HEADER RNA 27-OCT-22 8HB3 TITLE CRYSTAL STRUCTURE OF NAD-II RIBOSWITCH (TWO STRANDS) WITH NR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*AP*GP*AP*GP*CP*GP*UP*UP*GP*CP*GP*UP*CP*CP*GP*AP*AP*AP*GP*UP*(CBV) COMPND 4 P*GP*CP*C)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (31-MER); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PARASANGUINIS; SOURCE 4 ORGANISM_TAXID: 1318; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PARASANGUINIS; SOURCE 8 ORGANISM_TAXID: 1318 KEYWDS RIBOSWITCH, NAD, NMN, APTAMER, RNA EXPDTA X-RAY DIFFRACTION AUTHOR X.PENG,D.M.J.LILLEY,L.HUANG REVDAT 3 29-NOV-23 8HB3 1 REMARK REVDAT 2 19-APR-23 8HB3 1 JRNL REVDAT 1 22-MAR-23 8HB3 0 JRNL AUTH X.PENG,W.LIAO,X.LIN,D.M.J.LILLEY,L.HUANG JRNL TITL CRYSTAL STRUCTURES OF THE NAD+-II RIBOSWITCH REVEAL TWO JRNL TITL 2 DISTINCT LIGAND-BINDING POCKETS. JRNL REF NUCLEIC ACIDS RES. V. 51 2904 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 36840714 JRNL DOI 10.1093/NAR/GKAD102 REMARK 2 REMARK 2 RESOLUTION. 2.87 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) : 2.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 6188 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 298 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 29.8400 - 3.6200 1.00 2996 157 0.1791 0.1817 REMARK 3 2 3.6100 - 2.8700 1.00 2894 141 0.2714 0.3078 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) : 0.000 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.169 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 86.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 110.4 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 1359 REMARK 3 ANGLE : 1.568 2113 REMARK 3 CHIRALITY : 0.050 280 REMARK 3 PLANARITY : 0.007 59 REMARK 3 DIHEDRAL : 18.127 649 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.5298 -33.5025 12.9964 REMARK 3 T TENSOR REMARK 3 T11: 0.6557 T22: 1.1247 REMARK 3 T33: 0.7845 T12: -0.1870 REMARK 3 T13: -0.1604 T23: -0.0478 REMARK 3 L TENSOR REMARK 3 L11: 2.5471 L22: 4.7611 REMARK 3 L33: 4.3710 L12: 0.8231 REMARK 3 L13: 3.4335 L23: -0.2519 REMARK 3 S TENSOR REMARK 3 S11: 0.2765 S12: -0.5389 S13: -0.3668 REMARK 3 S21: -0.9120 S22: -0.1613 S23: 0.6092 REMARK 3 S31: 0.4594 S32: -0.8618 S33: -0.3141 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 24 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.3937 -25.9036 4.3052 REMARK 3 T TENSOR REMARK 3 T11: 0.7984 T22: 1.2437 REMARK 3 T33: 0.7266 T12: -0.0035 REMARK 3 T13: 0.1012 T23: 0.1268 REMARK 3 L TENSOR REMARK 3 L11: 2.8948 L22: 3.5948 REMARK 3 L33: 7.8721 L12: 3.0840 REMARK 3 L13: 0.4122 L23: -0.8550 REMARK 3 S TENSOR REMARK 3 S11: 0.0852 S12: 0.9935 S13: 0.5556 REMARK 3 S21: -0.5930 S22: 0.1377 S23: -0.1015 REMARK 3 S31: -0.0227 S32: -0.6767 S33: -0.0713 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 26 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.1666 -22.2285 -6.2838 REMARK 3 T TENSOR REMARK 3 T11: 1.2723 T22: 1.9316 REMARK 3 T33: 1.3065 T12: -0.0161 REMARK 3 T13: 0.1562 T23: 0.3877 REMARK 3 L TENSOR REMARK 3 L11: 8.3341 L22: 7.1782 REMARK 3 L33: 2.0592 L12: 1.7455 REMARK 3 L13: 0.5291 L23: 3.7554 REMARK 3 S TENSOR REMARK 3 S11: 2.0324 S12: -1.7005 S13: -0.8716 REMARK 3 S21: 0.3047 S22: -1.7520 S23: 2.1183 REMARK 3 S31: -1.1469 S32: -0.6911 S33: -0.5706 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 31 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.5639 -36.4328 11.8600 REMARK 3 T TENSOR REMARK 3 T11: 0.7584 T22: 2.0020 REMARK 3 T33: 0.7671 T12: -0.3159 REMARK 3 T13: 0.0581 T23: -0.1360 REMARK 3 L TENSOR REMARK 3 L11: 7.0698 L22: 2.1242 REMARK 3 L33: 3.0455 L12: -1.9220 REMARK 3 L13: -1.8816 L23: -0.4810 REMARK 3 S TENSOR REMARK 3 S11: -0.2632 S12: -0.4680 S13: -0.4824 REMARK 3 S21: 0.1126 S22: 0.0184 S23: 0.5350 REMARK 3 S31: 0.4964 S32: -2.6226 S33: 0.0301 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 41 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.6316 -33.9662 15.1504 REMARK 3 T TENSOR REMARK 3 T11: 0.5725 T22: 1.0368 REMARK 3 T33: 0.6992 T12: -0.1971 REMARK 3 T13: 0.0239 T23: -0.1314 REMARK 3 L TENSOR REMARK 3 L11: 5.1997 L22: 4.4883 REMARK 3 L33: 5.1333 L12: -0.4815 REMARK 3 L13: 1.2488 L23: 0.4178 REMARK 3 S TENSOR REMARK 3 S11: -0.1745 S12: -0.6270 S13: 0.0725 REMARK 3 S21: -0.0315 S22: -0.2491 S23: 1.1257 REMARK 3 S31: 0.0412 S32: -0.5068 S33: 0.3781 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 56 THROUGH 56 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.1866 -26.4773 16.6298 REMARK 3 T TENSOR REMARK 3 T11: 2.2855 T22: 3.1437 REMARK 3 T33: 1.9389 T12: -1.1873 REMARK 3 T13: -0.1317 T23: 0.2114 REMARK 3 L TENSOR REMARK 3 L11: 8.9995 L22: 4.2948 REMARK 3 L33: 4.2879 L12: 0.7000 REMARK 3 L13: -1.9184 L23: -4.2018 REMARK 3 S TENSOR REMARK 3 S11: 0.6738 S12: -0.5820 S13: 0.4835 REMARK 3 S21: 1.2300 S22: 0.4353 S23: -0.7692 REMARK 3 S31: -0.1817 S32: 0.0151 S33: -0.0211 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 8HB3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1300033205. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-AUG-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 : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6227 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.870 REMARK 200 RESOLUTION RANGE LOW (A) : 65.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.00 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.90 REMARK 200 R MERGE FOR SHELL (I) : 1.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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: 8HB1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.72667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.86333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.86333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.72667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 U A 7 C5 - C4 - O4 ANGL. DEV. = -3.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 8HB3 A 1 24 PDB 8HB3 8HB3 1 24 DBREF 8HB3 B 26 56 PDB 8HB3 8HB3 26 56 SEQRES 1 A 24 A G A G C G U U G C G U C SEQRES 2 A 24 C G A A A G U CBV G C C SEQRES 1 B 31 G C G A C A C G G C U C U SEQRES 2 B 31 U U A A A A A C A A A A G SEQRES 3 B 31 G A G A A HET CBV A 21 33 HET NNR A 101 33 HET NNR B 101 33 HETNAM CBV 5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM NNR NICOTINAMIDE RIBOSIDE HETSYN NNR 3-(AMINOCARBONYL)-1-BETA-D-RIBOFURANOSYLPYRIDINIUM FORMUL 1 CBV C9 H13 BR N3 O8 P FORMUL 3 NNR 2(C11 H15 N2 O5 1+) LINK O3' U A 20 P CBV A 21 1555 1555 1.62 LINK O3' CBV A 21 P G A 22 1555 1555 1.61 CRYST1 82.982 82.982 65.590 90.00 90.00 120.00 P 32 2 1 6 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 0.012051 0.006958 0.000000 0.00000 SCALE2 0.000000 0.013915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015246 0.00000