HEADER OXIDOREDUCTASE 10-DEC-23 8XCY TITLE CRYO-EM STRUCTURE OF GLUTAMATE DEHYDROGENASE FROM THERMOCOCCUS TITLE 2 PROFUNDUS INCORPORATING NADP AND GLU IN THE STEADY STAGE OF REACTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.4.1.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS PROFUNDUS; SOURCE 3 ORGANISM_TAXID: 49899; SOURCE 4 GENE: GDHA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, COENZYME, NADP, GLUTAMATE, OXIDOREDUCTASE EXPDTA ELECTRON MICROSCOPY AUTHOR T.WAKABAYASHI,M.OIDE,M.NAKASAKO REVDAT 1 27-DEC-23 8XCY 0 JRNL AUTH T.WAKABAYASHI,M.OIDE,M.NAKASAKO JRNL TITL CRYOEM-SAMPLING OF METASTABLE CONFORMATIONS APPEARING IN JRNL TITL 2 COFACTOR-LIGAND ASSOCIATION AND CATALYSIS OF GLUTAMATE JRNL TITL 3 DEHYDROGENASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, SERIALEM, CTFFIND, COOT, 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 : 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) : 2.910 REMARK 3 NUMBER OF PARTICLES : 86791 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 8XCY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1300043164. 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 GLUTAMATE REMARK 245 DEHYDROGENASE IN THE PRESENCE REMARK 245 OF NADP AND GLUTAMATE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 4.80 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : THE SAMPLE SOLUTION KEPT AT REMARK 245 ROOM TEMPERATURE WAS FLASH- REMARK 245 FROZEN 1-H AFTER MIXING GDH, REMARK 245 NADP AND GLUTAMATE SOLUTIONS. 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 : 7075 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) : 400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 47000.00 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) : 100.00 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 : GRID INFORMATION AS REMARK 245 FOLLOWING: COMPANY/MODEL: QUANTIFOIL CU 1.2/1.3 MATERIAL:CU GRID REMARK 245 MESH: 200 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 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 1 REMARK 465 VAL A 2 REMARK 465 GLU A 3 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 TRP A 30 CD1 REMARK 470 ARG A 265 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 266 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 244 -143.24 -132.34 REMARK 500 ARG A 246 -81.73 -83.17 REMARK 500 ASN A 344 31.14 -96.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAP A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38259 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF GLUTAMATE DEHYDROGENASE FROM THERMOCOCCUS REMARK 900 PROFUNDUS INCORPORATING NADP AND GLU IN THE STEADY STAGE OF REACTION DBREF 8XCY A 1 419 UNP O74024 DHE3_THEPR 1 419 SEQRES 1 A 419 MET VAL GLU ILE ASP PRO PHE GLU MET ALA VAL LYS GLN SEQRES 2 A 419 LEU GLU ARG ALA ALA GLN TYR MET ASP ILE SER GLU GLU SEQRES 3 A 419 ALA LEU GLU TRP LEU LYS LYS PRO MET ARG ILE VAL GLU SEQRES 4 A 419 VAL SER VAL PRO ILE GLU MET ASP ASP GLY SER VAL LYS SEQRES 5 A 419 VAL PHE THR GLY PHE ARG VAL GLN HIS ASN TRP ALA ARG SEQRES 6 A 419 GLY PRO THR LYS GLY GLY ILE ARG TRP HIS PRO ALA GLU SEQRES 7 A 419 THR LEU SER THR VAL LYS ALA LEU ALA THR TRP MET THR SEQRES 8 A 419 TRP LYS