HEADER TRANSFERASE 07-SEP-22 8B0M TITLE CRYO-EM STRUCTURE OF APOLIPOPROTEIN N-ACYLTRANSFERASE LNT FROM E. COLI TITLE 2 IN COMPLEX WITH PE (C387S MUTANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOLIPOPROTEIN N-ACYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALP N-ACYLTRANSFERASE,COPPER HOMEOSTASIS PROTEIN CUTE; COMPND 5 EC: 2.3.1.269; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: LNT, CUTE, B0657, JW0654; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LNT, APOLIPOPROTEIN N-ACYLTRANSFERASE, BACTERIAL LIPOPROTEIN, KEYWDS 2 TRANSFERASE, CRYO-EM EXPDTA ELECTRON MICROSCOPY AUTHOR O.DEGTJARIK,L.SMITHERS,C.BOLAND,M.CAFFREY,M.SHALEV BENAMI REVDAT 2 24-JUL-24 8B0M 1 REMARK REVDAT 1 12-JUL-23 8B0M 0 JRNL AUTH L.SMITHERS,O.DEGTJARIK,D.WEICHERT,C.Y.HUANG,C.BOLAND, JRNL AUTH 2 K.BOWEN,A.OLUWOLE,C.LUTOMSKI,C.V.ROBINSON,E.M.SCANLAN, JRNL AUTH 3 M.WANG,V.OLIERIC,M.SHALEV-BENAMI,M.CAFFREY JRNL TITL STRUCTURE SNAPSHOTS REVEAL THE MECHANISM OF A BACTERIAL JRNL TITL 2 MEMBRANE LIPOPROTEIN N -ACYLTRANSFERASE. JRNL REF SCI ADV V. 9 F5799 2023 JRNL REFN ESSN 2375-2548 JRNL PMID 37390210 JRNL DOI 10.1126/SCIADV.ADF5799 REMARK 2 REMARK 2 RESOLUTION. 3.01 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 : 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) : 3.010 REMARK 3 NUMBER OF PARTICLES : 123014 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: NULL REMARK 4 REMARK 4 8B0M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1292125390. 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 : APOLIPOPROTEIN N REMARK 245 -ACYLTRANSFERASE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 14.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.00 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 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 3300.00 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: 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ARG A 510 REMARK 465 ARG A 511 REMARK 465 LYS A 512 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PHE A 3 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 32 CG OD1 OD2 REMARK 470 ARG A 190 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 306 CG CD CE NZ REMARK 470 ARG A 309 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 347 CG CD1 CD2 REMARK 470 GLU A 348 CG CD OE1 OE2 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 ASP A 32 35.34 -94.34 REMARK 500 THR A 144 -1.86 66.40 REMARK 500 PHE A 146 71.51 -158.84 REMARK 500 GLN A 155 50.21 -91.20 REMARK 500 LEU A 160 52.44 -91.33 REMARK 500 PRO A 218 45.91 -76.95 REMARK 500 LYS A 220 30.63 -94.68 REMARK 500 ALA A 323 80.87 -161.52 REMARK 500 LEU A 347 -9.59 71.88 REMARK 500 SER A 387 -103.92 60.49 REMARK 500 PHE A 416 48.97 -92.