HEADER BIOSYNTHETIC PROTEIN 08-AUG-22 7YQM TITLE 2.9-ANGSTROM CRYO-EM STRUCTURE OF ECOLI MALATE SYNTHASE G COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALATE SYNTHASE G; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MSG; COMPND 5 EC: 2.3.3.9; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI DH5[ALPHA]; SOURCE 3 ORGANISM_TAXID: 668369; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: GLCB, GLC, B2976, JW2943; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS GLYOXYLATE, MALATE, MSG, CITRIC ACID CYCEL, MALATE SYNTHASE G, KEYWDS 2 BIOSYNTHETIC PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR K.-P.WU,Y.-M.WU,Y.-C.LU REVDAT 4 03-JUL-24 7YQM 1 REMARK REVDAT 3 19-APR-23 7YQM 1 JRNL REVDAT 2 12-APR-23 7YQM 1 JRNL REVDAT 1 29-MAR-23 7YQM 0 JRNL AUTH M.R.HO,Y.M.WU,Y.C.LU,T.P.KO,K.P.WU JRNL TITL CRYO-EM REVEALS THE STRUCTURE AND DYNAMICS OF A 723-RESIDUE JRNL TITL 2 MALATE SYNTHASE G. JRNL REF J.STRUCT.BIOL. V. 215 07958 2023 JRNL REFN ESSN 1095-8657 JRNL PMID 36997036 JRNL DOI 10.1016/J.JSB.2023.107958 REMARK 2 REMARK 2 RESOLUTION. 2.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, PHENIX, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, COOT REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1P7T 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) : 2.890 REMARK 3 NUMBER OF PARTICLES : 211582 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7YQM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031456. 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 : 2.9-ANGSTROM CRYO-EM STRUCTURE REMARK 245 OF 723-AA MALATE SYNTHASE G REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.30 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.60 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 K2 QUANTUM (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 5120.00 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 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 9 26.90 -149.43 REMARK 500 LEU A 178 59.83 -117.61 REMARK 500 LYS A 196 -1.07 70.46 REMARK 500 ALA A 263 -64.79 -94.59 REMARK 500 GLN A 308 -7.92 76.80 REMARK 500 ILE A 309 -62.18 -126.79 REMARK 500 PRO A 347 49.45 -82.21 REMARK 500 ASN A 380 -60.69 -92.80 REMARK 500 ALA A 442 33.74 -97.52 REMARK 500 ALA A 528 51.25 -93.51 REMARK 500 PRO A 580 49.69 -79.40 REMARK 500 ASP A 622 -168.56 -101.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-34029 RELATED DB: EMDB REMARK 900 2.9-ANGSTROM CRYO-EM STRUCTURE OF ECOLI MALATE SYNTHASE G DBREF 7YQM A 1 723 UNP P37330 MASZ_ECOLI 1 723 SEQRES 1 A 723 MET SER GLN THR ILE THR GLN SER ARG LEU ARG ILE ASP SEQRES 2 A 723 ALA ASN PHE LYS ARG PHE VAL ASP GLU GLU VAL LEU PRO SEQRES 3 A 723 GLY THR GLY LEU ASP ALA ALA ALA PHE TRP ARG ASN PHE SEQRES 4 A 723 ASP GLU ILE VAL HIS ASP LEU ALA PRO GLU ASN ARG GLN SEQRES 5 A 723 LEU LEU ALA GLU ARG ASP ARG ILE GLN ALA ALA LEU ASP SEQRES 6 A 723 GLU TRP HIS ARG SER ASN PRO GLY PRO VAL LYS ASP LYS SEQRES 7 A 723 ALA ALA