HEADER RNA 04-JUN-25 9OY3 TITLE STRUCTURE OF GEOBACILLUS STEAROTHERMOPHILUS RNASE P RIBOZYME TETRALOOP TITLE 2 MUTANT (SUB-CONFORMATION 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNASE P RNA COMPONENT TETRALOOP MUTANT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS RIBOZYME, RNA, RNASE P EXPDTA ELECTRON MICROSCOPY AUTHOR Y.-T.LEE,J.R.STAGNO,Y.-X.WANG REVDAT 1 20-MAY-26 9OY3 0 JRNL AUTH Y.T.LEE,M.F.S.DEGENHARDT,I.SKEPARNIAS,S.Y.CHEN,B.A.BHOGE, JRNL AUTH 2 S.G.TARASOV,M.A.DYBA,J.ZHANG,J.R.STAGNO,Y.X.WANG JRNL TITL STRUCTURAL BASIS FOR PROTEIN-FREE CATALYSIS BY RIBONUCLEASE JRNL TITL 2 P RIBOZYME. JRNL REF NAT COMMUN 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 41986363 JRNL DOI 10.1038/S41467-026-71597-4 REMARK 2 REMARK 2 RESOLUTION. 3.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2A64 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.130 REMARK 3 NUMBER OF PARTICLES : 125265 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9OY3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1000296672. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : RNASE P RNA TETRALOOP MUTANT IN REMARK 245 5 MM CA2+ REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : 4D-STEM REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5700.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 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 O2 U A 124 O6 G A 127 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 153 N3 - C2 - O2 ANGL. DEV. = -5.7 DEGREES REMARK 500 G A 173 N1 - C2 - N2 ANGL. DEV. = -5.6 DEGREES REMARK 500 U A 185 C2 - N1 - C1' ANGL. DEV. = 7.9 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 CA A 519 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 15 OP1 REMARK 620 2 G A 15 OP2 52.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 516 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 50 OP2 REMARK 620 2 A A 389 OP1 100.3 REMARK 620 3 A A 390 OP2 65.5 118.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 522 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 82 OP2 REMARK 620 2 G A 83 OP2 71.9 REMARK 620 3 G A 250 OP2 62.1 132.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 508 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 99 OP2 REMARK 620 2 U A 105 O4 58.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 511 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 139 OP1 REMARK 620 2 G A 140 OP2 76.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 512 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 275 OP1 REMARK 620 2 A A 277 OP1 75.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 509 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 276 O2' REMARK 620 2 C A 276 O2 69.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 510 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 277 O2' REMARK 620 2 C A 278 OP2 69.6 REMARK 620 3 A A 330 OP1 74.4 94.4 REMARK 620 4 G A 331 OP2 81.0 150.2 72.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 504 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 298 O6 REMARK 620 2 G A 299 O6 86.7 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-70995 RELATED DB: EMDB REMARK 900 STRUCTURE OF GEOBACILLUS STEAROTHERMOPHILUS RNASE P RIBOZYME REMARK 900 TETRALOOP MUTANT (SUB-CONFORMATION 2) DBREF 9OY3 A 1 417 GB 143442 M19021.1 1 417 SEQADV 9OY3 U A 126 GB 143442 C 126 CONFLICT SEQADV 9OY3 U A 215 GB 143442 G 215 ENGINEERED MUTATION SEQADV 9OY3 U A 216 GB 143442 A 216 ENGINEERED MUTATION SEQADV 9OY3 U A 217 GB 143442 A 217 ENGINEERED MUTATION SEQADV 9OY3 U A 218 GB 143442 A 218 ENGINEERED MUTATION SEQADV 9OY3 C A 417 GB 143442 G 417 ENGINEERED MUTATION SEQRES 1 