HEADER RNA 09-NOV-21 7Q7Z TITLE CRYSTAL STRUCTURE OF THE METHYLTRANSFERASE-RIBOZYME 1 (WITH 1- TITLE 2 BENZYLAMINE-ADENOSINE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA 1; COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA 2; COMPND 7 CHAIN: B, E; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: RNA 3; COMPND 11 CHAIN: C, F; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: GCUGGGACAACUAGACAUACAGUG 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 7Q7Z 1 REMARK REVDAT 3 11-MAY-22 7Q7Z 1 JRNL REVDAT 2 30-MAR-22 7Q7Z 1 JRNL REVDAT 1 23-MAR-22 7Q7Z 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. 3.26 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) : 3.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9568 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.450 REMARK 3 FREE R VALUE TEST SET COUNT : 521 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 44.5400 - 5.1800 1.00 2374 142 0.1693 0.2423 REMARK 3 2 5.1800 - 4.1100 1.00 2260 125 0.2588 0.2788 REMARK 3 3 4.1100 - 3.5900 1.00 2218 125 0.2701 0.2796 REMARK 3 4 3.5900 - 3.2600 0.99 2195 129 0.3524 0.3927 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) : 0.500 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.660 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 : 0.001 2978 REMARK 3 ANGLE : 0.303 4629 REMARK 3 CHIRALITY : 0.011 612 REMARK 3 PLANARITY : 0.001 128 REMARK 3 DIHEDRAL : 13.061 1470 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): 20.4042 -41.2435 -8.9227 REMARK 3 T TENSOR REMARK 3 T11: 0.8298 T22: 0.7939 REMARK 3 T33: 1.1314 T12: -0.0257 REMARK 3 T13: -0.0935 T23: 0.0430 REMARK 3 L TENSOR REMARK 3 L11: 3.3175 L22: 4.5979 REMARK 3 L33: 2.8780 L12: -1.5612 REMARK 3 L13: 1.0985 L23: -1.5586 REMARK 3 S TENSOR REMARK 3 S11: 0.3016 S12: 0.1664 S13: -0.5917 REMARK 3 S21: -0.3397 S22: -0.0860 S23: 0.5508 REMARK 3 S31: -0.0483 S32: -0.0941 S33: -0.2191 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 7Q7Z 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_1292118323. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAR-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 : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9584 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.260 REMARK 200 RESOLUTION RANGE LOW (A) : 44.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 15.40 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 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 : 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: 7Q7X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.63 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 2 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 41.63750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.81875 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 62.45625 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 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 41.63750 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 62.45625 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 20.81875 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 4740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 4690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 HOH B 201 O REMARK 620 2 HOH B 202 O 90.0 REMARK 620 3 HOH C 201 O 90.0 90.1 REMARK 620 4 HOH E 101 O 90.0 179.9 89.9 REMARK 620 5 HOH F 201 O 90.0 90.0 179.9 90.1 REMARK 620 6 HOH F 202 O 179.9 90.0 90.0 90.0 90.0 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7Q7X RELATED DB: PDB DBREF 7Q7Z A 1 14 PDB 7Q7Z 7Q7Z 1 14 DBREF 7Q7Z B 1 24 PDB 7Q7Z 7Q7Z 1 24 DBREF 7Q7Z C 25 48 PDB 7Q7Z 7Q7Z 25 48 DBREF 7Q7Z D 1 14 PDB 7Q7Z 7Q7Z 1 14 DBREF 7Q7Z E 1 24 PDB 7Q7Z 7Q7Z 1 24 DBREF 7Q7Z F 25 48 PDB 7Q7Z 7Q7Z 25 48 SEQRES 1 A 14 C C A C U G 9SI G A G C 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 SEQRES 1 D 14 C C A C U G 9SI G A G C U U SEQRES 2 D 14 C SEQRES 1 E 24 G G A A G C U C U G A C C SEQRES 2 E 24 G A C C C C C A G C C SEQRES 1 F 24 G C U G G G A C A A C U A SEQRES 2 F 24 G A C A U A C A G U G HET 9SI A 7 31 HET 9SI D 7 31 HET MG B 101 1 HET GUN C 101 11 HET MG C 102 1 HET GUN F 101 11 HET MG F 102 1 HETNAM 9SI [(2R,3S,4R,5R)-5-[1-[[4-(AMINOMETHYL)PHENYL]METHYL]-6- HETNAM 2 9SI AZANYL-PURIN-1-IUM-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2- HETNAM 3 9SI YL]METHYL DIHYDROGEN PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM GUN GUANINE HETSYN 9SI 1-BENZYLAMINE-ADENOSINE FORMUL 1 9SI 2(C18 H24 N6 O7 P 1+) FORMUL 7 MG 3(MG 2+) FORMUL 8 GUN 2(C5 H5 N5 O) FORMUL 12 HOH *6(H2 O) LINK O3' G A 6 P 9SI A 7 1555 1555 1.61 LINK O3' 9SI A 7 P G A 8 1555 1555 1.61 LINK O3' G D 6 P 9SI D 7 1555 1555 1.61 LINK O3' 9SI D 7 P G D 8 1555 1555 1.61 LINK MG MG B 101 O HOH B 201 1555 1555 2.18 LINK MG MG B 101 O HOH B 202 1555 1555 2.18 LINK MG MG B 101 O HOH C 201 1555 1555 2.18 LINK MG MG B 101 O HOH E 101 1555 1555 2.18 LINK MG MG B 101 O HOH F 201 1555 1555 2.18 LINK MG MG B 101 O HOH F 202 1555 1555 2.18 LINK O2 C C 32 MG MG C 102 1555 1555 2.54 LINK O2 C F 32 MG MG F 102 1555 1555 2.27 CRYST1 117.861 117.861 83.275 90.00 90.00 90.00 P 41 2 2 16 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 0.008485 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008485 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012008 0.00000