HEADER MEMBRANE PROTEIN 27-JUL-23 8TLU TITLE E. COLI MRAY MUTANT-T23P COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHO-N-ACETYLMURAMOYL-PENTAPEPTIDE-TRANSFERASE; COMPND 3 CHAIN: A, E; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: MRAY; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS PEPTIDOGLYCAN, PHOSPHOTRANSFERASE, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR A.K.ORTA,Y.E.LI,W.M.CLEMONS REVDAT 1 01-MAY-24 8TLU 0 JRNL AUTH L.S.MARMONT,A.K.ORTA,B.W.A.BAILEEVES,D.SYCHANTHA, JRNL AUTH 2 A.FERNANDEZ-GALLIANO,Y.E.LI,N.G.GREENE,R.A.COREY, JRNL AUTH 3 P.J.STANSFELD,W.M.CLEMONS JR.,T.G.BERNHARDT JRNL TITL SYNTHESIS OF LIPID-LINKED PRECURSORS OF THE BACTERIAL CELL JRNL TITL 2 WALL IS GOVERNED BY A FEEDBACK CONTROL MECHANISM IN JRNL TITL 3 PSEUDOMONAS AERUGINOSA. JRNL REF NAT MICROBIOL V. 9 763 2024 JRNL REFN ESSN 2058-5276 JRNL PMID 38336881 JRNL DOI 10.1038/S41564-024-01603-2 REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, DIGITALMICROGRAPH, SERIALEM, REMARK 3 CRYOSPARC, PHENIX, PHENIX, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 8G01 REMARK 3 REFINEMENT SPACE : REAL 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) : 3.800 REMARK 3 NUMBER OF PARTICLES : 287765 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 8TLU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1000276174. 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 MRAY T23P DIMER REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 5.00 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 : 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) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 5000.00 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) : 6000.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : 105000 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: A, E 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 VAL A 57 REMARK 465 ARG A 58 REMARK 465 ASN A 59 REMARK 465 ASP A 60 REMARK 465 GLY A 61 REMARK 465 PRO A 62 REMARK 465 GLU A 63 REMARK 465 LYS A 126 REMARK 465 GLY A 127 REMARK 465 LEU A 128 REMARK 465 ASN E 59 REMARK 465 ASP E 60 REMARK 465 GLY E 61 REMARK 465 PRO E 62 REMARK 465 GLU E 63 REMARK 465 ARG E 122 REMARK 465 LYS E 123 REMARK 465 ASP E 124 REMARK 465 THR E 125 REMARK 465 LYS E 126 REMARK 465 GLY E 127 REMARK 465 LEU E 128 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 O GLY E 353 OG1 THR E 356 2.06 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 ARG A 131 -12.80 72.58 REMARK 500 PHE A 164 -10.18 72.59 REMARK 500 THR A 258 -169.25 -79.59 REMARK 500 MET E 40 52.24 -93.03 REMARK 500 ASP E 195 -3.71 -59.92 REMARK 500 ASN E 257 57.32 -92.