HEADER HYDROLASE/RNA 12-APR-22 7UO0 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; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: PRECURSOR TRNA SUBSTRATE G(-1) G(-2); COMPND 13 CHAIN: C; COMPND 14 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; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 13 ORGANISM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 15 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 1 28-SEP-22 7UO0 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. 3.40 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 546283 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 7UO0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-22. REMARK 100 THE DEPOSITION ID IS D_1000262247. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 C B 85 OP1 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 O4 U B 97 N6 A B 99 2.12 REMARK 500 O2' G B 291 OP2 G B 293 2.14 REMARK 500 O2' A B 248 O2' A C 74 2.19 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 B 4 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 C B 5 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 G B 7 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 C B 9 OP1 - P - OP2 ANGL. DEV. = -9.7 DEGREES REMARK 500 C B 9 N1 - C1' - C2' ANGL. DEV. = -7.7 DEGREES REMARK 500 C B 9 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 C B 10 OP1 - P - OP2 ANGL. DEV. = -10.4 DEGREES REMARK 500 G B 12 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 C B 14 OP1 - P - OP2 ANGL. DEV. = -10.5 DEGREES REMARK 500 A B 15 O3' - P - OP2 ANGL. DEV. = 10.2 DEGREES REMARK 500 A B 15 O3' - P - OP1 ANGL. DEV. = -74.5 DEGREES REMARK 500 A B 15 OP1 - P - OP2 ANGL. DEV. = -19.4 DEGREES REMARK 500 G B 16 O3' - P - OP1 ANGL. DEV. = -70.7 DEGREES REMARK 500 C B 18 OP1 - P - OP2 ANGL. DEV. = -9.7 DEGREES REMARK 500 G B 19 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES REMARK 500 C B 20 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 C B 21 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 G B 22 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES REMARK 500 C B 23 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 C B 26 OP1 - P - OP2 ANGL. DEV. = -9.9 DEGREES REMARK 500 G B 27 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 C B 29 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 G B 30 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 C B 32 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES REMARK 500 G B 33 OP1 - P - OP2 ANGL. DEV. = -9.5 DEGREES REMARK 500 C B 35 OP1 - P - OP2 ANGL. DEV. = -11.7 DEGREES REMARK 500 C B 35 N1 - C1' - C2' ANGL. DEV. = 8.8 DEGREES REMARK 500 C B 35 C6 - N1 - C2 ANGL. DEV. = -3.1 DEGREES REMARK 500 C B 36 O3' - P - OP1 ANGL. DEV. = 9.0 DEGREES REMARK 500 C B 36 OP1 - P - OP2 ANGL. DEV. = -11.3 DEGREES REMARK 500 C B 38 OP1 - P - OP2 ANGL. DEV. = -11.0 DEGREES REMARK 500 C B 41 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 G B 42 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 G B 43 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES REMARK 500 G B 44 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 G B 45 OP1 - P - OP2 ANGL. DEV. = -9.6 DEGREES REMARK 500 G B 46 O3' - P - OP2 ANGL. DEV. = 7.3 DEGREES REMARK 500 G B 46 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 G B 46 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 G B 46 C4 - C5 - N7 