HEADER PLANT PROTEIN 20-APR-22 7XKW TITLE THE 3D STRCUTURE OF (-)-CYPERENE SYNTHASE WITH SUBSTRATE ANALOGUE FSPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: (-)-CYPERENE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTABOTRYS HEXAPETALUS; SOURCE 3 ORGANISM_TAXID: 225833; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 37762 KEYWDS (-)-CYPERENE SYNTHASE, CYCLIZATION MECHANISM, DIRECTED EVOLUTION, KEYWDS 2 ALPHAFOLD2, PLANT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.S.YU,P.ZHU,Y.B.LIU,S.G.MA,D.YE,Y.Z.SHAO,W.R.LI,Z.J.CUI REVDAT 3 03-APR-24 7XKW 1 JRNL REVDAT 2 27-MAR-24 7XKW 1 JRNL REVDAT 1 25-OCT-23 7XKW 0 JRNL AUTH D.YE,Y.Z.SHAO,W.R.LI,Z.J.CUI,T.GONG,J.L.YANG,H.Q.WANG, JRNL AUTH 2 J.G.DAI,K.P.FENG,M.MA,S.G.MA,Y.B.LIU,P.ZHU,S.S.YU JRNL TITL CHARACTERIZATION AND ENGINEERING OF TWO HIGHLY PARALOGOUS JRNL TITL 2 SESQUITERPENE SYNTHASES REVEAL A REGIOSELECTIVE JRNL TITL 3 REPROTONATION SWITCH. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 63 15674 2024 JRNL REFN ESSN 1521-3773 JRNL PMID 38327006 JRNL DOI 10.1002/ANIE.202315674 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.YE,Y.Z.SHAO,W.R.LI,Z.J.CUI,T.GONG,J.L.YANG,H.Q.WANG, REMARK 1 AUTH 2 J.G.DAI,K.P.FENG,M.MA,S.G.MA,Y.B.LIU,P.ZHU,S.S.YU REMARK 1 TITL CHARACTERISATION AND ENGINEERING OF TWO HIGHLY PARALOGOUS REMARK 1 TITL 2 SESQUITERPENE SYNTHASES REVEAL A REGIOSELECTIVE REMARK 1 TITL 3 REPROTONATION SWITCH. REMARK 1 REF ANGEW.CHEM.INT.ED.ENGL. 2024 REMARK 1 REFN ESSN 1521-3773 REMARK 1 DOI 10.1002/ANGE.202315674 REMARK 2 REMARK 2 RESOLUTION. 3.10 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 283635 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7XKW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-APR-22. REMARK 100 THE DEPOSITION ID IS D_1300029027. 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 : COMPLEX OF (-)-CYPERENE REMARK 245 SYNTHASE WITH SUBSTRATE REMARK 245 ANOLOGUE FSPP REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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 : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 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 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 5 REMARK 465 GLY A 6 REMARK 465 SER A 7 REMARK 465 SER A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 HIS A 11 REMARK 465 HIS A 12 REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 SER A 15 REMARK 465 SER A 16 REMARK 465 GLY A 17 REMARK 465 LEU A 18 REMARK 465 VAL A 19 REMARK 465 PRO A 20 REMARK 465 ARG A 21 REMARK 465 GLY A 22 REMARK 465 SER A 23 REMARK 465 HIS A 24 REMARK 465 MET A 25 REMARK 465 MET A 26 REMARK 465 GLY A 27 REMARK 465 ARG A 28 REMARK 465 SER A 29 REMARK 465 SER A 30 REMARK 465 ALA A 31 REMARK 465 ASN A 32 REMARK 465 PHE A 33 REMARK 465 HIS A 34 REMARK 465 PRO A 35 REMARK 465 ASN A 36 REMARK 465 VAL A 37 REMARK 465 TRP A 38 REMARK 465 GLY A 39 REMARK 465 ASP A 40 REMARK 465 ARG A 41 REMARK 465 PHE A 42 REMARK 465 VAL A 43 REMARK 465 MET A 44 REMARK 465 MET A 45 REMARK 465 PRO A 46 REMARK 465 SER A 47 REMARK 465 LYS A 48 REMARK 465 GLU A 49 REMARK 465 MET A 50 REMARK 465 GLU A 51 REMARK 465 THR A 52 REMARK 465 ASP A 53 REMARK 465 ALA A 54 REMARK 465 CYS A 540 REMARK 465 ARG A 541 REMARK 465 ASP A 542 REMARK 465 GLY A 543 REMARK 465 TYR A 544 REMARK 465 SER A 545 REMARK 465 ASP A 546 REMARK 465 SER A 547 REMARK 465 ALA A 548 REMARK 465 PHE A 549 REMARK 465 GLU A 550 REMARK 465 VAL A 565 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 O2B FPS A 601 MG MG A 603 1.55 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 LYS A 148 52.17 -92.59 REMARK 500 ASN A 151 -139.01 54.54 REMARK 500 SER A 446 1.44 -63.54 REMARK 500 LEU A 447 71.28 54.71 REMARK 500 CYS A 458 -87.82 -45.30 REMARK 500 ARG A 459 -62.70 -26.93 REMARK 500 ASN A 462 -79.11 -42.09 REMARK 500 ASP A 463 -69.76 -19.41 REMARK 500 PHE A 487 -137.92 59.12 REMARK 500 PRO A 516 71.07 -66.