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-41373 RELATED DB: EMDB REMARK 900 E. COLI MRAY MUTANT-T23P DBREF 8TLU A 1 360 UNP P0A6W3 MRAY_ECOLI 1 360 DBREF 8TLU E 1 360 UNP P0A6W3 MRAY_ECOLI 1 360 SEQADV 8TLU PRO A 23 UNP P0A6W3 THR 23 ENGINEERED MUTATION SEQADV 8TLU PRO E 23 UNP P0A6W3 THR 23 ENGINEERED MUTATION SEQRES 1 A 360 MET LEU VAL TRP LEU ALA GLU HIS LEU VAL LYS TYR TYR SEQRES 2 A 360 SER GLY PHE ASN VAL PHE SER TYR LEU PRO PHE ARG ALA SEQRES 3 A 360 ILE VAL SER LEU LEU THR ALA LEU PHE ILE SER LEU TRP SEQRES 4 A 360 MET GLY PRO ARG MET ILE ALA HIS LEU GLN LYS LEU SER SEQRES 5 A 360 PHE GLY GLN VAL VAL ARG ASN ASP GLY PRO GLU SER HIS SEQRES 6 A 360 PHE SER LYS ARG GLY THR PRO THR MET GLY GLY ILE MET SEQRES 7 A 360 ILE LEU THR ALA ILE VAL ILE SER VAL LEU LEU TRP ALA SEQRES 8 A 360 TYR PRO SER ASN PRO TYR VAL TRP CYS VAL LEU VAL VAL SEQRES 9 A 360 LEU VAL GLY TYR GLY VAL ILE GLY PHE VAL ASP ASP TYR SEQRES 10 A 360 ARG LYS VAL VAL ARG LYS ASP THR LYS GLY LEU ILE ALA SEQRES 11 A 360 ARG TRP LYS TYR PHE TRP MET SER VAL ILE ALA LEU GLY SEQRES 12 A 360 VAL ALA PHE ALA LEU TYR LEU ALA GLY LYS ASP THR PRO SEQRES 13 A 360 ALA THR GLN LEU VAL VAL PRO PHE PHE LYS ASP VAL MET SEQRES 14 A 360 PRO GLN LEU GLY LEU PHE TYR ILE LEU LEU ALA TYR PHE SEQRES 15 A 360 VAL ILE VAL GLY THR GLY ASN ALA VAL ASN LEU THR ASP SEQRES 16 A 360 GLY LEU ASP GLY LEU ALA ILE MET PRO THR VAL PHE VAL SEQRES 17 A 360 ALA GLY GLY PHE ALA LEU VAL ALA TRP ALA THR GLY ASN SEQRES 18 A 360 MET ASN PHE ALA SER TYR LEU HIS ILE PRO TYR LEU ARG SEQRES 19 A 360 HIS ALA GLY GLU LEU VAL ILE VAL CYS THR ALA ILE VAL SEQRES 20 A 360 GLY ALA GLY LEU GLY PHE LEU TRP PHE ASN THR TYR PRO SEQRES 21 A 360 ALA GLN VAL PHE MET GLY ASP VAL GLY SER LEU ALA LEU SEQRES 22 A 360 GLY GLY ALA LEU GLY ILE ILE ALA VAL LEU LEU ARG GLN SEQRES 23 A 360 GLU PHE LEU LEU VAL ILE MET GLY GLY VAL PHE VAL VAL SEQRES 24 A 360 GLU THR LEU SER VAL ILE LEU GLN VAL GLY SER PHE LYS SEQRES 25 A 360 LEU ARG GLY GLN ARG ILE PHE ARG MET ALA PRO ILE HIS SEQRES 26 A 360 HIS HIS TYR GLU LEU LYS GLY TRP PRO GLU PRO ARG VAL SEQRES 27 A 360 ILE VAL ARG PHE TRP ILE ILE SER LEU MET LEU VAL LEU SEQRES 28 A 360 ILE GLY LEU ALA THR LEU LYS VAL ARG SEQRES 1 E 360 MET LEU VAL TRP LEU ALA GLU HIS LEU VAL LYS TYR TYR SEQRES 2 E 360 SER GLY PHE ASN VAL PHE SER TYR LEU PRO PHE ARG ALA SEQRES 3 E 360 ILE VAL SER LEU LEU THR ALA LEU PHE ILE SER LEU TRP SEQRES 4 E 360 MET GLY PRO ARG MET ILE ALA HIS LEU GLN LYS LEU SER SEQRES 5 E 360 PHE GLY GLN VAL VAL ARG ASN ASP GLY PRO GLU SER HIS SEQRES 6 E 360 PHE SER LYS ARG GLY THR PRO THR MET GLY GLY ILE MET SEQRES 7 E 360 ILE LEU THR ALA ILE VAL ILE SER VAL LEU LEU TRP ALA SEQRES 