ANGL. DEV. = -2.6 DEGREES REMARK 500 G B 46 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 G B 46 N3 - C4 - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 G B 46 C6 - C5 - N7 ANGL. DEV. = 4.2 DEGREES REMARK 500 G B 46 N1 - C6 - O6 ANGL. DEV. = -4.6 DEGREES REMARK 500 G B 46 C5 - C6 - O6 ANGL. DEV. = 4.1 DEGREES REMARK 500 G B 46 C8 - N9 - C1' ANGL. DEV. = 8.1 DEGREES REMARK 500 G B 48 O3' - P - OP1 ANGL. DEV. = 8.3 DEGREES REMARK 500 G B 48 OP1 - P - OP2 ANGL. DEV. = -11.5 DEGREES REMARK 500 C B 50 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES REMARK 500 G B 51 O3' - P - OP1 ANGL. DEV. = 6.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 341 ANGLE DEVIATIONS. 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 PHE A 5 76.48 -155.85 REMARK 500 ARG A 57 69.27 61.12 REMARK 500 ARG A 61 -68.67 65.39 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 B 404 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 11 OP2 REMARK 620 2 A B 11 O5' 55.0 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-26636 RELATED DB: EMDB REMARK 900 E.COLI RNASEP HOLOENZYME WITH MG2+ DBREF 7UO0 A 0 118 UNP C3SLK7 C3SLK7_ECOLX 1 119 DBREF1 7UO0 B 1 373 GB CP053595.1 DBREF2 7UO0 B 1845291569 1320980 1321352 DBREF 7UO0 C -4 77 PDB 7UO0 7UO0 -4 77 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 373 G A A G C U G A C C A G A SEQRES 2 B 373 C A G U C G C C G C U U C SEQRES 3 B 373 G U C G U C G U C C U C U SEQRES 4 B 373 U C G G G G G A G A C G G SEQRES 5 B 373 G C G G A G G G G A G G A SEQRES 6 B 373 A A G U C C G G G C U C C SEQRES 7 B 373 A U A G G G C A G G G U G SEQRES 8 B 373 C C A G G U A A C G C C U SEQRES 9 B 373 G G G G G G G A A A C C C SEQRES 10 B 373 A C G A C C A G U G C A A SEQRES 11 B 373 C A G A G A G C A A A C C SEQRES 12 B 373 G C C G A U G G C C C G C SEQRES 13 B 373 G C A A G C G G G A U C A SEQRES 14 B 373 G G U A A G G G U G A A A SEQRES 15 B 373 G G G U G C G G U A A G A SEQRES 16 B 373 G C G C A C C G C G C G G SEQRES 17 B 373 C U G G U A A C A G U C C SEQRES 18 B 373 G U G G C A C G G U A A A SEQRES 19 B 373 C U C C A C C C G G A G C SEQRES 20 B 373 A A G G C C A A A U A G G SEQRES 21 B 373 G G U U C A U A A G G U A SEQRES 22 B 373 C G G C C C G U A C U G A SEQRES 23 B 373 A C C C G G G U A G G C U SEQRES 24 B 373 G C U U G A G C C A G U G SEQRES 25 B 373 A G C G A U U G C U G G C SEQRES 26 B 373 C U A G A U G A A U G A C SEQRES 27 B 373 U G U C C A C G A C A G A SEQRES 28 B 373 A C C C G G C U U A U C G SEQRES 29 B 373 G U C A G U U U C SEQRES 1 C 82 U C U G G G G C U A C G U SEQRES 2 C 82 A G C U C A G U U G G U U SEQRES 3 C 82 A G A G C A C A U C A C U SEQRES 4 C 82 C A U A A U G A U G G G G SEQRES 5 C 82 U C A C A G G U U C G A A SEQRES 6 C 82 U C C C G U C G U A G C C SEQRES 7 C 82 A C C A HET CA B 401 1 HET CA B 402 1 HET CA B 403 1 HET CA B 404 1 HET CA B 405 1 HET CA B 406 1 HET CA B 407 1 HETNAM CA CALCIUM ION FORMUL 4 CA 7(CA 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 ARG A 61 ARG A 75 1 15 HELIX 4 AA4 ASP A 96 ARG A 109 1 14 SHEET 1 AA1 4 GLN A 25 GLY A 28 0 SHEET 2 AA1 4 ILE A 32 GLY A 36 -1 O ILE A 34 N ALA A 27 SHEET 3 AA1 4 PHE A 84 ALA A 88 -1 O VAL A 87 N THR A 33 SHEET 4 AA1 4 ILE A 46 LEU A 48 1 N GLY A 47 O VAL A 86 LINK OP2 A B 11 CA CA B 404 1555 1555 2.45 LINK O5' A B 11 CA CA B 404 1555 1555 2.88 LINK OP2 A B 330 CA CA B 406 1555 1555 3.14 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