A 417 G U U A A U C A U G C U C SEQRES 2 A 417 G G G U A A U C G C U G C SEQRES 3 A 417 G G C C G G U U U C G G C SEQRES 4 A 417 C G U A G A G G A A A G U SEQRES 5 A 417 C C A U G C U C G C A C G SEQRES 6 A 417 G U G C U G A G A U G C C SEQRES 7 A 417 C G U A G U G U U C G U G SEQRES 8 A 417 C C U A G C G A A U C C A SEQRES 9 A 417 U A A G C U A G G G C A G SEQRES 10 A 417 C C U G G C U U U G G C U SEQRES 11 A 417 G G G C U G A C G G C G G SEQRES 12 A 417 G G A A A G A A C C U A C SEQRES 13 A 417 G U C C G G C U G G G A U SEQRES 14 A 417 A U G G U U C G A U U A C SEQRES 15 A 417 C C U G A A A G U G C C A SEQRES 16 A 417 C A G U G A C G G A G C U SEQRES 17 A 417 C U A A G G U U U U C C U SEQRES 18 A 417 U A G A G G U G G A A C G SEQRES 19 A 417 C G G U A A A C C C C A C SEQRES 20 A 417 G A G C G A G A A A C C C SEQRES 21 A 417 A A A U G A U G G U A G G SEQRES 22 A 417 G G C A C C U U C C C G A SEQRES 23 A 417 A G G A A A U G A A C G G SEQRES 24 A 417 A G G G A A G G A C A G G SEQRES 25 A 417 C G G C G C A U G C A G C SEQRES 26 A 417 C U G U A G A U A G A U G SEQRES 27 A 417 A U U A C C G C C G G A G SEQRES 28 A 417 U A C G A G G C G C A A A SEQRES 29 A 417 G C C G C U U G C A G U A SEQRES 30 A 417 C G A A G G U A C A G A A SEQRES 31 A 417 C A U G G C U U A U A G A SEQRES 32 A 417 G C A U G A U U A A C G U SEQRES 33 A 417 C HET CA A 501 1 HET CA A 502 1 HET CA A 503 1 HET CA A 504 1 HET CA A 505 1 HET CA A 506 1 HET CA A 507 1 HET CA A 508 1 HET CA A 509 1 HET CA A 510 1 HET CA A 511 1 HET CA A 512 1 HET CA A 513 1 HET CA A 514 1 HET CA A 515 1 HET CA A 516 1 HET CA A 517 1 HET CA A 518 1 HET CA A 519 1 HET CA A 520 1 HET CA A 521 1 HET CA A 522 1 HETNAM CA CALCIUM ION FORMUL 2 CA 22(CA 2+) LINK OP1 G A 15 CA CA A 519 1555 1555 2.53 LINK OP2 G A 15 CA CA A 519 1555 1555 3.15 LINK O4 U A 42 CA CA A 506 1555 1555 2.68 LINK OP2 A A 50 CA CA A 516 1555 1555 2.34 LINK OP2 A A 82 CA CA A 522 1555 1555 2.33 LINK OP2 G A 83 CA CA A 522 1555 1555 2.75 LINK OP2 A A 99 CA CA A 508 1555 1555 2.51 LINK O4 U A 105 CA CA A 508 1555 1555 3.19 LINK OP1 G A 139 CA CA A 511 1555 1555 2.42 LINK OP2 G A 140 CA CA A 511 1555 1555 2.37 LINK OP2 A A 240 CA CA A 507 1555 1555 2.78 LINK OP2 G A 250 CA CA A 522 1555 1555 2.91 LINK OP2 U A 270 CA CA A 521 1555 1555 2.68 LINK OP1 G A 275 CA CA A 512 1555 1555 2.35 LINK O2' C A 276 CA CA A 509 1555 1555 2.75 LINK O2 C A 276 CA CA A 509 1555 1555 2.55 LINK O2' A A 277 CA CA A 510 1555 1555 2.76 LINK OP1 A A 277 CA CA A 512 1555 1555 2.31 LINK OP2 C A 278 CA CA A 510 1555 1555 2.24 LINK O6 G A 289 CA CA A 515 1555 1555 2.46 LINK O6 G A 298 CA CA A 504 1555 1555 3.01 LINK O6 G A 299 CA CA A 504 1555 1555 2.36 LINK OP1 A A 330 CA CA A 510 1555 1555 2.57 LINK OP2 G A 331 CA CA A 510 1555 1555 2.20 LINK OP1 A A 389 CA CA A 516 1555 1555 2.72 LINK OP2 A A 390 CA CA A 516 1555 1555 2.68 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 CONECT 297 8973 CONECT 298 8973 CONECT 890 8960 CONECT 1052 8970 CONECT 1732 8976 CONECT 1754 8976 CONECT 2094 8962 CONECT 2235 8962 CONECT 2948 8965 CONECT 2972 8965 CONECT 5119 8961 CONECT 5330 8976 CONECT 5764 8975 CONECT 5874 8966 CONECT 5906 8963 CONECT 5910 8963 CONECT 5917 8966 CONECT 5926 8964 CONECT 5940 8964 CONECT 6185 8969 CONECT 6381 8958 CONECT 6404 8958 CONECT 7064 8964 CONECT 7087 8964 CONECT 8337 8970 CONECT 8360 8970 CONECT 8958 6381 6404 CONECT 8960 890 CONECT 8961 5119 CONECT 8962 2094 2235 CONECT 8963 5906 5910 CONECT 8964 5926 5940 7064 7087 CONECT 8965 2948 2972 CONECT 8966 5874 5917 CONECT 8969 6185 CONECT 8970 1052 8337 8360 CONECT 8973 297 298 CONECT 8975 5764 CONECT 8976 1732 1754 5330 MASTER 203 0 22 0 0 0 0 6 8975 1 39 33 END