HEADER ISOMERASE 23-APR-24 9F2K TITLE MYO-INOSITOL-1-PHOSPHATE SYNTHASE FROM THERMOCHAETOIDES THERMOPHILA IN TITLE 2 COMPLEX WITH NAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: INOSITOL-3-PHOSPHATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.5.1.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCHAETOIDES THERMOPHILA DSM 1495; SOURCE 3 ORGANISM_TAXID: 759272 KEYWDS INOSITOL METABOLISM, ENDOGENOUS, CONFORMATIONAL SELECTION, ISOMERASE EXPDTA ELECTRON MICROSCOPY AUTHOR T.K.TRAEGER,F.L.KYRILIS,F.HAMDI,P.L.KASTRITIS REVDAT 2 28-AUG-24 9F2K 1 JRNL REVDAT 1 14-AUG-24 9F2K 0 JRNL AUTH T.K.TRAGER,F.L.KYRILIS,F.HAMDI,C.TUTING,M.ALFES,T.HOFMANN, JRNL AUTH 2 C.SCHMIDT,P.L.KASTRITIS JRNL TITL DISORDER-TO-ORDER ACTIVE SITE CAPPING REGULATES THE JRNL TITL 2 RATE-LIMITING STEP OF THE INOSITOL PATHWAY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 121 12121 2024 JRNL REFN ESSN 1091-6490 JRNL PMID 39145930 JRNL DOI 10.1073/PNAS.2400912121 REMARK 2 REMARK 2 RESOLUTION. 2.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, UCSF REMARK 3 CHIMERAX, PHENIX, UCSF CHIMERAX, COOT, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : SIMULTANEOUS ITERATIVE (SIRT) REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE 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) : 2.480 REMARK 3 NUMBER OF PARTICLES : 255354 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 9F2K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-APR-24. REMARK 100 THE DEPOSITION ID IS D_1292138055. 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 : NATIVE HOMOTETRAMER OF THE MYO REMARK 245 -INOSITOL-1-PHOSPHATE SYNTHASE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.60 REMARK 245 SAMPLE SUPPORT DETAILS : 15 MA REMARK 245 SAMPLE VITRIFICATION DETAILS : 6 S BLOT TIME WITH A BLOT FORCE REMARK 245 OF -1 REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 6261 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS GLACIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2800.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : 240000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 302.08000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 302.08000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 302.08000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 302.08000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 302.08000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 302.08000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLN A 347 OD1 ASP A 436 2.03 REMARK 500 OG SER A 136 OD1 ASP A 468 2.13 REMARK 500 O SER A 501 OG SER A 504 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 342 172.93 68.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-50149 RELATED DB: EMDB REMARK 900 MYO-INOSITOL-1-PHOSPHATE SYNTHASE FROM THERMOCHAETOIDES THERMOPHILA REMARK 900 IN COMPLEX WITH NAD DBREF 9F2K A 40 552 UNP G0SDP4 G0SDP4_CHATD 40 552 SEQADV 9F2K LYS A 237 UNP G0SDP4 ALA 237 CONFLICT SEQRES 1 A 513 ILE PHE LYS VAL ASN SER PRO ASN VAL VAL TYR THR ASP SEQRES 2 A 513 ASP GLU ILE ARG SER LYS TYR VAL TYR ARG THR THR GLU SEQRES 3 A 513 VAL THR THR ALA GLU ASP GLY SER LEU ILE ALA THR PRO SEQRES 4 A 513 ARG GLU THR VAL TYR ASP PHE LYS VAL ASP ARG LYS LEU SEQRES 5 A 513 PRO LYS LEU GLY VAL MET LEU VAL GLY TRP GLY GLY ASN SEQRES 6 A 513 ASN GLY SER THR ILE THR ALA GLY ILE ILE ALA ASN ARG SEQRES 7 A 513 ARG GLY LEU VAL TRP GLU THR ARG ASN GLY LYS GLN GLU SEQRES 8 A 513 ALA ASN TYR TYR GLY SER VAL ILE MET GLY SER THR ILE SEQRES 9 A 513 LYS LEU GLY THR ASP ALA LYS THR HIS LYS ASP ILE ASN SEQRES 10 A 513 ILE PRO PHE HIS SER VAL LEU PRO MET VAL HIS PRO ASN SEQRES 11 A 513 ASP ILE VAL ILE GLY GLY TRP ASP ILE