 11223 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 554 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 34.4300 - 3.4900 0.98 2836 152 0.1494 0.1954 REMARK 3 2 3.4900 - 2.7700 0.97 2724 125 0.2535 0.2648 REMARK 3 3 2.7700 - 2.4200 0.99 2690 163 0.3757 0.3977 REMARK 3 4 2.4200 - 2.2000 0.87 2419 114 0.4526 0.5395 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) : 0.384 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.828 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 71.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 92.29 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 1733 REMARK 3 ANGLE : 1.096 2694 REMARK 3 CHIRALITY : 0.046 362 REMARK 3 PLANARITY : 0.007 73 REMARK 3 DIHEDRAL : 15.464 863 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.1608 -3.5279 15.3939 REMARK 3 T TENSOR REMARK 3 T11: 0.7509 T22: 0.5249 REMARK 3 T33: 0.8039 T12: -0.0265 REMARK 3 T13: 0.0477 T23: -0.0515 REMARK 3 L TENSOR REMARK 3 L11: 1.7338 L22: 0.3950 REMARK 3 L33: 1.5061 L12: -0.5365 REMARK 3 L13: 1.4581 L23: -0.6287 REMARK 3 S TENSOR REMARK 3 S11: 0.1079 S12: -0.3038 S13: 0.2510 REMARK 3 S21: 0.2586 S22: 0.2161 S23: -0.1346 REMARK 3 S31: 0.2142 S32: -0.6399 S33: 0.0100 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 17 THROUGH 31 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.0593 -8.5138 40.8123 REMARK 3 T TENSOR REMARK 3 T11: 0.8954 T22: 2.5549 REMARK 3 T33: 0.8837 T12: -0.0045 REMARK 3 T13: 0.0101 T23: 0.3694 REMARK 3 L TENSOR REMARK 3 L11: 0.6179 L22: 1.2048 REMARK 3 L33: 0.5023 L12: -0.3656 REMARK 3 L13: 0.4091 L23: -0.1678 REMARK 3 S TENSOR REMARK 3 S11: -0.2669 S12: -2.3000 S13: 0.0424 REMARK 3 S21: 0.6800 S22: 0.5952 S23: 0.0763 REMARK 3 S31: -0.6997 S32: -0.7796 S33: -0.0656 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 32 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): -41.4243 2.5781 19.1355 REMARK 3 T TENSOR REMARK 3 T11: 0.8702 T22: 0.9576 REMARK 3 T33: 0.9197 T12: 0.2082 REMARK 3 T13: 0.0352 T23: 0.0680 REMARK 3 L TENSOR REMARK 3 L11: 0.2603 L22: 0.0758 REMARK 3 L33: 0.1694 L12: -0.0438 REMARK 3 L13: 0.0228 L23: 0.0185 REMARK 3 S TENSOR REMARK 3 S11: 0.3890 S12: -1.1376 S13: 0.4450 REMARK 3 S21: 0.1877 S22: 0.2737 S23: 0.1529 REMARK 3 S31: 0.1926 S32: -0.4913 S33: 0.0016 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 37 THROUGH 72 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.9882 -6.5875 23.3912 REMARK 3 T TENSOR REMARK 3 T11: 0.6953 T22: 0.5803 REMARK 3 T33: 0.7768 T12: 0.0502 REMARK 3 T13: -0.0045 T23: -0.0243 REMARK 3 L TENSOR REMARK 3 L11: 4.5117 L22: 1.6688 REMARK 3 L33: 0.5711 L12: -0.3630 REMARK 3 L13: 1.8235 L23: -0.4585 REMARK 3 S TENSOR REMARK 3 S11: 0.1128 S12: -0.9819 S13: 0.1350 REMARK 3 S21: 0.2837 S22: 0.2238 S23: -0.2050 REMARK 3 S31: 0.2350 S32: -0.8507 S33: -0.0032 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 8KEB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 22-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300040176. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11351 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 64.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.03100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 1.70400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.600 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 (%): 49.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08 M SODIUM CHLORIDE, 0.01 M REMARK 280 POTASSIUM CHLORIDE, 0.01 M MAGNESIUM CHLORIDE HEXAHYDRATE 0.04 M REMARK 280 SODIUM CACODYLATE TRIHYDRATE PH 6.4, 30% V/V (+/-)-2-METHYL-2,4- REMARK 280 PENTANEDIOL, 0.012 M SPERMINE TETRAHYDROCHLORIDE, 0.1M GLYCINE., REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 69.75800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.41700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 69.75800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.41700 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 G A 1 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 C A 65 C6 - N1 - C2 ANGL. DEV. = -2.5 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 NA A 105 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 2 O6 REMARK 620 2 U A 70 O4 72.1 REMARK 620 N 1 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 U A 10 O2' REMARK 620 2 GNG A 102 O6 74.0 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 202 O REMARK 620 2 HOH A 203 O 70.0 REMARK 620 3 HOH A 204 O 95.0 146.7 REMARK 620 4 HOH A 205 O 72.6 82.0 64.9 REMARK 620 5 HOH A 206 O 137.6 102.0 68.5 65.1 REMARK 620 N 1 2 3 4 DBREF 8KEB A 1 72 PDB 8KEB 8KEB 1 72 SEQRES 1 A 72 G G A U U C G U A U A U C SEQRES 2 A 72 C U U A A U G A U A U G G SEQRES 3 A 72 U U U A A G G G C A A U A SEQRES 4 A 72 C A U A G A G A C C A C A SEQRES 5 A 72 A A U U U C U U A C U G C SEQRES 6 A 72 G A A U U C U HET GTP A 101 32 HET GNG A 102 19 HET MG A 103 1 HET MG A 104 1 HET NA A 105 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM GNG 2'-DEOXY-GUANOSINE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 2 GTP C10 H16 N5 O14 P3 FORMUL 3 GNG C10 H13 N5 O4 FORMUL 4 MG 2(MG 2+) FORMUL 6 NA NA 1+ FORMUL 7 HOH *6(H2 O) LINK P G A 2 O3' GTP A 101 1555 1555 1.56 LINK O6 G A 2 NA NA A 105 1555 1555 2.96 LINK O2' U A 10 MG MG A 104 1555 1555 2.64 LINK O4 U A 70 NA NA A 105 1555 1555 3.01 LINK O6 GNG A 102 MG MG A 104 1555 1555 2.68 LINK MG MG A 103 O HOH A 202 1555 1555 2.05 LINK MG MG A 103 O HOH A 203 1555 1555 2.38 LINK MG MG A 103 O HOH A 204 1555 1555 2.95 LINK MG MG A 103 O HOH A 205 1555 1555 2.65 LINK MG MG A 103 O HOH A 206 1555 1555 2.22 CRYST1 139.516 26.834 65.227 90.00 112.71 90.00 C 1 2 1 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 0.007168 0.000000 0.003000 0.00000 SCALE2 0.000000 0.037266 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016620 0.00000