HEADER RNA/HYDROLASE 02-JUN-25 9OWS TITLE STRUCTURE OF GEOBACILLUS STEAROTHERMOPHILUS RNASE P HOLOENZYME IN 5 MM TITLE 2 MG2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNASE P RNA (417-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RIBONUCLEASE P PROTEIN COMPONENT; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: RNASE P PROTEIN,RNASEP PROTEIN,PROTEIN C5; COMPND 9 EC: 3.1.26.5; COMPND 10 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; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 8 ORGANISM_TAXID: 1422; SOURCE 9 GENE: RNPA, B4114_2986; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS RIBOZYME, RNA, RNASE P., RNA-HYDROLASE COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR Y.-T.LEE,J.R.STAGNO,Y.-X.WANG REVDAT 1 10-JUN-26 9OWS 0 JRNL AUTH Y.-T.LEE,M.F.S.DEGENHARDT,I.SKEPARNIAS,S.-Y.CHEN,B.A.BHOGE, JRNL AUTH 2 J.ZHANG,J.R.STAGNO,Y.-X.WANG JRNL TITL STRUCTURES OF RNASE P RIBOZYME CATALYSIS IN APO AND HOLO JRNL TITL 2 STATES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 2.870 REMARK 3 NUMBER OF PARTICLES : 998359 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 9OWS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1000296548. 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 AND PROTEIN REMARK 245 COMPONENTS IN 5 MM 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 OP2 U A 293 MG MG A 511 1.25 REMARK 500 OP2 G A 331 MG MG A 510 1.66 REMARK 500 OP1 A A 50 MG MG A 515 1.66 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 G A 68 O3' - P - OP1 ANGL. DEV. = 7.7 DEGREES REMARK 500 A A 147 O3' - P - OP1 ANGL. DEV. = 7.4 DEGREES REMARK 500 U A 180 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 A A 263 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 U A 264 O3' - P - OP1 ANGL. DEV. = 7.2 DEGREES REMARK 500 C A 278 O3' - P - OP2 ANGL. DEV. = 10.7 DEGREES REMARK 500 A A 300 O3' - P - O5' ANGL. DEV. = -12.0 DEGREES REMARK 500 A A 300 O3' - P - OP1 ANGL. DEV. = 7.3 DEGREES REMARK 500 A A 389 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 G A 394 O3' - P - OP1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ASP B 80 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR B 5 33.12 -75.26 REMARK 500 ASN B 25 -66.98 -100.99 REMARK 500 ARG B 26 -30.00 -140.18 REMARK 500 LEU B 71 39.31 -98.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 6 0.31 SIDE CHAIN 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 522 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 82 OP2 REMARK 620 2 G A 250 OP2 62.1 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 102.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 508 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 275 OP1 REMARK 620 2 A A 277 OP1 98.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 510 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 277 O2' REMARK 620 2 C A 278 OP2 101.2 REMARK 620 3 A A 330 OP1 79.7 79.8 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 389 O5' REMARK 620 2 A A 390 OP2 84.6 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-70942 RELATED DB: EMDB REMARK 900 STRUCTURE OF GEOBACILLUS STEAROTHERMOPHILUS RNASE P HOLOENZYME IN 5 REMARK 900 MM MG2+ DBREF 9OWS A 1 417 PDB 9OWS 9OWS 1 417 DBREF1 9OWS B 1 115 UNP A0A150N245_GEOSE DBREF2 9OWS B A0A150N245 1 115 SEQADV 9OWS GLY B 0 UNP A0A150N24 EXPRESSION TAG SEQADV 9OWS ILE B 64 UNP A0A150N24 VAL 64 CONFLICT 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 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 SEQRES 1 B 116 GLY MET LYS LYS LYS TYR ARG ILE LYS LYS ASN GLU GLU SEQRES 2 B 116 PHE GLN GLU VAL PHE GLN GLN GLY VAL SER VAL ALA ASN SEQRES 3 B 116 ARG GLN PHE VAL VAL TYR THR LEU ASP ARG PRO GLU GLN SEQRES 4 B 116 PRO TYR PHE ARG ILE GLY LEU SER VAL SER LYS LYS LEU SEQRES 5 B 116 GLY LYS ALA VAL VAL ARG ASN ARG ILE LYS ARG TYR ILE SEQRES 6 B 116 ARG GLN CYS PHE LEU GLU LEU LYS GLU GLU VAL ALA PRO SEQRES 7 B 116 GLY LYS ASP TYR VAL ILE ILE ALA ARG GLN PRO ALA ALA SEQRES 8 B 116 GLU MET GLY TYR ALA GLU VAL LYS LYS SER LEU ILE HIS SEQRES 9 B 116 VAL LEU ARG LYS ALA GLY GLY LEU LYS LYS GLU ALA 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 HETNAM MG MAGNESIUM ION FORMUL 3 MG 22(MG 2+) HELIX 1 AA1 ASN B 10 GLY B 20 1 11 HELIX 2 AA2 LYS B 53 LEU B 71 1 19 HELIX 3 AA3 GLN B 87 ALA B 90 5 4 HELIX 4 AA4 GLY B 93 ALA B 108 1 16 SHEET 1 AA1 4 VAL B 21 ALA B 24 0 SHEET 2 AA1 4 PHE B 28 ASP B 34 -1 O VAL B 30 N VAL B 23 SHEET 3 AA1 4 LYS B 79 ALA B 85 -1 O ILE B 84 N VAL B 29 SHEET 4 AA1 4 ARG B 42 LEU B 45 1 N GLY B 44 O TYR B 81 LINK N7 G A 27 MG MG A 502 1555 1555 2.80 LINK OP2 A A 82 MG MG A 522 1555 1555 2.15 LINK OP2 G A 250 MG MG A 522 1555 1555 2.94 LINK N1 A A 253 MG MG A 521 1555 1555 2.86 LINK OP1 A A 257 MG MG A 520 1555 1555 2.24 LINK OP2 C A 258 MG MG A 520 1555 1555 1.92 LINK OP1 G A 275 MG MG A 508 1555 1555 1.73 LINK OP1 A A 277 MG MG A 508 1555 1555 2.00 LINK O2' A A 277 MG MG A 510 1555 1555 2.00 LINK OP2 C A 278 MG MG A 510 1555 1555 1.96 LINK N7 G A 294 MG MG A 511 1555 1555 1.94 LINK OP1 A A 330 MG MG A 510 1555 1555 2.72 LINK O5' A A 389 MG MG A 515 1555 1555 2.92 LINK OP2 A A 390 MG MG A 515 1555 1555 2.09 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 566 9913 CONECT 1732 9933 CONECT 5339 9933 CONECT 5421 9932 CONECT 5493 9931 CONECT 5516 9931 CONECT 5883 9919 CONECT 5926 9919 CONECT 5935 9921 CONECT 5949 9921 CONECT 6300 9922 CONECT 7073 9921 CONECT 8348 9926 CONECT 8369 9926 CONECT 9913 566 CONECT 9919 5883 5926 CONECT 9921 5935 5949 7073 CONECT 9922 6300 CONECT 9926 8348 8369 CONECT 9931 5493 5516 CONECT 9932 5421 CONECT 9933 1732 5339 MASTER 220 0 22 4 4 0 0 6 9931 2 22 42 END