HEADER RNA 29-MAY-25 9OVB TITLE STRUCTURE OF GEOBACILLUS STEAROTHERMOPHILUS RNASE P RIBOZYME IN 5 MM TITLE 2 MG2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNASE P RNA COMPONENT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: 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 9OVB 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. 3.21 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) : 3.210 REMARK 3 NUMBER OF PARTICLES : 334369 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 9OVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1000296486. 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 COMPONENT IN 5 MM REMARK 245 MG2+ 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 C A 29 N2 G A 38 2.18 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 MG A 511 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 50 OP1 REMARK 620 2 A A 50 O5' 68.4 REMARK 620 3 A A 389 OP1 162.1 95.7 REMARK 620 4 A A 390 OP2 114.9 139.0 82.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 507 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 82 OP2 REMARK 620 2 G A 83 OP2 71.0 REMARK 620 3 G A 250 OP2 84.5 154.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 527 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 139 OP1 REMARK 620 2 G A 140 OP2 103.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 514 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 275 OP1 REMARK 620 2 A A 277 OP1 102.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 512 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 276 O2 REMARK 620 2 A A 332 OP2 138.1 REMARK 620 3 U A 333 O4 121.0 98.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 515 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 277 O2' REMARK 620 2 C A 278 OP2 95.1 REMARK 620 3 A A 330 OP1 69.6 87.4 REMARK 620 4 G A 331 OP2 88.8 152.3 68.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 517 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 293 OP2 REMARK 620 2 G A 294 N7 77.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 509 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 385 OP1 REMARK 620 2 C A 386 OP2 93.5 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-70896 RELATED DB: EMDB REMARK 900 STRUCTURE OF GEOBACILLUS STEAROTHERMOPHILUS RNASE P RIBOZYME IN 5 REMARK 900 MM MG2+ DBREF 9OVB A 1 417 GB 143442 M19021.1 1 417 SEQADV 9OVB 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 C 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 G A A A 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 MG A 501 1 HET MG A 502 1 HET MG A 503 1 HET MG A 504 1 HET MG A 505 1 HET MG A 506 1 HET MG A 507 1 HET MG A 508 1 HET MG A 509 1 HET MG A 510 1 HET MG A 511 1 HET MG A 512 1 HET MG A 513 1 HET MG A 514 1 HET MG A 515 1 HET MG A 516 1 HET MG A 517 1 HET MG A 518 1 HET MG A 519 1 HET MG A 520 1 HET MG A 521 1 HET MG A 522 1 HET MG A 523 1 HET MG A 524 1 HET MG A 525 1 HET MG A 526 1 HET MG A 527 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 27(MG 2+) LINK N7 G A 46 MG MG A 506 1555 1555 2.12 LINK OP2 G A 47 MG MG A 510 1555 1555 1.98 LINK OP1 A A 50 MG MG A 511 1555 1555 2.35 LINK O5' A A 50 MG MG A 511 1555 1555 2.02 LINK N7 G A 71 MG MG A 508 1555 1555 2.52 LINK OP2 A A 82 MG MG A 507 1555 1555 2.02 LINK OP2 G A 83 MG MG A 507 1555 1555 2.88 LINK OP1 G A 139 MG MG A 527 1555 1555 2.68 LINK OP2 G A 140 MG MG A 527 1555 1555 2.21 LINK OP2 G A 250 MG MG A 507 1555 1555 2.95 LINK OP1 G A 275 MG MG A 514 1555 1555 1.98 LINK O2 C A 276 MG MG A 512 1555 1555 2.01 LINK OP1 A A 277 MG MG A 514 1555 1555 2.01 LINK O2' A A 277 MG MG A 515 1555 1555 2.04 LINK OP2 C A 278 MG MG A 515 1555 1555 1.96 LINK OP2 G A 288 MG MG A 504 1555 1555 2.44 LINK OP2 U A 293 MG MG A 517 1555 1555 2.38 LINK N7 G A 294 MG MG A 517 1555 1555 2.70 LINK OP1 A A 330 MG MG A 515 1555 1555 2.86 LINK OP2 G A 331 MG MG A 515 1555 1555 1.94 LINK OP2 A A 332 MG MG A 512 1555 1555 2.07 LINK O4 U A 333 MG MG A 512 1555 1555 2.77 LINK OP1 A A 385 MG MG A 509 1555 1555 2.34 LINK OP2 C A 386 MG MG A 509 1555 1555 1.98 LINK OP1 A A 389 MG MG A 511 1555 1555 2.68 LINK OP2 A A 390 MG MG A 511 1555 1555 2.24 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 974 8969 CONECT 985 8973 CONECT 1051 8974 CONECT 1053 8974 CONECT 1508 8971 CONECT 1732 8970 CONECT 1754 8970 CONECT 2948 8990 CONECT 2972 8990 CONECT 5339 8970 CONECT 5883 8977 CONECT 5919 8975 CONECT 5926 8977 CONECT 5935 8978 CONECT 5949 8978 CONECT 6156 8967 CONECT 6268 8980 CONECT 6300 8980 CONECT 7073 8978 CONECT 7096 8978 CONECT 7119 8975 CONECT 7156 8975 CONECT 8259 8972 CONECT 8282 8972 CONECT 8346 8974 CONECT 8369 8974 CONECT 8967 6156 CONECT 8969 974 CONECT 8970 1732 1754 5339 CONECT 8971 1508 CONECT 8972 8259 8282 CONECT 8973 985 CONECT 8974 1051 1053 8346 8369 CONECT 8975 5919 7119 7156 CONECT 8977 5883 5926 CONECT 8978 5935 5949 7073 7096 CONECT 8980 6268 6300 CONECT 8990 2948 2972 MASTER 177 0 27 0 0 0 0 6 8989 1 38 33 END