HEADER OXIDOREDUCTASE 26-MAY-24 8ZNC TITLE CRYO-EM STRUCTURE OF W89F MUTATED GLUTAMATE DEHYDROGENASE FROM TITLE 2 THERMOCOCCUS PROFUNDUS INCORPORATING NADPH, AKG IN THE STEADY STAGE TITLE 3 OF REACTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GDH; COMPND 5 EC: 1.4.1.3; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS PROFUNDUS; SOURCE 3 ORGANISM_TAXID: 49899; SOURCE 4 GENE: GDHA, GDH; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, COMPLEX, NADPH, 2-OXOGLUTARATE, MUTANT EXPDTA ELECTRON MICROSCOPY AUTHOR T.WAKABAYASHI,M.NAKASAKO REVDAT 1 12-JUN-24 8ZNC 0 JRNL AUTH T.WAKABAYASHI,M.OIDE,Y.MATSUI,M.NAKASAKO JRNL TITL MECHANISM FOR DRASTIC REDUCTION IN CATALYTIC ACTIVITY OF JRNL TITL 2 TRP89PHE-MUTATED GLUTAMATE DEHYDROGENASE REVEALED BY CRYSTAL JRNL TITL 3 STRUCTURE AND CRYOEM-SAMPLING OF METASTABLE CONFORMATION IN JRNL TITL 4 ACTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, SERIALEM, CTFFIND, PHENIX, REMARK 3 PHENIX, RELION, RELION, RELION, RELION 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) : 2.410 REMARK 3 NUMBER OF PARTICLES : 444903 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 8ZNC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1300046497. 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 : HEXAMER OF W89F MUTATED REMARK 245 GLUTAMATE DEHYDROGENASE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 9.00 REMARK 245 SAMPLE SUPPORT DETAILS : BOTH SIDES OF THE GRID WERE REMARK 245 GLOW-DISCHARGED FOR 45 S AT 20 REMARK 245 MA AND 20 PA. REMARK 245 SAMPLE VITRIFICATION DETAILS : THE SAMPLE SOLUTION WAS FLASH REMARK 245 -FROZEN 2-H AFTER MIXING THE REMARK 245 PROTEIN SOLUTION AND BUFFER REMARK 245 SOLUTION. 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 : 7651 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : JEOL CRYO ARM 300 REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 350.00 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) : 5000.00 REMARK 245 ILLUMINATION MODE : OTHER 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 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 LYS A 418 -77.28 -93.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8ZMU RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THE SAME PROTEIN IN UNLIGANDED STATE REMARK 900 RELATED ID: EMD-60267 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF W89F MUTATED GLUTAMATE DEHYDROGENASE FROM REMARK 900 THERMOCOCCUS PROFUNDUS INCORPORATING NADPH, AKG IN THE STEADY STAGE REMARK 900 OF REACTION DBREF 8ZNC A 4 419 UNP O74024 DHE3_THEPR 4 419 SEQADV 8ZNC PHE A 89 UNP O74024 TRP 89 ENGINEERED MUTATION SEQRES 1 A 416 ILE ASP PRO PHE GLU MET ALA VAL LYS GLN LEU GLU ARG SEQRES 2 A 416 ALA ALA GLN TYR MET ASP ILE SER GLU GLU ALA LEU GLU SEQRES 3 A 416 TRP LEU LYS LYS PRO MET ARG ILE VAL GLU VAL SER VAL SEQRES 4 A 416 PRO ILE GLU MET ASP ASP GLY SER VAL LYS VAL PHE THR SEQRES 5 A 416 GLY PHE ARG VAL GLN HIS ASN TRP ALA ARG GLY PRO THR SEQRES 6 A 416 LYS GLY GLY ILE ARG TRP HIS PRO ALA GLU THR LEU SER SEQRES 7 A 416 THR VAL LYS ALA LEU ALA THR PHE MET THR TRP LYS VAL SEQRES 8 A 416 ALA VAL VAL ASP LEU PRO TYR GLY GLY GLY LYS GLY GLY SEQRES 9 A 416 ILE ILE VAL ASN PRO LYS GLU LEU SER GLU ARG