HEADER HYDROLASE/RNA 12-APR-22 7UO2 TITLE E.COLI RNASEP HOLOENZYME WITH MG2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE P PROTEIN COMPONENT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE P PROTEIN,RNASEP PROTEIN,PROTEIN C5; COMPND 5 EC: 3.1.26.5; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNASE P RNA; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 8 ORGANISM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 10 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS RIBOZYME, PROTEIN-RNA COMPLEX, DIVALENT ION, RNA, HYDROLASE-RNA KEYWDS 2 COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR W.HUANG,D.J.TAYLOR REVDAT 2 12-JUN-24 7UO2 1 REMARK REVDAT 1 28-SEP-22 7UO2 0 JRNL AUTH J.ZHU,W.HUANG,J.ZHAO,L.HUYNH,D.J.TAYLOR,M.E.HARRIS JRNL TITL STRUCTURAL AND MECHANISTIC BASIS FOR RECOGNITION OF JRNL TITL 2 ALTERNATIVE TRNA PRECURSOR SUBSTRATES BY BACTERIAL JRNL TITL 3 RIBONUCLEASE P. JRNL REF NAT COMMUN V. 13 5120 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36045135 JRNL DOI 10.1038/S41467-022-32843-7 REMARK 2 REMARK 2 RESOLUTION. 3.10 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 : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 538466 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 7UO2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-22. REMARK 100 THE DEPOSITION ID IS D_1000262280. 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 : E.COLI RNASE P HOLOENZYME WITH REMARK 245 MG2+ REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.10 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 TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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) : 4000.00 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: DIMERIC 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 0 REMARK 465 VAL A 1 REMARK 465 LEU A 114 REMARK 465 ALA A 115 REMARK 465 ARG A 116 REMARK 465 GLY A 117 REMARK 465 SER A 118 REMARK 465 G B 127 REMARK 465 C B 128 REMARK 465 A B 129 REMARK 465 A B 130 REMARK 465 C B 131 REMARK 465 A B 132 REMARK 465 G B 133 REMARK 465 A B 134 REMARK 465 G B 135 REMARK 465 A B 136 REMARK 465 G B 137 REMARK 465 C B 138 REMARK 465 A B 139 REMARK 465 A B 140 REMARK 465 A B 141 REMARK 465 C B 142 REMARK 465 C B 143 REMARK 465 G B 144 REMARK 465 C B 145 REMARK 465 C B 146 REMARK 465 G B 147 REMARK 465 A B 148 REMARK 465 U B 149 REMARK 465 G B 150 REMARK 465 G B 151 REMARK 465 C B 152 REMARK 465 C B 153 REMARK 465 C B 154 REMARK 465 G B 155 REMARK 465 C B 156 REMARK 465 G B 157 REMARK 465 C B 158 REMARK 465 A B 159 REMARK 465 A B 160 REMARK 465 G B 161 REMARK 465 C B 162 REMARK 465 G B 163 REMARK 465 G B 164 REMARK 465 G B 165 REMARK 465 A B 166 REMARK 465 U B 167 REMARK 465 C B 168 REMARK 465 A B 169 REMARK 465 G B 170 REMARK 465 G B 171 REMARK 465 U B 172 REMARK 465 A B 173 REMARK 465 A B 174 REMARK 465 G B 175 REMARK 465 G B 176 REMARK 465 G B 177 REMARK 465 U B 178 REMARK 465 G B 179 REMARK 465 A B 180 REMARK 465 A B 181 REMARK 465 A B 182 REMARK 465 G B 183 REMARK 465 G B 184 REMARK 465 G B 185 REMARK 465 U B 186 REMARK 465 G B 187 REMARK 465 C B 188 REMARK 465 G B 189 REMARK 465 G B 190 REMARK 465 U B 191 REMARK 465 A B 192 REMARK 465 A B 193 REMARK 465 G B 194 REMARK 465 A B 195 REMARK 465 G B 196 REMARK 465 C B 197 REMARK 465 G B 198 REMARK 465 C B 199 REMARK 465 A B 200 REMARK 465 C B 201 REMARK 465 C B 202 REMARK 465 G B 203 REMARK 465 C B 204 REMARK 465 G B 205 REMARK 465 C B 206 REMARK 465 G B 207 REMARK 465 G B 208 REMARK 465 C B 209 REMARK 465 U B 210 REMARK 465 G B 211 REMARK 465 G B 212 REMARK 465 U B 213 REMARK 465 A B 214 REMARK 465 A B 215 REMARK 465 C B 216 REMARK 465 A B 217 REMARK 465 G B 218 REMARK 465 U B 219 REMARK 465 C B 220 REMARK 465 C B 221 REMARK 465 G B 222 REMARK 465 U B 223 REMARK 465 G B 224 REMARK 465 G B 225 REMARK 465 C B 226 REMARK 465 A B 227 REMARK 465 C B 228 REMARK 465 G B 229 REMARK 465 G B 230 REMARK 465 U B 231 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' A B 112 OP1 C B 