SER GLY LEU ASN SEQRES 12 A 513 LEU ALA ASP ALA MET ASP ARG ALA GLN VAL LEU GLU PRO SEQRES 13 A 513 SER LEU LYS ALA LEU VAL ARG LYS GLU MET ALA SER MET SEQRES 14 A 513 LYS PRO LEU PRO SER ILE TYR TYR PRO ASP PHE ILE ALA SEQRES 15 A 513 ALA ASN GLN GLU ASP ARG ALA ASP ASN ILE LEU PRO GLY SEQRES 16 A 513 ASN LYS LYS CYS TRP GLU HIS VAL GLU GLU ILE ARG LYS SEQRES 17 A 513 ASN ILE ARG ASP PHE LYS ALA ALA ASN GLY LEU ASP LYS SEQRES 18 A 513 VAL ILE VAL LEU TRP THR ALA ASN THR GLU ARG TYR ALA SEQRES 19 A 513 SER ILE ILE GLU GLY VAL ASN ASP THR ALA ASP ASN LEU SEQRES 20 A 513 LEU ASN ALA ILE LYS ASN GLY HIS GLU GLU VAL SER PRO SEQRES 21 A 513 SER THR VAL PHE ALA VAL SER SER ILE LEU GLU GLY VAL SEQRES 22 A 513 PRO PHE ILE ASN GLY SER PRO GLN ASN THR PHE VAL PRO SEQRES 23 A 513 GLY CYS ILE GLU LEU ALA GLU ARG HIS GLY ALA PHE ILE SEQRES 24 A 513 GLY GLY ASP ASP PHE LYS SER GLY GLN THR LYS MET LYS SEQRES 25 A 513 SER ALA LEU VAL ASP PHE LEU ILE ASN ALA GLY ILE LYS SEQRES 26 A 513 LEU THR SER ILE ALA SER TYR ASN HIS LEU GLY ASN ASN SEQRES 27 A 513 ASP GLY LYS ASN LEU SER SER GLN ARG GLN PHE ARG SER SEQRES 28 A 513 LYS GLU ILE SER LYS SER ASN VAL VAL ASP ASP MET VAL SEQRES 29 A 513 GLU ALA ASN THR VAL LEU TYR LYS PRO GLY GLU HIS PRO SEQRES 30 A 513 ASP HIS ILE VAL VAL ILE LYS TYR VAL PRO ALA VAL GLY SEQRES 31 A 513 ASP SER LYS ARG ALA MET ASP GLU TYR HIS GLY GLU ILE SEQRES 32 A 513 PHE LEU GLY GLY HIS GLN THR ILE SER ILE ALA ASN VAL SEQRES 33 A 513 CYS GLU ASP SER LEU LEU ALA SER PRO LEU ILE ILE ASP SEQRES 34 A 513 LEU VAL ILE VAL ALA GLU LEU MET THR ARG ILE GLN TRP SEQRES 35 A 513 ARG LEU HIS LYS GLU ASP ALA THR GLU ALA ASP TRP LYS SEQRES 36 A 513 TYR PHE HIS SER VAL LEU SER ILE LEU SER TYR MET LEU SEQRES 37 A 513 LYS ALA PRO MET THR PRO PRO GLY THR PRO VAL VAL ASN SEQRES 38 A 513 ALA LEU ALA LYS GLN ARG ALA ALA MET ALA ASN ILE PHE SEQRES 39 A 513 ARG ALA CYS LEU GLY LEU ASP PRO GLU ASN ASP MET THR SEQRES 40 A 513 LEU GLU HIS LYS LEU PHE HET NAD A 601 44 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 2 NAD C21 H27 N7 O14 P2 HELIX 1 AA1 GLY A 103 GLY A 119 1 17 HELIX 2 AA2 SER A 136 SER A 141 1 6 HELIX 3 AA3 HIS A 160 VAL A 162 5 3 HELIX 4 AA4 HIS A 167 ILE A 171 5 5 HELIX 5 AA5 ASN A 182 GLN A 191 1 10 HELIX 6 AA6 GLU A 194 ALA A 206 1 13 HELIX 7 AA7 ALA A 221 GLU A 225 5 5 HELIX 8 AA8 CYS A 238 GLY A 257 1 20 HELIX 9 AA9 THR A 282 GLY A 293 1 12 HELIX 10 AB1 SER A 298 GLY A 311 1 14 HELIX 11 AB2 GLY A 326 GLY A 335 1 10 HELIX 12 AB3 GLY A 346 ASN A 360 1 15 HELIX 13 AB4 ASN A 376 LEU A 382 1 7 HELIX 14 AB5 SER A 384 ASN A 397 1 14 HELIX 15 AB6 VAL A 399 ASN A 406 1 8 HELIX 16 AB7 PHE A 443 GLY A 445 5 3 HELIX 17 AB8 ASP A 458 THR A 477 1 20 HELIX 18 AB9 THR A 489 TRP A 493 5 5 HELIX 19 AC1 LEU A 500 LEU A 507 5 8 HELIX 20 AC2 ALA A 521 CYS A 536 1 16 SHEET 1 AA1 4 SER A 57 THR A 68 0 SHEET 2 AA1 4 LEU A 74 VAL A 87 -1 O THR A 81 N TYR A 61 SHEET 3 AA1 4 ILE A 479 LEU A 483 -1 O ARG A 482 N ASP A 84 SHEET 4 AA1 4 LYS A 494 TYR A 495 -1 O LYS A 494 N TRP A 481 SHEET 1 AA2 4 VAL A 172 TRP A 176 0 SHEET 2 AA2 4 LEU A 94 VAL A 99 1 N LEU A 98 O GLY A 174 SHEET 3 AA2 4 LYS A 260 TRP A 265 1 O ILE A 262 N MET A 97 SHEET 4 AA2 4 PHE A 314 ASN A 316 1 O ILE A 315 N TRP A 265 SHEET 1 AA3 2 VAL A 121 THR A 124 0 SHEET 2 AA3 2 GLY A 127 GLU A 130 -1 O GLY A 127 N THR A 124 SHEET 1 AA4 2 THR A 142 THR A 147 0 SHEET 2 AA4 2 ASP A 154 PRO A 158 -1 O ILE A 155 N GLY A 146 SHEET 1 AA5 4 ASP A 417 TYR A 424 0 SHEET 2 AA5 4 LYS A 364 LEU A 374 1 N ILE A 368 O ASP A 417 SHEET 3 AA5 4 SER A 431 ILE A 442 -1 O MET A 435 N TYR A 371 SHEET 4 AA5 4 GLY A 446 GLU A 457 -1 O ASN A 454 N ALA A 434 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