HEADER RIBOSOME 19-DEC-18 6IZI TITLE CRYSTAL STRUCTURE OF E. COLI PEPTIDE DEFORMYLASE AND METHIONINE TITLE 2 AMINOPEPTIDASE FITTED INTO THE CRYO-EM DENSITY MAP OF THE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: P; COMPND 4 SYNONYM: PDF,POLYPEPTIDE DEFORMYLASE; COMPND 5 EC: 3.5.1.88; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: METHIONINE AMINOPEPTIDASE; COMPND 9 CHAIN: Q; COMPND 10 SYNONYM: METAP,PEPTIDASE M; COMPND 11 EC: 3.4.11.18; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: DEF, FMS, B3287, JW3248; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 10 ORGANISM_TAXID: 83333; SOURCE 11 STRAIN: K-12; SOURCE 12 GENE: MAP, B0168, JW0163; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E. COLI 70S RIBOSOME, PROTEIN BIOGENESIS, PEPTIDE DEFORMYLASE, KEYWDS 2 METHIONINE AMINOPEPTIDASE, POLYPEPTIDE EXIT TUNNEL, RIBOSOME EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN P, Q AUTHOR J.SENGUPTA,S.BHAKTA,S.AKBAR REVDAT 2 27-MAR-24 6IZI 1 REMARK REVDAT 1 17-APR-19 6IZI 0 JRNL AUTH S.BHAKTA,S.AKBAR,J.SENGUPTA JRNL TITL CRYO-EM STRUCTURES REVEAL RELOCALIZATION OF METAP IN THE JRNL TITL 2 PRESENCE OF OTHER PROTEIN BIOGENESIS FACTORS AT THE JRNL TITL 3 RIBOSOMAL TUNNEL EXIT. JRNL REF J. MOL. BIOL. V. 431 1426 2019 JRNL REFN ESSN 1089-8638 JRNL PMID 30753870 JRNL DOI 10.1016/J.JMB.2019.02.002 REMARK 2 REMARK 2 RESOLUTION. 11.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1BS7 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) : 11.80 REMARK 3 NUMBER OF PARTICLES : 35000 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 6IZI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1300010200. 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 70S RIBOSOME IN COMPLEX REMARK 245 WITH PEPTIDE DEFORMYLASE AND REMARK 245 METHIONINE AMINOPEPTIDASE 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 : 7.40 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 POLARA 300 REMARK 245 DETECTOR TYPE : FEI EAGLE (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 1000.00 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: P, Q 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 P 0 REMARK 465 MET Q 1 REMARK 465 GLU Q 264 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-9750 RELATED DB: EMDB REMARK 900 CRYO-EM DENSITY MAP OF E. COLI 70S RIBOSOME IN COMPLEX WITH PEPTIDE REMARK 900 DEFORMYLASE ENZYME REMARK 900 RELATED ID: EMD-9752 RELATED DB: EMDB REMARK 900 CRYO-EM DENSITY MAP OF E. COLI 70S RIBOSOME IN COMPLEX WITH REMARK 900 METHIONINE AMINOPEPTIDASE REMARK 900 RELATED ID: EMD-9753 RELATED DB: EMDB REMARK 900 CRYO-EM DENSITY MAP OF PEPTIDE DEFORMYLASE AND METHIONINE REMARK 900 AMINOPEPTIDASE BOUND