HEADER RNA 30-DEC-21 7TD7 TITLE CRYSTAL STRUCTURE OF AN E. COLI THIM RIBOSWITCH BOUND TO THIAMINE, TITLE 2 MANGANESE IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIM RIBOSWITCH RNA (78-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 4 ORGANISM_TAXID: 562 KEYWDS RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.NUTHANAKANTI,A.SERGANOV REVDAT 3 18-OCT-23 7TD7 1 REMARK REVDAT 2 02-MAR-22 7TD7 1 JRNL REVDAT 1 16-FEB-22 7TD7 0 JRNL AUTH M.J.ZELLER,A.NUTHANAKANTI,K.LI,J.AUBE,A.SERGANOV,K.M.WEEKS JRNL TITL SUBSITE LIGAND RECOGNITION AND COOPERATIVITY IN THE TPP JRNL TITL 2 RIBOSWITCH: IMPLICATIONS FOR FRAGMENT-LINKING IN RNA LIGAND JRNL TITL 3 DISCOVERY. JRNL REF ACS CHEM.BIOL. V. 17 438 2022 JRNL REFN ESSN 1554-8937 JRNL PMID 35060698 JRNL DOI 10.1021/ACSCHEMBIO.1C00880 REMARK 2 REMARK 2 RESOLUTION. 2.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 4766 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.810 REMARK 3 FREE R VALUE TEST SET COUNT : 857 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 29.3000 - 5.3700 0.98 1341 144 0.1942 0.2926 REMARK 3 2 5.3600 - 4.2600 0.99 1338 147 0.2462 0.2504 REMARK 3 3 4.2600 - 3.7200 0.98 1348 146 0.2680 0.2492 REMARK 3 4 3.7200 - 3.3800 0.98 1328 144 0.2092 0.3421 REMARK 3 5 3.3800 - 3.1400 0.98 1325 152 0.2769 0.2829 REMARK 3 6 3.1400 - 2.9500 0.88 1195 124 0.3235 0.4200 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.549 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 89.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 110.0 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 1800 REMARK 3 ANGLE : 1.076 2799 REMARK 3 CHIRALITY : 0.052 369 REMARK 3 PLANARITY : 0.007 75 REMARK 3 DIHEDRAL : 16.577 888 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): 10.6305 19.5574 -5.6171 REMARK 3 T TENSOR REMARK 3 T11: 0.5412 T22: 1.0121 REMARK 3 T33: 0.6368 T12: 0.1067 REMARK 3 T13: -0.0186 T23: -0.0040 REMARK 3 L TENSOR REMARK 3 L11: 2.9665 L22: 1.3692 REMARK 3 L33: 1.8812 L12: -0.2323 REMARK 3 L13: 0.3124 L23: -0.4747 REMARK 3 S TENSOR REMARK 3 S11: -0.1997 S12: -1.0342 S13: -0.2387 REMARK 3 S21: 0.3308 S22: 0.2618 S23: 0.0005 REMARK 3 S31: -0.1510 S32: 0.0745 S33: 0.0008 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 7TD7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1000262080. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0-6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4766 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.950 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 47.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.55500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.14_3260 REMARK 200 STARTING MODEL: 2HOJ REMARK 200 REMARK 200 REMARK: ROD-SHAPED CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RNA (0.15 MM) WAS INCUBATED IN A REMARK 280 BUFFER CONTAINING 5 MM TRIS-HCL, PH 8.0, 3 MM MGCL2, 10 MM NACL, REMARK 280 0.1 M KCL, AND 0.5 MM SPERMINE WITH 1.0 MM OF THIAMINE. THE REMARK 280 RESERVOIR SOLUTION WAS 50 MM BIS-TRIS HCL, PH 6.5, 0.5 M NH4CL, REMARK 280 10 MM MNCL2, AND 30% (V/V) PEG2000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 1 2 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+1/3 REMARK 290 5555 -X+Y,Y,-Z+2/3 REMARK 290 6555 X,X-Y,-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 -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 68.94400 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 34.47200 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 34.47200 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 68.94400 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 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 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 U A 25 REMARK 465 U A 26 REMARK 465 C A 27 REMARK 465 U A 28 REMARK 465 G A 29 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 C A 30 P OP1 OP2 O5' REMARK 470 U A 46 P OP1 OP2 O5' C5' C4' O4' REMARK 470 U A 46 C2' O2' C1' N1 C2 O2 N3 REMARK 470 U A 46 C4 O4 C5 C6 REMARK 470 U A 54 C5' C4' O4' C3' O3' C2' O2' REMARK 470 U A 54 C1' N1 C2 O2 N3 C4 O4 REMARK 470 U A 54 C5 C6 REMARK 470 C A 55 P OP1 OP2 O5' C5' C4' O4' REMARK 470 C A 55 C2' O2' C1' N1 C2 O2 N3 REMARK 470 C A 55 C4 N4 C5 C6 REMARK 470 U A 62 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U A 62 C6 REMARK 470 U A 79 O4' C2' O2' C1' N1 C2 O2 REMARK 470 U A 79 N3 C4 O4 C5 C6 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 N6 A A 61 O2 C A 77 2.15 REMARK 500 REMARK 500 REMARK: NULL DBREF 7TD7 A 9 91 PDB 7TD7 7TD7 9 91 SEQRES 1 A 83 G C G A C U C G G G G U G SEQRES 2 A 83 C C C U U C U G C G U G A SEQRES 3 A 83 A G G C U G A G A A A U A SEQRES 4 A 83 C C C G U A U C A C C U G SEQRES 5 A 83 A U C U G G A U A A U G C SEQRES 6 A 83 C A G C G U A G G G A A G SEQRES 7 A 83 U C G C A HET MN A 101 1 HET MG A 102 1 HET MG A 103 1 HET VIB A 104 18 HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM VIB 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY- HETNAM 2 VIB ETHYL)-4-METHYL-THIAZOL-3-IUM HETSYN VIB THIAMIN; VITAMIN B1 FORMUL 2 MN MN 2+ FORMUL 3 MG 2(MG 2+) FORMUL 5 VIB C12 H17 N4 O S 1+ LINK OP2 A A 35 MG MG A 103 1555 1555 2.67 LINK N7 A A 41 MN MN A 101 1555 1555 1.78 CRYST1 61.110 61.110 103.416 90.00 90.00 120.00 P 32 1 2 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 0.016364 0.009448 0.000000 0.00000 SCALE2 0.000000 0.018895 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009670 0.00000