PDB Short entry for 1R2W HEADER RNA BINDING PROTEIN/RNA 30-SEP-03 1R2W TITLE COORDINATES OF L11 WITH 58NTS OF 23S RRNA FITTED INTO THE CRYO-EM MAP TITLE 2 OF THE 70S RIBOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: 58NTS OF 23S RRNA; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 50S RIBOSOMAL PROTEIN L11; COMPND 7 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 5 ORGANISM_TAXID: 2336 KEYWDS RNA, RIBOSOMAL PROTEIN, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN A; P ATOMS ONLY, CHAIN C AUTHOR M.VALLE,A.ZAVIALOV,W.LI,S.M.STAGG,J.SENGUPTA,R.C.NIELSEN,P.NISSEN, AUTHOR 2 S.C.HARVEY,M.EHRENBERG,J.FRANK REVDAT 3 14-FEB-24 1R2W 1 REMARK SEQADV REVDAT 2 24-FEB-09 1R2W 1 VERSN REVDAT 1 04-NOV-03 1R2W 0 JRNL AUTH M.VALLE,A.ZAVIALOV,W.LI,S.M.STAGG,J.SENGUPTA,R.C.NIELSEN, JRNL AUTH 2 P.NISSEN,S.C.HARVEY,M.EHRENBERG,J.FRANK JRNL TITL INCORPORATION OF AMINOACYL-TRNA INTO THE RIBOSOME AS SEEN BY JRNL TITL 2 CRYO-ELECTRON MICROSCOPY JRNL REF NAT.STRUCT.BIOL. V. 10 899 2003 JRNL REFN ISSN 1072-8368 JRNL PMID 14566331 JRNL DOI 10.1038/NSB1003 REMARK 2 REMARK 2 RESOLUTION. 9.00 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 : OTHER REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--MANUAL USING O 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) : 9.000 REMARK 3 NUMBER OF PARTICLES : 52181 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 1R2W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020369. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : 70S RIBOSOME; 50S RIBOSOMAL REMARK 245 PROTEIN L11; A SITE TRNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 32.00 REMARK 245 SAMPLE SUPPORT DETAILS : QUANTIFOIL HOLLEY CARBON COATED REMARK 245 GRIDS REMARK 245 SAMPLE VITRIFICATION DETAILS : RAPID FREEZING IN LIQUID ETHANE REMARK 245 SAMPLE BUFFER : POLYMIX BUFFER REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : STRUCTURAL CONSTITUENT OF REMARK 245 RIBOSOME REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 93.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 20000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 50000 REMARK 245 CALIBRATED MAGNIFICATION : 49640 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 APPLY THE FOLLOWING TO CHAINS: C, 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 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 G C 0 REMARK 465 ALA A -5 REMARK 465 LYS A -4 REMARK 465 LYS A -3 REMARK 465 VAL A -2 REMARK 465 ALA A -1 REMARK 465 ALA A 0 REMARK 465 ASP A 135 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 CA GLU A 66 CA PRO A 68 1.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FFK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA REMARK 900 MARISMORTUI AT 2.4 ANGSTROM RESOLUTION REMARK 900 RELATED ID: 1QZB RELATED DB: PDB REMARK 900 COORDINATES OF THE A-SITE TRNA MODEL FITTED INTO THE CRYO-EM MAP OF REMARK 900 70S RIBOSOME IN THE PRE-TRANSLOCATIONAL STATE REMARK 900 RELATED ID: 1QZC RELATED DB: PDB REMARK 900 COORDINATES OF S12, SH44, LH69 AND SRL SEPARATELY FITTED INTO THE REMARK 900 CRYO-EM MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S REMARK 900 RIBOSOME REMARK 900 RELATED ID: 1QZD RELATED DB: PDB REMARK 900 EF-TU.KIRROMYCIN COORDINATES FITTED INTO THE CRYO-EM MAP OF EF-TU REMARK 900 TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S RIBOSOME REMARK 900 RELATED ID: 1R2X RELATED DB: PDB REMARK 900 COORDINATES OF L11 WITH 58NTS OF 23S RRNA FITTED INTO THE CRYO-EM REMARK 900 MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S RIBOSOME REMARK 900 RELATED ID: EMD-1056 RELATED DB: EMDB REMARK 999 REMARK 999 SEQUENCE THE PROTEIN STRUCTURE CONTAINS CA ATOMS AND THE RNA REMARK 999 STRUCTURE CONTAINS P ATOMS ONLY DBREF 1R2W A -5 135 UNP P29395 RL11_THEMA 1 140 DBREF 1R2W C 0 57 PDB 1R2W 1R2W 0 57 SEQADV 1R2W GLU A 66 UNP P29395 INSERTION SEQRES 1 C 58 G C U G G G A U G U U G G SEQRES 2 C 58 C U U A G A A G C A G C C SEQRES 3 C 58 A U C A U U U A A A G A G SEQRES 4 C 58 U G C G U A A C A G C U C SEQRES 5 C 58 A C C A G C SEQRES 1 A 141 ALA LYS LYS VAL ALA ALA GLN ILE LYS LEU GLN LEU PRO SEQRES 2 A 141 ALA GLY LYS ALA THR PRO ALA PRO PRO VAL GLY PRO ALA SEQRES 3 A 141 LEU GLY GLN HIS GLY VAL ASN ILE MET GLU PHE CYS LYS SEQRES 4 A 141 ARG PHE ASN ALA GLU THR ALA ASP LYS ALA GLY MET ILE SEQRES 5 A 141 LEU PRO VAL VAL ILE THR VAL TYR GLU ASP LYS SER PHE SEQRES 6 A 141 THR PHE ILE ILE LYS THR GLU PRO PRO ALA SER PHE LEU SEQRES 7 A 141 LEU LYS LYS ALA ALA GLY ILE GLU LYS GLY SER SER GLU SEQRES 8 A 141 PRO LYS ARG LYS ILE VAL GLY LYS VAL THR ARG LYS GLN SEQRES 9 A 141 ILE GLU GLU ILE ALA LYS THR LYS MET PRO ASP LEU ASN SEQRES 10 A 141 ALA ASN SER LEU GLU ALA ALA MET LYS ILE ILE GLU GLY SEQRES 11 A 141 THR ALA LYS SER MET GLY ILE GLU VAL VAL ASP CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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