TYR LYS SER PHE LEU ARG GLU LEU GLY TYR LEU SEQRES 8 A 723 VAL PRO GLN PRO GLU ARG VAL THR VAL GLU THR THR GLY SEQRES 9 A 723 ILE ASP SER GLU ILE THR SER GLN ALA GLY PRO GLN LEU SEQRES 10 A 723 VAL VAL PRO ALA MET ASN ALA ARG TYR ALA LEU ASN ALA SEQRES 11 A 723 ALA ASN ALA ARG TRP GLY SER LEU TYR ASP ALA LEU TYR SEQRES 12 A 723 GLY SER ASP ILE ILE PRO GLN GLU GLY ALA MET VAL SER SEQRES 13 A 723 GLY TYR ASP PRO GLN ARG GLY GLU GLN VAL ILE ALA TRP SEQRES 14 A 723 VAL ARG ARG PHE LEU ASP GLU SER LEU PRO LEU GLU ASN SEQRES 15 A 723 GLY SER TYR GLN ASP VAL VAL ALA PHE LYS VAL VAL ASP SEQRES 16 A 723 LYS GLN LEU ARG ILE GLN LEU LYS ASN GLY LYS GLU THR SEQRES 17 A 723 THR LEU ARG THR PRO ALA GLN PHE VAL GLY TYR ARG GLY SEQRES 18 A 723 ASP ALA ALA ALA PRO THR CYS ILE LEU LEU LYS ASN ASN SEQRES 19 A 723 GLY LEU HIS ILE GLU LEU GLN ILE ASP ALA ASN GLY ARG SEQRES 20 A 723 ILE GLY LYS ASP ASP PRO ALA HIS ILE ASN ASP VAL ILE SEQRES 21 A 723 VAL GLU ALA ALA ILE SER THR ILE LEU ASP CYS GLU ASP SEQRES 22 A 723 SER VAL ALA ALA VAL ASP ALA GLU ASP LYS ILE LEU LEU SEQRES 23 A 723 TYR ARG ASN LEU LEU GLY LEU MET GLN GLY THR LEU GLN SEQRES 24 A 723 GLU LYS MET GLU LYS ASN GLY ARG GLN ILE VAL ARG LYS SEQRES 25 A 723 LEU ASN ASP ASP ARG HIS TYR THR ALA ALA ASP GLY SER SEQRES 26 A 723 GLU ILE SER LEU HIS GLY ARG SER LEU LEU PHE ILE ARG SEQRES 27 A 723 ASN VAL GLY HIS LEU MET THR ILE PRO VAL ILE TRP ASP SEQRES 28 A 723 SER GLU GLY ASN GLU ILE PRO GLU GLY ILE LEU ASP GLY SEQRES 29 A 723 VAL MET THR GLY ALA ILE ALA LEU TYR ASP LEU LYS VAL SEQRES 30 A 723 GLN LYS ASN SER ARG THR GLY SER VAL TYR ILE VAL LYS SEQRES 31 A 723 PRO LYS MET HIS GLY PRO GLN GLU VAL ALA PHE ALA ASN SEQRES 32 A 723 LYS LEU PHE THR ARG ILE GLU THR MET LEU GLY MET ALA SEQRES 33 A 723 PRO ASN THR LEU LYS MET GLY ILE MET ASP GLU GLU ARG SEQRES 34 A 723 ARG THR SER LEU ASN LEU ARG SER CYS ILE ALA GLN ALA SEQRES 35 A 723 ARG ASN ARG VAL ALA PHE ILE ASN THR GLY PHE LEU ASP SEQRES 36 A 723 ARG THR GLY ASP GLU MET HIS SER VAL MET GLU ALA GLY SEQRES 37 A 723 PRO MET LEU ARG LYS ASN GLN MET LYS SER THR PRO TRP SEQRES 38 A 723 ILE LYS ALA TYR GLU ARG ASN ASN VAL LEU SER GLY LEU SEQRES 39 A 723 PHE CYS GLY LEU ARG GLY LYS ALA GLN ILE GLY LYS GLY SEQRES 40 A 723 MET TRP ALA MET PRO ASP LEU MET ALA ASP MET TYR SER SEQRES 41 A 723 GLN LYS GLY ASP GLN LEU ARG ALA GLY ALA ASN THR ALA SEQRES 42 A 723 TRP VAL PRO SER PRO THR ALA ALA THR LEU HIS ALA LEU SEQRES 43 A 723 HIS TYR HIS GLN THR ASN VAL GLN SER VAL GLN ALA ASN SEQRES 44 A 723 ILE ALA GLN THR GLU PHE ASN ALA GLU PHE GLU PRO LEU SEQRES 45 A 723 LEU ASP ASP LEU LEU THR ILE PRO VAL ALA GLU ASN ALA SEQRES 46 A 723 ASN TRP SER ALA GLN GLU ILE GLN GLN GLU LEU ASP ASN SEQRES 47 A 723 ASN VAL GLN GLY ILE LEU GLY TYR VAL VAL ARG TRP VAL SEQRES 48 A 723 GLU GLN GLY ILE GLY CYS SER LYS VAL PRO ASP ILE HIS SEQRES 49 A 723 ASN VAL ALA LEU MET GLU ASP ARG ALA THR LEU ARG ILE SEQRES 50 A 723 SER SER GLN HIS ILE ALA ASN TRP LEU ARG HIS GLY ILE SEQRES 