HEADER RIBOSOMAL PROTEIN 26-FEB-18 6FU8 TITLE UL23 BETA HAIRPIN LOOP DELETION OF E.COLI RIBOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L23; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI O157:H7; SOURCE 3 ORGANISM_TAXID: 83334; SOURCE 4 GENE: RPLW, Z4689, ECS4183; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UL23, LOOP DELETION, RIBOSOMAL TUNNEL, RIBOSOMAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR R.KUDVA,G.VON HEIJNE,M.CARRONI REVDAT 2 26-DEC-18 6FU8 1 JRNL REVDAT 1 05-DEC-18 6FU8 0 JRNL AUTH R.KUDVA,P.TIAN,F.PARDO-AVILA,M.CARRONI,R.B.BEST, JRNL AUTH 2 H.D.BERNSTEIN,G.VON HEIJNE JRNL TITL THE SHAPE OF THE BACTERIAL RIBOSOME EXIT TUNNEL AFFECTS JRNL TITL 2 COTRANSLATIONAL PROTEIN FOLDING. JRNL REF ELIFE V. 7 2018 JRNL REFN ESSN 2050-084X JRNL PMID 30475203 JRNL DOI 10.7554/ELIFE.36326 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CTFFIND, UCSF CHIMERA, CRYOSPARC, REMARK 3 COOT REMARK 3 RECONSTRUCTION SCHEMA : BACK PROJECTION REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 132029 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: ALL PROCESSING FROM AB INITIO TO REFINEMENT AND REMARK 3 SHARPENING PERFORMED IN CRYOSPARC REMARK 4 REMARK 4 6FU8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1200008478. 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 RIBOSOME WITH BETA REMARK 245 -HAIRPIN OF UL23 DELETED 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 : 7.50 REMARK 245 SAMPLE DETAILS : DEPOSITED PDB IS OF THE UL23 REMARK 245 WITH THE BETA-HAIRPIN LOOP DELETED. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 3500 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON II (4K X 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 1.17 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ARG C 6 NE - CZ - NH1 ANGL. DEV. = 4.3 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 SER C 17 45.74 -166.52 REMARK 500 GLU C 18 -59.32 52.23 REMARK 500 SER C 27 25.15 -142.22 REMARK 500 ASP C 37 -83.09 -88.36 REMARK 500 ALA C 38 -171.34 45.02 REMARK 500 GLU C 52 16.47 58.65 REMARK 500 LYS C 77 -71.28 -86.95 REMARK 500 GLU C 78 -49.89 -146.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA C 13 PRO C 14 149.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-4319 RELATED DB: EMDB REMARK 900 UL23 BETA HAIRPIN LOOP DELETION OF E.COLI RIBOSOME DBREF 6FU8 C 1 82 UNP P0ADZ2 RL23_ECO57 1 93 SEQADV 6FU8 C UNP P0ADZ2 GLY 65 DELETION SEQADV 6FU8 C UNP P0ADZ2 LYS 66 DELETION SEQADV 6FU8 C UNP P0ADZ2 VAL 67 DELETION SEQADV 6FU8 C UNP P0ADZ2 LYS 68 DELETION SEQADV 6FU8 C UNP P0ADZ2 ARG 69 DELETION SEQADV 6FU8 C UNP P0ADZ2 HIS 70 DELETION SEQADV 6FU8 C UNP P0ADZ2 GLY 71 DELETION SEQADV 6FU8 C UNP P0ADZ2 GLN 72 DELETION SEQADV 6FU8 C UNP P0ADZ2 ARG 73 DELETION SEQADV 6FU8 C UNP P0ADZ2 ILE 74 DELETION SEQADV 6FU8 C UNP P0ADZ2 GLY 75 DELETION SEQRES 1 C 82 MET ILE ARG GLU GLU ARG LEU LEU LYS VAL LEU ARG ALA SEQRES 2 C 82 PRO HIS VAL SER GLU LYS ALA SER THR ALA MET GLU LYS SEQRES 3 C 82 SER ASN THR ILE VAL LEU LYS VAL ALA LYS ASP ALA THR SEQRES 4 C 82 LYS ALA GLU ILE LYS ALA ALA VAL GLN LYS LEU PHE GLU SEQRES 5 C 82 VAL GLU VAL GLU VAL VAL ASN THR LEU VAL VAL LYS ARG SEQRES 6 C 82 ARG SER ASP TRP LYS LYS ALA TYR VAL THR LEU LYS GLU SEQRES 7 C 82 GLY GLN ASN LEU HELIX 1 AA1 ARG C 3 VAL C 10 1 8 HELIX 2 AA2 GLU C 18 ASN C 28 1 11 HELIX 3 AA3 THR C 39 PHE C 51 1 13 SHEET 1 AA1 4 LEU C 11 PRO C 14 0 SHEET 2 AA1 4 THR C 29 VAL C 34 -1 O LYS C 33 N ARG C 12 SHEET 3 AA1 4 LYS C 70 LEU C 76 -1 O ALA C 72 N LEU C 32 SHEET 4 AA1 4 VAL C 55 VAL C 62 -1 N ASN C 59 O TYR C 73 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