TO THE E. COLI 70S RIBOSOME REMARK 900 RELATED ID: EMD-9759 RELATED DB: EMDB REMARK 900 CRYO-EM DENSITY MAP OF METHIONINE AMINOPEPTIDASE ENZYME AND REMARK 900 CHAPERONE TRIGGER FACTOR BOUND TO THE E. COLI 70S RIBOSOME DBREF 6IZI P 0 168 UNP P0A6K3 DEF_ECOLI 1 169 DBREF 6IZI Q 1 264 UNP P0AE18 MAP1_ECOLI 1 264 SEQADV 6IZI GLN Q 175 UNP P0AE18 ARG 175 ENGINEERED MUTATION SEQRES 1 P 169 MET SER VAL LEU GLN VAL LEU HIS ILE PRO ASP GLU ARG SEQRES 2 P 169 LEU ARG LYS VAL ALA LYS PRO VAL GLU GLU VAL ASN ALA SEQRES 3 P 169 GLU ILE GLN ARG ILE VAL ASP ASP MET PHE GLU THR MET SEQRES 4 P 169 TYR ALA GLU GLU GLY ILE GLY LEU ALA ALA THR GLN VAL SEQRES 5 P 169 ASP ILE HIS GLN ARG ILE ILE VAL ILE ASP VAL SER GLU SEQRES 6 P 169 ASN ARG ASP GLU ARG LEU VAL LEU ILE ASN PRO GLU LEU SEQRES 7 P 169 LEU GLU LYS SER GLY GLU THR GLY ILE GLU GLU GLY CYS SEQRES 8 P 169 LEU SER ILE PRO GLU GLN ARG ALA LEU VAL PRO ARG ALA SEQRES 9 P 169 GLU LYS VAL LYS ILE ARG ALA LEU ASP ARG ASP GLY LYS SEQRES 10 P 169 PRO PHE GLU LEU GLU ALA ASP GLY LEU LEU ALA ILE CYS SEQRES 11 P 169 ILE GLN HIS GLU MET ASP HIS LEU VAL GLY LYS LEU PHE SEQRES 12 P 169 MET ASP TYR LEU SER PRO LEU LYS GLN GLN ARG ILE ARG SEQRES 13 P 169 GLN LYS VAL GLU LYS LEU ASP ARG LEU LYS ALA ARG ALA SEQRES 1 Q 264 MET ALA ILE SER ILE LYS THR PRO GLU ASP ILE GLU LYS SEQRES 2 Q 264 MET ARG VAL ALA GLY ARG LEU ALA ALA GLU VAL LEU GLU SEQRES 3 Q 264 MET ILE GLU PRO TYR VAL LYS PRO GLY VAL SER THR GLY SEQRES 4 Q 264 GLU LEU ASP ARG ILE CYS ASN ASP TYR ILE VAL ASN GLU SEQRES 5 Q 264 GLN HIS ALA VAL SER ALA CYS LEU GLY TYR HIS GLY TYR SEQRES 6 Q 264 PRO LYS SER VAL CYS ILE SER ILE ASN GLU VAL VAL CYS SEQRES 7 Q 264 HIS GLY ILE PRO ASP ASP ALA LYS LEU LEU LYS ASP GLY SEQRES 8 Q 264 ASP ILE VAL ASN ILE ASP VAL THR VAL ILE LYS ASP GLY SEQRES 9 Q 264 PHE HIS GLY ASP THR SER LYS MET PHE ILE VAL GLY LYS SEQRES 10 Q 264 PRO THR ILE MET GLY GLU ARG LEU CYS ARG ILE THR GLN SEQRES 11 Q 264 GLU SER LEU TYR LEU ALA LEU ARG MET VAL LYS PRO GLY SEQRES 12 Q 264 ILE ASN LEU ARG GLU ILE GLY ALA ALA ILE GLN LYS PHE SEQRES 13 Q 264 VAL GLU ALA GLU GLY PHE SER VAL VAL ARG GLU TYR CYS SEQRES 14 Q 264 GLY HIS GLY ILE GLY GLN GLY PHE HIS GLU GLU PRO GLN SEQRES 15 Q 264 VAL LEU HIS TYR ASP SER ARG GLU THR ASN VAL VAL LEU SEQRES 16 Q 264 LYS PRO GLY MET THR PHE THR ILE GLU PRO MET VAL ASN SEQRES 17 Q 264 ALA GLY LYS LYS GLU ILE ARG THR MET LYS ASP GLY TRP SEQRES 18 Q 264 THR VAL LYS THR LYS ASP ARG SER LEU SER ALA GLN TYR SEQRES 19 Q 264 GLU HIS THR ILE VAL VAL THR ASP ASN GLY CYS GLU ILE SEQRES 20 Q 264 LEU THR LEU ARG LYS ASP ASP THR ILE PRO ALA ILE ILE SEQRES 21 Q 264 SER HIS ASP GLU 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