GLU GLN SEQRES 10 A 416 GLU ARG LEU ALA ARG ALA TYR ILE ARG ALA VAL TYR ASP SEQRES 11 A 416 VAL ILE GLY PRO TRP THR ASP ILE PRO ALA PRO ASP VAL SEQRES 12 A 416 TYR THR ASN PRO LYS ILE MET GLY TRP MET MET ASP GLU SEQRES 13 A 416 TYR GLU THR ILE MET ARG ARG LYS GLY PRO ALA PHE GLY SEQRES 14 A 416 VAL ILE THR GLY LYS PRO LEU SER ILE GLY GLY SER LEU SEQRES 15 A 416 GLY ARG GLY THR ALA THR ALA GLN GLY ALA ILE PHE THR SEQRES 16 A 416 ILE ARG GLU ALA ALA LYS ALA LEU GLY ILE ASP LEU LYS SEQRES 17 A 416 GLY LYS LYS ILE ALA VAL GLN GLY TYR GLY ASN ALA GLY SEQRES 18 A 416 TYR TYR THR ALA LYS LEU ALA LYS GLU GLN LEU GLY MET SEQRES 19 A 416 THR VAL VAL ALA VAL SER ASP SER ARG GLY GLY ILE TYR SEQRES 20 A 416 ASN PRO ASP GLY LEU ASP PRO ASP GLU VAL LEU LYS TRP SEQRES 21 A 416 LYS ARG GLU HIS GLY SER VAL LYS ASP PHE PRO GLY ALA SEQRES 22 A 416 THR ASN ILE THR ASN GLU GLU LEU LEU GLU LEU GLU VAL SEQRES 23 A 416 ASP VAL LEU ALA PRO ALA ALA ILE GLU GLU VAL ILE THR SEQRES 24 A 416 GLU LYS ASN ALA ASP ASN ILE LYS ALA LYS ILE VAL ALA SEQRES 25 A 416 GLU VAL ALA ASN GLY PRO VAL THR PRO GLU ALA ASP ASP SEQRES 26 A 416 ILE LEU ARG GLU LYS GLY ILE LEU GLN ILE PRO ASP PHE SEQRES 27 A 416 LEU CYS ASN ALA GLY GLY VAL THR VAL SER TYR PHE GLU SEQRES 28 A 416 TRP VAL GLN ASN ILE ASN GLY TYR TYR TRP THR GLU GLU SEQRES 29 A 416 GLU VAL ARG GLU LYS LEU ASP LYS LYS MET THR LYS ALA SEQRES 30 A 416 PHE TRP GLU VAL TYR ASN THR HIS LYS ASP LYS ASN ILE SEQRES 31 A 416 HIS MET ARG ASP ALA ALA TYR VAL VAL ALA VAL SER ARG SEQRES 32 A 416 VAL TYR GLN ALA MET LYS ASP ARG GLY TRP VAL LYS LYS HET NDP A 501 48 HET AKG A 502 10 HET NH4 A 503 1 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM AKG 2-OXOGLUTARIC ACID HETNAM NH4 AMMONIUM ION FORMUL 2 NDP C21 H30 N7 O17 P3 FORMUL 3 AKG C5 H6 O5 FORMUL 4 NH4 H4 N 1+ FORMUL 5 HOH *24(H2 O) HELIX 1 AA1 ASP A 5 GLN A 19 1 15 HELIX 2 AA2 SER A 24 LYS A 32 1 9 HELIX 3 AA3 THR A 79 VAL A 97 1 19 HELIX 4 AA4 ASN A 111 LEU A 115 5 5 HELIX 5 AA5 SER A 116 TYR A 132 1 17 HELIX 6 AA6 ASP A 133 ILE A 135 5 3 HELIX 7 AA7 ASN A 149 ARG A 165 1 17 HELIX 8 AA8 PRO A 169 ILE A 174 5 6 HELIX 9 AA9 THR A 189 GLY A 207 1 19 HELIX 10 AB1 GLY A 221 GLN A 234 1 14 HELIX 11 AB2 ASP A 256 GLY A 268 1 13 HELIX 12 AB3 THR A 280 GLU A 286 1 7 HELIX 13 AB4 ASN A 305 ILE A 309 5 5 HELIX 14 AB5 THR A 323 GLY A 334 1 12 HELIX 15 AB6 PRO A 339 ASN A 344 1 6 HELIX 16 AB7 ALA A 345 GLY A 361 1 17 HELIX 17 AB8 THR A 365 ASN A 392 1 28 HELIX 18 AB9 HIS A 394 ARG A 414 1 21 SHEET 1 AA1 5 ARG A 36 GLU A 45 0 SHEET 2 AA1 5 VAL A 51 ASN A 62 -1 O PHE A 54 N VAL A 42 SHEET 3 AA1 5 GLY A 102 ILE A 109 -1 O LYS A 105 N VAL A 59 SHEET 4 AA1 5 THR A 68 HIS A 75 1 N LYS A 69 O GLY A 104 SHEET 5 AA1 5 ASP A 140 PRO A 144 1 O ILE A 141 N THR A 68 SHEET 1 AA2 7 THR A 277 ILE A 279 0 SHEET 2 AA2 7 GLY A 248 TYR A 250 -1 N GLY A 248 O ILE A 279 SHEET 3 AA2 7 THR A 238 SER A 243 -1 N VAL A 242 O ILE A 249 SHEET 4 AA2 7 LYS A 214 GLN A 218 1 N ILE A 215 O VAL A 240 SHEET 5 AA2 7 VAL A 291 PRO A 294 1 O VAL A 291 N ALA A 216 SHEET 6 AA2 7 ILE A 313 ALA A 315 1 O ILE A 313 N LEU A 292 SHEET 7 AA2 7 LEU A 336 ILE A 338 1 O LEU A 336 N VAL A 314 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