51 A 723 LEU THR LYS GLU GLN VAL GLN ALA SER LEU GLU ASN MET SEQRES 52 A 723 ALA LYS VAL VAL ASP GLN GLN ASN ALA GLY ASP PRO ALA SEQRES 53 A 723 TYR ARG PRO MET ALA GLY ASN PHE ALA ASN SER CYS ALA SEQRES 54 A 723 PHE LYS ALA ALA SER ASP LEU ILE PHE LEU GLY VAL LYS SEQRES 55 A 723 GLN PRO ASN GLY TYR THR GLU PRO LEU LEU HIS ALA TRP SEQRES 56 A 723 ARG LEU ARG GLU LYS GLU SER HIS HELIX 1 AA1 ALA A 14 VAL A 24 1 11 HELIX 2 AA2 ASP A 31 ASN A 71 1 41 HELIX 3 AA3 ASP A 77 LEU A 88 1 12 HELIX 4 AA4 ASP A 106 SER A 111 1 6 HELIX 5 AA5 ASN A 123 ALA A 133 1 11 HELIX 6 AA6 LEU A 138 TYR A 143 1 6 HELIX 7 AA7 ASP A 159 LEU A 178 1 20 HELIX 8 AA8 THR A 212 ALA A 214 5 3 HELIX 9 AA9 ASP A 279 GLY A 296 1 18 HELIX 10 AB1 GLU A 359 GLN A 378 1 20 HELIX 11 AB2 HIS A 394 GLY A 414 1 21 HELIX 12 AB3 GLU A 428 LEU A 433 1 6 HELIX 13 AB4 ASN A 434 ALA A 440 1 7 HELIX 14 AB5 PHE A 453 VAL A 464 1 12 HELIX 15 AB6 MET A 465 GLY A 468 5 4 HELIX 16 AB7 ARG A 472 SER A 478 5 7 HELIX 17 AB8 THR A 479 CYS A 496 1 18 HELIX 18 AB9 LEU A 514 LYS A 522 1 9 HELIX 19 AC1 GLY A 523 ALA A 528 1 6 HELIX 20 AC2 SER A 537 THR A 551 1 15 HELIX 21 AC3 ASN A 552 GLN A 562 1 11 HELIX 22 AC4 THR A 563 ALA A 567 5 5 HELIX 23 AC5 GLU A 568 LEU A 577 1 10 HELIX 24 AC6 SER A 588 GLN A 613 1 26 HELIX 25 AC7 ARG A 632 HIS A 648 1 17 HELIX 26 AC8 THR A 652 ASN A 671 1 20 HELIX 27 AC9 ASN A 683 ASN A 686 5 4 HELIX 28 AD1 SER A 687 LEU A 699 1 13 HELIX 29 AD2 GLY A 700 TYR A 707 5 8 HELIX 30 AD3 THR A 708 HIS A 723 1 16 SHEET 1 AA1 4 THR A 4 THR A 6 0 SHEET 2 AA1 4 ARG A 11 ASP A 13 -1 O ILE A 12 N ILE A 5 SHEET 3 AA1 4 THR A 345 TRP A 350 -1 O TRP A 350 N ARG A 11 SHEET 4 AA1 4 GLU A 356 PRO A 358 -1 O ILE A 357 N ILE A 349 SHEET 1 AA2 8 GLN A 503 GLY A 505 0 SHEET 2 AA2 8 VAL A 446 THR A 451 1 N ILE A 449 O GLY A 505 SHEET 3 AA2 8 LEU A 420 ASP A 426 1 N MET A 422 O ALA A 447 SHEET 4 AA2 8 VAL A 386 LYS A 390 1 N VAL A 386 O LYS A 421 SHEET 5 AA2 8 LEU A 334 ARG A 338 1 N ILE A 337 O VAL A 389 SHEET 6 AA2 8 SER A 266 ASP A 270 1 N THR A 267 O PHE A 336 SHEET 7 AA2 8 GLN A 116 PRO A 120 1 N VAL A 119 O ILE A 268 SHEET 8 AA2 8 TRP A 534 VAL A 535 1 O VAL A 535 N GLN A 116 SHEET 1 AA3 7 TRP A 135 SER A 137 0 SHEET 2 AA3 7 ILE A 256 GLU A 262 -1 O VAL A 261 N GLY A 136 SHEET 3 AA3 7 LEU A 236 ILE A 242 -1 N GLU A 239 O ILE A 260 SHEET 4 AA3 7 PRO A 226 ASN A 233 -1 N THR A 227 O ILE A 242 SHEET 5 AA3 7 PHE A 216 GLY A 221 -1 N GLY A 218 O LEU A 230 SHEET 6 AA3 7 ARG A 317 ALA A 321 -1 O THR A 320 N TYR A 219 SHEET 7 AA3 7 GLU A 326 LEU A 329 -1 O LEU A 329 N ARG A 317 SHEET 1 AA4 3 VAL A 188 VAL A 194 0 SHEET 2 AA4 3 GLN A 197 LEU A 202 -1 O GLN A 201 N VAL A 189 SHEET 3 AA4 3 GLU A 207 THR A 208 -1 O THR A 208 N ILE A 200 SHEET 1 AA5 2 GLN A 299 GLU A 300 0 SHEET 2 AA5 2 ARG A 311 LYS A 312 -1 O ARG A 311 N GLU A 300 SHEET 1 AA6 2 VAL A 620 PRO A 621 0 SHEET 2 AA6 2 ALA A 627 LEU A 628 -1 O LEU A 628 N VAL A 620 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