8 E 360 TYR PRO SER ASN PRO TYR VAL TRP CYS VAL LEU VAL VAL SEQRES 9 E 360 LEU VAL GLY TYR GLY VAL ILE GLY PHE VAL ASP ASP TYR SEQRES 10 E 360 ARG LYS VAL VAL ARG LYS ASP THR LYS GLY LEU ILE ALA SEQRES 11 E 360 ARG TRP LYS TYR PHE TRP MET SER VAL ILE ALA LEU GLY SEQRES 12 E 360 VAL ALA PHE ALA LEU TYR LEU ALA GLY LYS ASP THR PRO SEQRES 13 E 360 ALA THR GLN LEU VAL VAL PRO PHE PHE LYS ASP VAL MET SEQRES 14 E 360 PRO GLN LEU GLY LEU PHE TYR ILE LEU LEU ALA TYR PHE SEQRES 15 E 360 VAL ILE VAL GLY THR GLY ASN ALA VAL ASN LEU THR ASP SEQRES 16 E 360 GLY LEU ASP GLY LEU ALA ILE MET PRO THR VAL PHE VAL SEQRES 17 E 360 ALA GLY GLY PHE ALA LEU VAL ALA TRP ALA THR GLY ASN SEQRES 18 E 360 MET ASN PHE ALA SER TYR LEU HIS ILE PRO TYR LEU ARG SEQRES 19 E 360 HIS ALA GLY GLU LEU VAL ILE VAL CYS THR ALA ILE VAL SEQRES 20 E 360 GLY ALA GLY LEU GLY PHE LEU TRP PHE ASN THR TYR PRO SEQRES 21 E 360 ALA GLN VAL PHE MET GLY ASP VAL GLY SER LEU ALA LEU SEQRES 22 E 360 GLY GLY ALA LEU GLY ILE ILE ALA VAL LEU LEU ARG GLN SEQRES 23 E 360 GLU PHE LEU LEU VAL ILE MET GLY GLY VAL PHE VAL VAL SEQRES 24 E 360 GLU THR LEU SER VAL ILE LEU GLN VAL GLY SER PHE LYS SEQRES 25 E 360 LEU ARG GLY GLN ARG ILE PHE ARG MET ALA PRO ILE HIS SEQRES 26 E 360 HIS HIS TYR GLU LEU LYS GLY TRP PRO GLU PRO ARG VAL SEQRES 27 E 360 ILE VAL ARG PHE TRP ILE ILE SER LEU MET LEU VAL LEU SEQRES 28 E 360 ILE GLY LEU ALA THR LEU LYS VAL ARG HELIX 1 AA1 MET A 1 HIS A 8 1 8 HELIX 2 AA2 GLY A 15 SER A 20 5 6 HELIX 3 AA3 TYR A 21 PHE A 53 1 33 HELIX 4 AA4 GLY A 76 ALA A 91 1 16 HELIX 5 AA5 ASN A 95 VAL A 121 1 27 HELIX 6 AA6 ARG A 131 GLY A 152 1 22 HELIX 7 AA7 LEU A 174 THR A 194 1 21 HELIX 8 AA8 ILE A 202 ASN A 221 1 20 HELIX 9 AA9 ASN A 221 HIS A 229 1 9 HELIX 10 AB1 GLU A 238 PHE A 256 1 19 HELIX 11 AB2 GLY A 266 ARG A 285 1 20 HELIX 12 AB3 GLN A 286 GLY A 294 1 9 HELIX 13 AB4 GLY A 294 ARG A 314 1 21 HELIX 14 AB5 PRO A 323 GLY A 332 1 10 HELIX 15 AB6 PRO A 334 VAL A 359 1 26 HELIX 16 AB7 LEU E 2 LEU E 9 1 8 HELIX 17 AB8 TYR E 13 SER E 20 5 8 HELIX 18 AB9 TYR E 21 MET E 40 1 20 HELIX 19 AC1 GLY E 41 GLY E 54 1 14 HELIX 20 AC2 GLY E 75 ALA E 91 1 17 HELIX 21 AC3 ASN E 95 VAL E 121 1 27 HELIX 22 AC4 ALA E 130 GLY E 152 1 23 HELIX 23 AC5 THR E 155 GLN E 159 5 5 HELIX 24 AC6 GLY E 173 ASP E 195 1 23 HELIX 25 AC7 ILE E 202 ASN E 221 1 20 HELIX 26 AC8 ASN E 221 HIS E 229 1 9 HELIX 27 AC9 HIS E 235 GLY E 237 5 3 HELIX 28 AD1 GLU E 238 TRP E 255 1 18 HELIX 29 AD2 MET E 265 LEU E 284 1 20 HELIX 30 AD3 GLN E 286 GLY E 294 1 9 HELIX 31 AD4 GLY E 294 ARG E 314 1 21 HELIX 32 AD5 PRO E 323 GLY E 332 1 10 HELIX 33 AD6 PRO E 334 ARG E 360 1 27 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