115 2.13 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 U B 17 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 U B 17 C2 - N1 - C1' ANGL. DEV. = 7.4 DEGREES REMARK 500 G B 271 O4' - C1' - N9 ANGL. DEV. = 4.4 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 PRO A 6 -166.62 -74.48 REMARK 500 GLU A 8 23.66 -78.38 REMARK 500 ALA A 27 62.66 -163.60 REMARK 500 PRO A 30 38.59 -72.37 REMARK 500 GLN A 31 -50.67 -159.18 REMARK 500 ASN A 39 -148.66 -134.30 REMARK 500 SER A 40 0.07 -151.68 REMARK 500 ARG A 56 -144.67 -87.91 REMARK 500 ARG A 57 94.29 57.28 REMARK 500 ARG A 61 -51.74 62.38 REMARK 500 GLU A 78 -59.80 -132.86 REMARK 500 LYS A 89 -145.64 -87.55 REMARK 500 LYS A 90 -93.67 -74.00 REMARK 500 ASP A 96 -158.42 -92.12 REMARK 500 HIS A 111 43.54 -101.44 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 B 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 67 OP1 REMARK 620 2 A B 67 O5' 62.7 REMARK 620 3 G B 350 O3' 167.9 106.0 REMARK 620 4 A B 351 OP1 122.4 118.1 57.1 REMARK 620 5 A B 352 OP2 78.9 141.5 112.0 79.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 249 OP1 REMARK 620 2 G B 250 OP1 122.7 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-26638 RELATED DB: EMDB REMARK 900 E.COLI RNASEP HOLOENZYME WITH MG2+ DBREF 7UO2 A 0 118 UNP C3SLK7 C3SLK7_ECOLX 1 119 DBREF1 7UO2 B 1 376 GB CP053595.1 DBREF2 7UO2 B 1845291569 1320980 1321356 SEQADV 7UO2 B GB 184529156 A 21353 DELETION SEQRES 1 A 119 MET VAL LYS LEU ALA PHE PRO ARG GLU LEU ARG LEU LEU SEQRES 2 A 119 THR PRO SER GLN PHE THR PHE VAL PHE GLN GLN PRO GLN SEQRES 3 A 119 ARG ALA GLY THR PRO GLN ILE THR ILE LEU GLY ARG LEU SEQRES 4 A 119 ASN SER LEU GLY HIS PRO ARG ILE GLY LEU THR VAL ALA SEQRES 5 A 119 LYS LYS ASN VAL ARG ARG ALA HIS GLU ARG ASN ARG ILE SEQRES 6 A 119 LYS ARG LEU THR ARG GLU SER PHE ARG LEU ARG GLN HIS SEQRES 7 A 119 GLU LEU PRO ALA MET ASP PHE VAL VAL VAL ALA LYS LYS SEQRES 8 A 119 GLY VAL ALA ASP LEU ASP ASN ARG ALA LEU SER GLU ALA SEQRES 9 A 119 LEU GLU LYS LEU TRP ARG ARG HIS CYS ARG LEU ALA ARG SEQRES 10 A 119 GLY SER SEQRES 1 B 376 G A A G C U G A C C A G A SEQRES 2 B 376 C A G U C G C C G C U U C SEQRES 3 B 376 G U C G U C G U C C U C U SEQRES 4 B 376 U C G G G G G A G A C G G SEQRES 5 B 376 G C G G A G G G G A G G A SEQRES 6 B 376 A A G U C C G G G C U C C SEQRES 7 B 376 A U A G G G C A G G G U G SEQRES 8 B 376 C C A G G U A A C G C C U SEQRES 9 B 376 G G G G G G G A A A C C C SEQRES 10 B 376 A C G A C C A G U G C A A SEQRES 11 B 376 C A G A G A G C A A A C C SEQRES 12 B 376 G C C G A U G G C C C G C SEQRES 13 B 376 G C A A G C G G G A U C A SEQRES 14 B 376 G G U A A G G G U G A A A SEQRES 15 B 376 G G G U G C G G U A A G A SEQRES 16 B 376 G C G C A C C G C G C G G SEQRES 17 B 376 C U G G U A A C A G U C C SEQRES 18 B 376 G U G G C A C G G U A A A SEQRES 19 B 376 C U C C A C C C G G A G C SEQRES 20 B 376 A A G G C C A A A U A G G SEQRES 21 B 376 G G U U C A U A A G G U A SEQRES 22 B 376 C G G C C C G U A C U G A SEQRES 23 B 376 A C C C G G G U A G G C U SEQRES 24 B 376 G C U U G A G C C A G U G SEQRES 25 B 376 A G C G A U U G C U G G C SEQRES 26 B 376 C U A G A U G A A U G A C SEQRES 27 B 376 U G U C C A C G A C A G A SEQRES 28 B 376 A C C C G G C U U A U C G SEQRES 29 B 376 G U C A G U U U C C C U HET MG B 401 1 HET MG B 402 1 HET MG B 403 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 3(MG 2+) HELIX 1 AA1 PRO A 6 ARG A 10 5 5 HELIX 2 AA2 THR A 13 GLN A 23 1 11 HELIX 3 AA3 ALA A 58 ARG A 73 1 16 HELIX 4 AA4 ASP A 96 TRP A 108 1 13 SHEET 1 AA1 3 ILE A 32 LEU A 35 0 SHEET 2 AA1 3 ASP A 83 ALA A 88 -1 O VAL A 85 N LEU A 35 SHEET 3 AA1 3 ARG A 45 LEU A 48 1 N ARG A 45 O PHE A 84 LINK OP1 A B 67 MG MG B 401 1555 1555 2.05 LINK O5' A B 67 MG MG B 401 1555 1555 2.64 LINK OP1 A B 249 MG MG B 403 1555 1555 2.55 LINK OP1 G B 250 MG MG B 403 1555 1555 2.03 LINK O3' G B 350 MG MG B 401 1555 1555 2.93 LINK OP1 A B 351 MG MG B 401 1555 1555 2.07 LINK OP2 A B 352 MG MG B 401 1555 1555 2.37 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