VAL ALA VAL VAL ASP LEU PRO TYR GLY GLY GLY SEQRES 9 A 419 LYS GLY GLY ILE ILE VAL ASN PRO LYS GLU LEU SER GLU SEQRES 10 A 419 ARG GLU GLN GLU ARG LEU ALA ARG ALA TYR ILE ARG ALA SEQRES 11 A 419 VAL TYR ASP VAL ILE GLY PRO TRP THR ASP ILE PRO ALA SEQRES 12 A 419 PRO ASP VAL TYR THR ASN PRO LYS ILE MET GLY TRP MET SEQRES 13 A 419 MET ASP GLU TYR GLU THR ILE MET ARG ARG LYS GLY PRO SEQRES 14 A 419 ALA PHE GLY VAL ILE THR GLY LYS PRO LEU SER ILE GLY SEQRES 15 A 419 GLY SER LEU GLY ARG GLY THR ALA THR ALA GLN GLY ALA SEQRES 16 A 419 ILE PHE THR ILE ARG GLU ALA ALA LYS ALA LEU GLY ILE SEQRES 17 A 419 ASP LEU LYS GLY LYS LYS ILE ALA VAL GLN GLY TYR GLY SEQRES 18 A 419 ASN ALA GLY TYR TYR THR ALA LYS LEU ALA LYS GLU GLN SEQRES 19 A 419 LEU GLY MET THR VAL VAL ALA VAL SER ASP SER ARG GLY SEQRES 20 A 419 GLY ILE TYR ASN PRO ASP GLY LEU ASP PRO ASP GLU VAL SEQRES 21 A 419 LEU LYS TRP LYS ARG GLU HIS GLY SER VAL LYS ASP PHE SEQRES 22 A 419 PRO GLY ALA THR ASN ILE THR ASN GLU GLU LEU LEU GLU SEQRES 23 A 419 LEU GLU VAL ASP VAL LEU ALA PRO ALA ALA ILE GLU GLU SEQRES 24 A 419 VAL ILE THR GLU LYS ASN ALA ASP ASN ILE LYS ALA LYS SEQRES 25 A 419 ILE VAL ALA GLU VAL ALA ASN GLY PRO VAL THR PRO GLU SEQRES 26 A 419 ALA ASP ASP ILE LEU ARG GLU LYS GLY ILE LEU GLN ILE SEQRES 27 A 419 PRO ASP PHE LEU CYS ASN ALA GLY GLY VAL THR VAL SER SEQRES 28 A 419 TYR PHE GLU TRP VAL GLN ASN ILE ASN GLY TYR TYR TRP SEQRES 29 A 419 THR GLU GLU GLU VAL ARG GLU LYS LEU ASP LYS LYS MET SEQRES 30 A 419 THR LYS ALA PHE TRP GLU VAL TYR ASN THR HIS LYS ASP SEQRES 31 A 419 LYS ASN ILE HIS MET ARG ASP ALA ALA TYR VAL VAL ALA SEQRES 32 A 419 VAL SER ARG VAL TYR GLN ALA MET LYS ASP ARG GLY TRP SEQRES 33 A 419 VAL LYS LYS HET NAP A 500 31 HET GGL A 501 10 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM GGL GAMMA-L-GLUTAMIC ACID HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE HETSYN GGL L-GLUTAMIC ACID FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 GGL C5 H9 N O4 FORMUL 4 HOH *8(H2 O) HELIX 1 AA1 ASP A 5 TYR A 20 1 16 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 LEU A 235 1 15 HELIX 11 AB2 ASP A 256 GLY A 268 1 13 HELIX 12 AB3 THR A 280 LEU A 285 1 6 HELIX 13 AB4 ASN A 305 ILE A 309 5 5 HELIX 14 AB5 THR A 323 LYS A 333 1 11 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 4 ARG A 36 GLU A 45 0 SHEET 2 AA1 4 VAL A 51 ASN A 62 -1 O PHE A 54 N VAL A 42 SHEET 3 AA1 4 GLY A 102 ILE A 109 -1 O LYS A 105 N VAL A 59 SHEET 4 AA1 4 ILE A 72 HIS A 75 1 N ARG A 73 O ILE A 108 SHEET 1 AA2 5 ARG A 36 GLU A 45 0 SHEET 2 AA2 5 VAL A 51 ASN A 62 -1 O PHE A 54 N VAL A 42 SHEET 3 AA2 5 GLY A 102 ILE A 109 -1 O LYS A 105 N VAL A 59 SHEET 4 AA2 5 THR A 68 LYS A 69 1 N LYS A 69 O GLY A 104 SHEET 5 AA2 5 ASP A 140 ILE A 141 1 O ILE A 141 N THR A 68 SHEET 1 AA3 5 THR A 238 SER A 243 0 SHEET 2 AA3 5 LYS A 214 GLN A 218 1 N VAL A 217 O ALA A 241 SHEET 3 AA3 5 VAL A 291 PRO A 294 1 O ALA A 293 N ALA A 216 SHEET 4 AA3 5 ILE A 313 ALA A 315 1 O ALA A 315 N LEU A 292 SHEET 5 AA3 5 LEU A 336 ILE A 338 1 O ILE A 338 N VAL A 314 SHEET 1 AA4 2 GLY A 248 TYR A 250 0 SHEET 2 AA4 2 THR A 277 ILE A 279 -1 O ILE A 279 N GLY A 248 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