HEADER RNA 09-NOV-21 7Q7Y TITLE CRYSTAL STRUCTURE OF THE METHYLTRANSFERASE-RIBOZYME 1 (1-BENZYL- TITLE 2 ADENOSINE DERIVATIVE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA 2; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: RNA 3; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS MTR1, METHYLTRANSFERASE RIBOZYME, RIBOZYME, RNA EXPDTA X-RAY DIFFRACTION AUTHOR M.MIECZKOWSKI,C.HOEBARTNER REVDAT 4 31-JAN-24 7Q7Y 1 REMARK REVDAT 3 11-MAY-22 7Q7Y 1 JRNL REVDAT 2 30-MAR-22 7Q7Y 1 JRNL REVDAT 1 23-MAR-22 7Q7Y 0 JRNL AUTH C.P.M.SCHEITL,M.MIECZKOWSKI,H.SCHINDELIN,C.HOBARTNER JRNL TITL STRUCTURE AND MECHANISM OF THE METHYLTRANSFERASE RIBOZYME JRNL TITL 2 MTR1. JRNL REF NAT.CHEM.BIOL. V. 18 547 2022 JRNL REFN ESSN 1552-4469 JRNL PMID 35301481 JRNL DOI 10.1038/S41589-022-00976-X REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.1_4122: ???) 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 5091 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.520 REMARK 3 FREE R VALUE TEST SET COUNT : 230 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 29.7600 - 3.6500 1.00 2498 116 0.1705 0.2356 REMARK 3 2 3.6500 - 2.9000 1.00 2363 114 0.2966 0.2745 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.260 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 1496 REMARK 3 ANGLE : 0.425 2334 REMARK 3 CHIRALITY : 0.024 306 REMARK 3 PLANARITY : 0.002 64 REMARK 3 DIHEDRAL : 12.564 733 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): 45.1143 13.0435 42.1005 REMARK 3 T TENSOR REMARK 3 T11: 0.5242 T22: 0.5163 REMARK 3 T33: 0.6603 T12: -0.0143 REMARK 3 T13: 0.0347 T23: 0.0153 REMARK 3 L TENSOR REMARK 3 L11: 2.6906 L22: 7.0213 REMARK 3 L33: 2.7296 L12: 3.0493 REMARK 3 L13: -1.4179 L23: -1.6810 REMARK 3 S TENSOR REMARK 3 S11: 0.4220 S12: -0.1860 S13: 0.2097 REMARK 3 S21: 0.0460 S22: -0.3949 S23: 0.0088 REMARK 3 S31: 0.0746 S32: 0.3526 S33: -0.0361 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 7Q7Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292118316. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-21 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 : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9716 REMARK 200 MONOCHROMATOR : M 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5134 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 43.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.08 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 : 1.200 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: 7Q7X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 36-42% MPD, 50MM MES PH 6.4-6.7, 100MM REMARK 280 NACL, 100MM LICL, 10MM MGCL2, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 41.54500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.63250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.63250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.77250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.63250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.63250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 62.31750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.63250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.63250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.77250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.63250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.63250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 62.31750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 41.54500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 B 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 12 O2' REMARK 620 2 C B 12 O2 100.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 201 O REMARK 620 2 HOH B 203 O 90.0 REMARK 620 3 HOH B 204 O 90.0 89.9 REMARK 620 4 HOH B 205 O 90.1 179.7 89.7 REMARK 620 5 HOH B 207 O 179.8 90.0 90.2 90.0 REMARK 620 6 HOH C 205 O 89.8 90.3 179.7 90.1 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 202 O REMARK 620 2 HOH B 206 O 90.3 REMARK 620 3 HOH C 201 O 179.5 89.3 REMARK 620 4 HOH C 202 O 90.3 90.0 89.4 REMARK 620 5 HOH C 203 O 89.8 179.9 90.6 89.9 REMARK 620 6 HOH C 204 O 90.1 90.4 90.2 179.4 89.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U C 47 O4 REMARK 620 2 G C 48 O6 84.9 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7Q7X RELATED DB: PDB DBREF 7Q7Y A 1 14 PDB 7Q7Y 7Q7Y 1 14 DBREF 7Q7Y B 1 24 PDB 7Q7Y 7Q7Y 1 24 DBREF 7Q7Y C 25 48 PDB 7Q7Y 7Q7Y 25 48 SEQRES 1 A 14 C C A C U G 9SY G A G U U U SEQRES 2 A 14 C SEQRES 1 B 24 G G A A G C U C U G A C C SEQRES 2 B 24 G A C C C C C A G C C SEQRES 1 C 24 G C U G G G A C A A C U A SEQRES 2 C 24 G A C A U A C A G U G HET 9SY A 7 29 HET MG B 101 1 HET MG B 102 1 HET MG C 101 1 HET MG C 102 1 HET GUN C 103 11 HET MG C 104 1 HETNAM 9SY [(2R,3S,4R,5R)-5-[6-AZANYL-1-(PHENYLMETHYL)PURIN-1-IUM- HETNAM 2 9SY 9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL DIHYDROGEN HETNAM 3 9SY PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM GUN GUANINE HETSYN 9SY 1-BENZYL-ADENOSINE DERIVATIVE FORMUL 1 9SY C17 H21 N5 O7 P 1+ FORMUL 4 MG 5(MG 2+) FORMUL 8 GUN C5 H5 N5 O FORMUL 10 HOH *12(H2 O) LINK O3' G A 6 P 9SY A 7 1555 1555 1.61 LINK O3' 9SY A 7 P G A 8 1555 1555 1.61 LINK O2' C B 12 MG MG B 101 1555 1555 2.25 LINK O2 C B 12 MG MG B 101 1555 1555 2.60 LINK MG MG B 102 O HOH B 201 1555 1555 2.18 LINK MG MG B 102 O HOH B 203 1555 1555 2.18 LINK MG MG B 102 O HOH B 204 1555 1555 2.18 LINK MG MG B 102 O HOH B 205 1555 1555 2.18 LINK MG MG B 102 O HOH B 207 1555 1555 2.18 LINK MG MG B 102 O HOH C 205 1555 1555 2.18 LINK O HOH B 202 MG MG C 104 1555 1555 2.18 LINK O HOH B 206 MG MG C 104 1555 1555 2.18 LINK O2 C C 32 MG MG C 101 1555 1555 2.45 LINK O4 U C 47 MG MG C 102 1555 1555 2.35 LINK O6 G C 48 MG MG C 102 1555 1555 2.19 LINK MG MG C 104 O HOH C 201 1555 1555 2.18 LINK MG MG C 104 O HOH C 202 1555 1555 2.18 LINK MG MG C 104 O HOH C 203 1555 1555 2.18 LINK MG MG C 104 O HOH C 204 1555 1555 2.18 CRYST1 71.265 71.265 83.090 90.00 90.00 90.00 P 41 21 2 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 0.014032 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014032 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012035 0.00000