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-15788 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF APOLIPOPROTEIN N-ACYLTRANSFERASE LNT FROM E. REMARK 900 COLI IN COMPLEX WITH PE (C387S MUTANT) DBREF 8B0M A 1 512 UNP P23930 LNT_ECOLI 1 512 SEQADV 8B0M MET A -19 UNP P23930 INITIATING METHIONINE SEQADV 8B0M GLY A -18 UNP P23930 EXPRESSION TAG SEQADV 8B0M SER A -17 UNP P23930 EXPRESSION TAG SEQADV 8B0M SER A -16 UNP P23930 EXPRESSION TAG SEQADV 8B0M HIS A -15 UNP P23930 EXPRESSION TAG SEQADV 8B0M HIS A -14 UNP P23930 EXPRESSION TAG SEQADV 8B0M HIS A -13 UNP P23930 EXPRESSION TAG SEQADV 8B0M HIS A -12 UNP P23930 EXPRESSION TAG SEQADV 8B0M HIS A -11 UNP P23930 EXPRESSION TAG SEQADV 8B0M HIS A -10 UNP P23930 EXPRESSION TAG SEQADV 8B0M SER A -9 UNP P23930 EXPRESSION TAG SEQADV 8B0M SER A -8 UNP P23930 EXPRESSION TAG SEQADV 8B0M GLY A -7 UNP P23930 EXPRESSION TAG SEQADV 8B0M LEU A -6 UNP P23930 EXPRESSION TAG SEQADV 8B0M VAL A -5 UNP P23930 EXPRESSION TAG SEQADV 8B0M PRO A -4 UNP P23930 EXPRESSION TAG SEQADV 8B0M ARG A -3 UNP P23930 EXPRESSION TAG SEQADV 8B0M GLY A -2 UNP P23930 EXPRESSION TAG SEQADV 8B0M SER A -1 UNP P23930 EXPRESSION TAG SEQADV 8B0M HIS A 0 UNP P23930 EXPRESSION TAG SEQADV 8B0M SER A 387 UNP P23930 CYS 387 ENGINEERED MUTATION SEQRES 1 A 532 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 532 LEU VAL PRO ARG GLY SER HIS MET ALA PHE ALA SER LEU SEQRES 3 A 532 ILE GLU ARG GLN ARG ILE ARG LEU LEU LEU ALA LEU LEU SEQRES 4 A 532 PHE GLY ALA CYS GLY THR LEU ALA PHE SER PRO TYR ASP SEQRES 5 A 532 VAL TRP PRO ALA ALA ILE ILE SER LEU MET GLY LEU GLN SEQRES 6 A 532 ALA LEU THR PHE ASN ARG ARG PRO LEU GLN SER ALA ALA SEQRES 7 A 532 ILE GLY PHE CYS TRP GLY PHE GLY LEU PHE GLY SER GLY SEQRES 8 A 532 ILE ASN TRP VAL TYR VAL SER ILE ALA THR PHE GLY GLY SEQRES 9 A 532 MET PRO GLY PRO VAL ASN ILE PHE LEU VAL VAL LEU LEU SEQRES 10 A 532 ALA ALA TYR LEU SER LEU TYR THR GLY LEU PHE ALA GLY SEQRES 11 A 532 VAL LEU SER ARG LEU TRP PRO LYS THR THR TRP LEU ARG SEQRES 12 A 532 VAL ALA ILE ALA ALA PRO ALA LEU TRP GLN VAL THR GLU SEQRES 13 A 532 PHE LEU ARG GLY TRP VAL LEU THR GLY PHE PRO TRP LEU SEQRES 14 A 532 GLN PHE GLY TYR SER GLN ILE ASP GLY PRO LEU LYS GLY SEQRES 15 A 532 LEU ALA PRO ILE MET GLY VAL GLU ALA ILE ASN PHE LEU SEQRES 16 A 532 LEU MET MET VAL SER GLY LEU LEU ALA LEU ALA LEU VAL SEQRES 17 A 532 LYS ARG ASN TRP ARG PRO LEU VAL VAL ALA VAL VAL LEU SEQRES 18 A 532 PHE ALA LEU PRO PHE PRO LEU ARG TYR ILE GLN TRP PHE SEQRES 19 A 532 THR PRO GLN PRO GLU LYS THR ILE GLN VAL SER MET VAL SEQRES 20 A 532 GLN GLY ASP ILE PRO GLN SER LEU LYS TRP ASP GLU GLY SEQRES 21 A 532 GLN LEU LEU ASN THR LEU LYS ILE TYR TYR ASN ALA THR SEQRES 22 A 532 ALA PRO LEU MET GLY LYS SER SER LEU ILE ILE TRP PRO SEQRES 23 A 532 GLU SER ALA ILE THR ASP LEU GLU ILE ASN GLN GLN PRO SEQRES 24 A 532 PHE LEU LYS ALA LEU ASP GLY GLU LEU ARG ASP LYS GLY SEQRES 25 A 532 SER SER LEU VAL THR GLY ILE VAL ASP ALA ARG LEU ASN SEQRES 26 A 532 LYS GLN ASN ARG TYR ASP THR TYR ASN THR ILE ILE THR SEQRES 27 A 532 LEU GLY LYS GLY ALA PRO TYR SER TYR GLU SER ALA ASP SEQRES 28 A 532 ARG TYR ASN LYS ASN HIS LEU VAL PRO PHE GLY GLU PHE