HEADER RNA 29-MAY-25 9OVC TITLE STRUCTURE OF GEOBACILLUS STEAROTHERMOPHILUS RNASE P RIBOZYME IN 10 MM TITLE 2 MG2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNASE P RIBOZYME; 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,I.SKEPARNIAS,J.R.STAGNO,Y.-X.WANG REVDAT 1 20-MAY-26 9OVC 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. 2.97 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) : 2.970 REMARK 3 NUMBER OF PARTICLES : 130123 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 9OVC 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_1000296488. 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 10 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 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 : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5474.00 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) : 300 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: 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 U A 87 C5 - C6 - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 C A 209 O3' - P - OP1 ANGL. DEV. = 6.9 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 MG A 511 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 50 OP1 REMARK 620 2 A A 389 OP1 106.3 REMARK 620 3 A A 390 OP2 81.2 106.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 529 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 91 N7 REMARK 620 2 G A 91 O6 72.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 520 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 257 OP1 REMARK 620 2 C A 258 OP2 89.3 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 85.5 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 U A 333 O4 160.9 REMARK 620 N 1 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 84.1 REMARK 620 3 A A 330 OP1 85.3 85.3 REMARK 620 4 G A 331 OP2 92.3 158.8 73.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 535 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 300 OP2 REMARK 620 2 G A 301 N7 95.8 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 92.1 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-70897 RELATED DB: EMDB REMARK 900 STRUCTURE OF GEOBACILLUS STEAROTHERMOPHILUS RNASE P RIBOZYME IN 10 REMARK 900 MM MG2+ DBREF 9OVC A 1 417 GB 143442 M19021.1 1 417 SEQADV 9OVC 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 HET MG A 528 1 HET MG A 529 1 HET MG A 530 1 HET MG A 531 1 HET MG A 532 1 HET MG A 533 1 HET MG A 534 1 HET MG A 535 1 HET MG A 536 1 HET MG A 537 1 HET MG A 538 1 HET MG A 539 1 HET MG A 540 1 HET MG A 541 1 HET MG A 542 1 HET MG A 543 1 HET MG A 544 1 HET MG A 545 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 45(MG 2+) LINK N7 G A 46 MG MG A 506 1555 1555 2.13 LINK OP2 G A 47 MG MG A 510 1555 1555 2.01 LINK OP1 A A 50 MG MG A 511 1555 1555 2.10 LINK OP2 A A 82 MG MG A 507 1555 1555 2.01 LINK N7 G A 91 MG MG A 529 1555 1555 2.12 LINK O6 G A 91 MG MG A 529 1555 1555 2.92 LINK OP2 C A 103 MG MG A 532 1555 1555 2.10 LINK OP1 G A 139 MG MG A 528 1555 1555 2.82 LINK OP1 A A 257 MG MG A 520 1555 1555 2.03 LINK OP2 C A 258 MG MG A 520 1555 1555 2.15 LINK OP1 G A 275 MG MG A 514 1555 1555 2.02 LINK O2 C A 276 MG MG A 512 1555 1555 2.12 LINK OP1 A A 277 MG MG A 514 1555 1555 2.34 LINK O2' A A 277 MG MG A 515 1555 1555 2.09 LINK OP2 C A 278 MG MG A 515 1555 1555 2.16 LINK OP2 G A 288 MG MG A 504 1555 1555 2.97 LINK O6 G A 299 MG MG A 534 1555 1555 2.31 LINK OP2 A A 300 MG MG A 535 1555 1555 2.14 LINK N7 G A 301 MG MG A 535 1555 1555 2.11 LINK OP1 A A 330 MG MG A 515 1555 1555 2.70 LINK OP2 G A 331 MG MG A 515 1555 1555 1.98 LINK O4 U A 333 MG MG A 512 1555 1555 2.57 LINK OP1 A A 385 MG MG A 509 1555 1555 2.12 LINK OP2 C A 386 MG MG A 509 1555 1555 2.03 LINK OP1 A A 389 MG MG A 511 1555 1555 2.61 LINK OP2 A A 389 MG MG A 526 1555 1555 2.54 LINK OP2 A A 390 MG MG A 511 1555 1555 2.17 LINK OP2 A A 392 MG MG A 522 1555 1555 2.97 LINK O4 U A 393 MG MG A 523 1555 1555 2.00 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 1732 8970 CONECT 1935 8992 CONECT 1938 8992 CONECT 2178 8995 CONECT 2948 8991 CONECT 5493 8983 CONECT 5516 8983 CONECT 5883 8977 CONECT 5919 8975 CONECT 5926 8977 CONECT 5935 8978 CONECT 5949 8978 CONECT 6156 8967 CONECT 6413 8997 CONECT 6421 8998 CONECT 6455 8998 CONECT 7073 8978 CONECT 7096 8978 CONECT 7156 8975 CONECT 8259 8972 CONECT 8282 8972 CONECT 8346 8974 CONECT 8347 8989 CONECT 8369 8974 CONECT 8411 8985 CONECT 8448 8986 CONECT 8967 6156 CONECT 8969 974 CONECT 8970 1732 CONECT 8972 8259 8282 CONECT 8973 985 CONECT 8974 1051 8346 8369 CONECT 8975 5919 7156 CONECT 8977 5883 5926 CONECT 8978 5935 5949 7073 7096 CONECT 8983 5493 5516 CONECT 8985 8411 CONECT 8986 8448 CONECT 8989 8347 CONECT 8991 2948 CONECT 8992 1935 1938 CONECT 8995 2178 CONECT 8997 6413 CONECT 8998 6421 6455 MASTER 183 0 45 0 0 0 0 6 9007 1 47 33 END