HEADER OXIDOREDUCTASE 14-MAR-19 6JND TITLE CRYO-EM STRUCTURE OF GLUTAMATE DEHYDROGENASE FROM THERMOCOCCUS TITLE 2 PROFUNDUS 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 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 ENZYME, MULTI-DOMAIN PROTEIN, OXIDOREDUCTASE EXPDTA ELECTRON MICROSCOPY AUTHOR M.OIDE,T.KATO,T.OROGUCHI,M.NAKASAKO REVDAT 3 27-MAR-24 6JND 1 REMARK REVDAT 2 02-SEP-20 6JND 1 JRNL REVDAT 1 12-FEB-20 6JND 0 JRNL AUTH M.OIDE,T.KATO,T.OROGUCHI,M.NAKASAKO JRNL TITL ENERGY LANDSCAPE OF DOMAIN MOTION IN GLUTAMATE DEHYDROGENASE JRNL TITL 2 DEDUCED FROM CRYO-ELECTRON MICROSCOPY. JRNL REF FEBS J. V. 287 3472 2020 JRNL REFN ISSN 1742-464X JRNL PMID 31976609 JRNL DOI 10.1111/FEBS.15224 REMARK 2 REMARK 2 RESOLUTION. 3.90 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) : 3.900 REMARK 3 NUMBER OF PARTICLES : 97022 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 6JND COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1300011406. 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 : GLUTAMATE DEHYDROGENASE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL 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 : JEOL CRYO ARM 200 REMARK 245 DETECTOR TYPE : GATAN K2 BASE (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 1000.00 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) : 200 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 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 ASP A 22 CG OD1 OD2 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 58 115.00 -161.24 REMARK 500 TRP A 63 35.61 -99.24 REMARK 500 ASP A 145 -155.67 -149.75 REMARK 500 LYS A 167 52.41 -94.21 REMARK 500 ALA A 295 17.93 -141.50 REMARK 500 THR A 302 -169.66 -126.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6JN9 RELATED DB: PDB REMARK 900 6JN9 CONTAINS THE SAME PROTEIN IN A DIFFERENT CONFORMATION. REMARK 900 RELATED ID: 6JNA RELATED DB: PDB REMARK 900 6JNA CONTAINS THE SAME PROTEIN IN A DIFFERENT CONFORMATION. REMARK 900 RELATED ID: 6JNC RELATED DB: PDB REMARK 900 6JNC CONTAINS THE SAME PROTEIN IN A DIFFERENT CONFORMATION. REMARK 900 RELATED ID: EMD-9848 RELATED DB: EMDB DBREF 6JND 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 TRS A 901 8 HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 TRS C4 H12 N O3 1+ HELIX 1 AA1 ASP A 5 ALA A 17 1 13 HELIX 2 AA2 THR A 79 ALA A 95 1 17 HELIX 3 AA3 ASN A 111 LEU A 115 5 5 HELIX 4 AA4 SER A 116 ARG A 129 1 14 HELIX 5 AA5 VAL A 131 ILE A 135 5 5 HELIX 6 AA6 ASN A 149 ARG A 165 1 17 HELIX 7 AA7 PRO A 169 VAL A 173 5 5 HELIX 8 AA8 THR A 189 GLY A 207 1 19 HELIX 9 AA9 GLY A 221 GLN A 234 1 14 HELIX 10 AB1 ASP A 256 ARG A 265 1 10 HELIX 11 AB2 THR A 280 GLU A 286 1 7 HELIX 12 AB3 ALA A 326 GLU A 332 1 7 HELIX 13 AB4 PRO A 339 ASN A 344 1 6 HELIX 14 AB5 ALA A 345 GLY A 361 1 17 HELIX 15 AB6 THR A 365 ASN A 392 1 28 HELIX 16 AB7 HIS A 394 LYS A 412 1 19 SHEET 1 AA1 4 ARG A 36 GLU A 45 0 SHEET 2 AA1 4 VAL A 51 GLN A 60 -1 O PHE A 54 N VAL A 42 SHEET 3 AA1 4 GLY A 104 ILE A 108 -1 O GLY A 107 N PHE A 57 SHEET 4 AA1 4 ILE A 72 TRP A 74 1 N ARG A 73 O GLY A 106 SHEET 1 AA2 2 THR A 68 LYS A 69 0 SHEET 2 AA2 2 ASP A 140 ILE A 141 1 O ILE A 141 N THR A 68 SHEET 1 AA3 5 GLY A 248 TYR A 250 0 SHEET 2 AA3 5 THR A 238 SER A 243 -1 N VAL A 242 O ILE A 249 SHEET 3 AA3 5 LYS A 214 GLN A 218 1 N ILE A 215 O THR A 238 SHEET 4 AA3 5 VAL A 291 PRO A 294 1 O ALA A 293 N ALA A 216 SHEET 5 AA3 5 ILE A 313 VAL A 314 1 O ILE A 313 N LEU A 292 SITE 1 AC1 2 ALA A 143 PRO A 144 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 0.005155 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005155 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005131 0.00000