SEQRES 29 A 532 VAL PRO LEU GLU SER ILE LEU ARG PRO LEU ALA PRO PHE SEQRES 30 A 532 PHE ASP LEU PRO MET SER SER PHE SER ARG GLY PRO TYR SEQRES 31 A 532 ILE GLN PRO PRO LEU SER ALA ASN GLY ILE GLU LEU THR SEQRES 32 A 532 ALA ALA ILE SER TYR GLU ILE ILE LEU GLY GLU GLN VAL SEQRES 33 A 532 ARG ASP ASN PHE ARG PRO ASP THR ASP TYR LEU LEU THR SEQRES 34 A 532 ILE SER ASN ASP ALA TRP PHE GLY LYS SER ILE GLY PRO SEQRES 35 A 532 TRP GLN HIS PHE GLN MET ALA ARG MET ARG ALA LEU GLU SEQRES 36 A 532 LEU ALA ARG PRO LEU LEU ARG SER THR ASN ASN GLY ILE SEQRES 37 A 532 THR ALA VAL ILE GLY PRO GLN GLY GLU ILE GLN ALA MET SEQRES 38 A 532 ILE PRO GLN PHE THR ARG GLU VAL LEU THR THR ASN VAL SEQRES 39 A 532 THR PRO THR THR GLY LEU THR PRO TYR ALA ARG THR GLY SEQRES 40 A 532 ASN TRP PRO LEU TRP VAL LEU THR ALA LEU PHE GLY PHE SEQRES 41 A 532 ALA ALA VAL LEU MET SER LEU ARG GLN ARG ARG LYS HET PTY A 601 50 HETNAM PTY PHOSPHATIDYLETHANOLAMINE FORMUL 2 PTY C40 H80 N O8 P HELIX 1 AA1 ALA A 2 ILE A 7 1 6 HELIX 2 AA2 ARG A 9 CYS A 23 1 15 HELIX 3 AA3 GLY A 24 PHE A 28 5 5 HELIX 4 AA4 TRP A 34 LEU A 47 1 14 HELIX 5 AA5 ARG A 52 GLY A 69 1 18 HELIX 6 AA6 TRP A 74 THR A 81 1 8 HELIX 7 AA7 PRO A 86 TRP A 116 1 31 HELIX 8 AA8 THR A 120 ILE A 126 1 7 HELIX 9 AA9 ALA A 127 GLY A 140 1 14 HELIX 10 AB1 TRP A 141 GLY A 145 5 5 HELIX 11 AB2 GLN A 150 GLN A 155 1 6 HELIX 12 AB3 ILE A 156 ASP A 157 5 2 HELIX 13 AB4 GLY A 158 GLY A 162 5 5 HELIX 14 AB5 LEU A 163 GLY A 168 1 6 HELIX 15 AB6 GLY A 168 LYS A 189 1 22 HELIX 16 AB7 TRP A 192 LEU A 204 1 13 HELIX 17 AB8 PRO A 205 ILE A 211 5 7 HELIX 18 AB9 ASP A 238 GLY A 240 5 3 HELIX 19 AC1 GLN A 241 MET A 257 1 17 HELIX 20 AC2 GLN A 277 GLY A 292 1 16 HELIX 21 AC3 VAL A 345 SER A 349 5 5 HELIX 22 AC4 ILE A 350 ALA A 355 1 6 HELIX 23 AC5 PRO A 356 ASP A 359 5 4 HELIX 24 AC6 ILE A 386 ILE A 391 5 6 HELIX 25 AC7 LEU A 392 PHE A 400 1 9 HELIX 26 AC8 ASN A 412 GLY A 417 5 6 HELIX 27 AC9 ILE A 420 ALA A 437 1 18 HELIX 28 AD1 THR A 481 GLY A 487 1 7 HELIX 29 AD2 ASN A 488 ARG A 508 1 21 SHEET 1 AA1 2 THR A 215 PRO A 216 0 SHEET 2 AA1 2 THR A 477 THR A 478 -1 O THR A 478 N THR A 215 SHEET 1 AA2 3 ILE A 270 LEU A 273 0 SHEET 2 AA2 3 SER A 294 ASP A 301 1 O GLY A 298 N ILE A 270 SHEET 3 AA2 3 TYR A 313 GLY A 320 -1 O ILE A 317 N THR A 297 SHEET 1 AA3 5 ILE A 270 LEU A 273 0 SHEET 2 AA3 5 SER A 294 ASP A 301 1 O GLY A 298 N ILE A 270 SHEET 3 AA3 5 LEU A 262 ILE A 264 1 N ILE A 263 O VAL A 296 SHEET 4 AA3 5 ILE A 222 GLN A 228 1 N VAL A 227 O ILE A 264 SHEET 5 AA3 5 GLU A 468 VAL A 474 -1 O LEU A 470 N MET A 226 SHEET 1 AA4 6 LEU A 375 ALA A 377 0 SHEET 2 AA4 6 ILE A 380 ALA A 384 -1 O LEU A 382 N LEU A 375 SHEET 3 AA4 6 TYR A 406 SER A 411 1 O LEU A 408 N THR A 383 SHEET 4 AA4 6 LEU A 440 THR A 444 1 O LEU A 441 N LEU A 407 SHEET 5 AA4 6 ALA A 450 ILE A 452 -1 O ILE A 452 N LEU A 440 SHEET 6 AA4 6 ILE A 458 MET A 461 -1 O GLN A 459 N VAL A 451 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