HEADER RNA 22-APR-22 7URM TITLE ALLO-TRNAUTU1A IN THE P SITE OF THE E. COLI RIBOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALLO-TRNAUTU1A; COMPND 3 CHAIN: v; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: METAGENOME; SOURCE 4 ORGANISM_TAXID: 256318; SOURCE 5 OTHER_DETAILS: OIL POLLUTED MARINE MICROBIAL COMMUNITIES FROM COAL SOURCE 6 OIL POINT, SANTA BARBARA, CALIFORNIA, USA - SANTA BARBARA OIL SEEP SOURCE 7 SAMPLE 6 (CRUDE OIL METAGENOME 6, ASSEMBLY_DATE=20131204) KEYWDS TRNA, SELENOCYSTEINE, RIBOSOME, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR J.ZHANG,A.PRABHAKAR,N.KRAHN,O.VARGAS-RODRIGUEZ,M.KRUPKIN,Z.FU, AUTHOR 2 F.J.ACOSTA-REYES,X.GE,J.CHOI,A.CRNKOVIC,M.EHRENBERG,E.VIANI PUGLISI, AUTHOR 3 D.SOLL,J.PUGLISI REVDAT 3 12-JUN-24 7URM 1 REMARK REVDAT 2 26-OCT-22 7URM 1 JRNL REVDAT 1 10-AUG-22 7URM 0 JRNL AUTH A.PRABHAKAR,N.KRAHN,J.ZHANG,O.VARGAS-RODRIGUEZ,M.KRUPKIN, JRNL AUTH 2 Z.FU,F.J.ACOSTA-REYES,X.GE,J.CHOI,A.CRNKOVIC,M.EHRENBERG, JRNL AUTH 3 E.V.PUGLISI,D.SOLL,J.PUGLISI JRNL TITL UNCOVERING TRANSLATION ROADBLOCKS DURING THE DEVELOPMENT OF JRNL TITL 2 A SYNTHETIC TRNA. JRNL REF NUCLEIC ACIDS RES. V. 50 10201 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 35882385 JRNL DOI 10.1093/NAR/GKAC576 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CTFFIND 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) : 3.000 REMARK 3 NUMBER OF PARTICLES : 23609 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7URM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-22. REMARK 100 THE DEPOSITION ID IS D_1000264743. 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 : 3D ARRAY REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : E. COLI 70S RIBOSOME WITH ALLO REMARK 245 -TRNAUTU1A IN THE P SITE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FOR 3 SECONDS BEFORE REMARK 245 PLUNGING REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 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 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: v 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 A v 8 C3' - O3' - P ANGL. DEV. = 21.2 DEGREES REMARK 500 U v 9 O3' - P - O5' ANGL. DEV. = 13.5 DEGREES REMARK 500 U v 9 O5' - P - OP2 ANGL. DEV. = -14.0 DEGREES REMARK 500 A v 46 O5' - C5' - C4' ANGL. DEV. = -5.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7URI RELATED DB: PDB REMARK 900 7URI CONTAINS SAME TRNA IN THE A SITE OF THE RIBOSOME REMARK 900 RELATED ID: EMD-26714 RELATED DB: EMDB REMARK 900 ALLO-TRNAUTU1A IN THE P SITE OF THE E. COLI RIBOSOME DBREF 7URM v 1 76 PDB 7URM 7URM 1 76 SEQRES 1 v 90 G G A G G G G A A A U U C SEQRES 2 v 90 U A U C U G G U G A U A G SEQRES 3 v 90 A C G G G A A C U C U A A SEQRES 4 v 90 A U U C C U U G A A A U G SEQRES 5 v 90 C C U C G C C G C A U U G SEQRES 6 v 90 G G U U C G A U U C C C U SEQRES 7 v 90 U C C C C U C C G C C A 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