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 318 OD1 REMARK 620 2 FPS A 601 O3B 127.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 604 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 470 OE1 REMARK 620 2 FPS A 601 O1B 99.8 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33209 RELATED DB: EMDB DBREF 7XKW A 5 565 PDB 7XKW 7XKW 5 565 SEQRES 1 A 561 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 561 LEU VAL PRO ARG GLY SER HIS MET MET GLY ARG SER SER SEQRES 3 A 561 ALA ASN PHE HIS PRO ASN VAL TRP GLY ASP ARG PHE VAL SEQRES 4 A 561 MET MET PRO SER LYS GLU MET GLU THR ASP ALA SER THR SEQRES 5 A 561 LYS GLN ARG ALA GLU MET LEU LYS GLN GLU VAL LYS LYS SEQRES 6 A 561 MET LEU HIS ASP VAL SER GLY SER LEU GLN GLU LEU ASN SEQRES 7 A 561 LEU ILE ASN GLU ILE GLN ARG LEU GLY VAL ALA TYR HIS SEQRES 8 A 561 PHE GLU ALA GLU ILE SER ASN ALA LEU GLU ARG ILE TYR SEQRES 9 A 561 ASN ARG GLU LYS ASN GLU ASN GLY ILE ASN ASP CYS ASP SEQRES 10 A 561 LEU HIS ALA VAL ALA LEU ARG PHE ARG LEU LEU ARG GLN SEQRES 11 A 561 HIS GLY TYR ASN VAL SER SER ASP VAL PHE LYS LYS PHE SEQRES 12 A 561 LYS ASP GLU ASN GLY GLU PHE GLU ALA ARG PHE ARG ASN SEQRES 13 A 561 ASP VAL ARG GLY LEU LEU SER LEU TYR GLU ALA ALA TYR SEQRES 14 A 561 PHE GLY THR GLN GLU ASP GLY HIS LEU ASP GLU ALA ILE SEQRES 15 A 561 ALA PHE THR THR LYS HIS LEU LYS SER LEU LEU PRO HIS SEQRES 16 A 561 LEU SER SER PRO LEU SER ASP LEU VAL LYS LEU ALA LEU SEQRES 17 A 561 ASP LEU PRO LEU LEU LYS ARG ILE GLU ARG LEU GLN SER SEQRES 18 A 561 LYS HIS PHE ILE SER ILE TYR GLN GLN ASP GLU ASP ARG SEQRES 19 A 561 ASN ASN VAL LEU LEU GLU PHE ALA LYS ILE ASP PHE ASN SEQRES 20 A 561 ILE LEU GLN ALA LEU HIS ARG LYS GLU LEU ASN GLU ILE SEQRES 21 A 561 THR ARG TRP TRP ASN GLU SER ASP LEU PRO ARG LYS LEU SEQRES 22 A 561 PRO PHE ILE ARG ASP ARG LEU VAL GLU CYS TYR ILE TRP SEQRES 23 A 561 MET LEU GLU LEU TYR TYR GLU PRO GLN TYR SER GLN SER SEQRES 24 A 561 ARG ARG MET THR THR ILE LEU LEU ILE LEU THR SER SER SEQRES 25 A 561 MET ASP ASP ILE TYR ASP VAL TYR GLY LYS LEU GLU GLU SEQRES 26 A 561 LEU GLU ARG TYR THR VAL ALA VAL GLU ARG TRP GLU ARG SEQRES 27 A 561 GLU ALA LEU ASP GLN LEU PRO ASP TYR MET ARG VAL HIS SEQRES 28 A 561 LEU GLY VAL LEU LEU THR VAL VAL GLU ASN PHE GLU ASP SEQRES 29 A 561 GLU LEU GLY LYS GLU GLY LYS SER PHE HIS LEU ALA TYR SEQRES 30 A 561 VAL LYS LYS ALA PHE ALA GLU LEU THR LYS ALA TYR ILE SEQRES 31 A 561 LYS GLU ALA ARG TRP ALA ASN ALA GLU HIS VAL PRO ALA SEQRES 32 A 561 LEU GLU GLU TYR VAL ASP ASN ALA VAL VAL SER SER ALA SEQRES 33 A 561 TYR PRO LEU ILE THR THR MET SER LEU LEU GLY MET GLY SEQRES 34 A 561 LYS VAL ALA THR LYS GLU ALA PHE GLU TRP THR ILE SER SEQRES 35 A 561 LEU PRO ASN ALA VAL ARG GLN CYS SER MET ILE CYS ARG SEQRES 36 A 561 LEU VAL ASN ASP ILE MET SER ASN GLN SER GLU GLN GLU SEQRES 37 A 561 ARG VAL HIS VAL ALA SER ALA VAL GLN CYS CYS MET LYS SEQRES 38 A 561 GLU PHE SER THR THR TYR GLU GLU ALA CYS LYS ILE LEU SEQRES 39 A 561 GLN GLU LYS ILE ALA ARG ALA TRP LYS ASP LEU ASN LYS SEQRES 40 A 561 GLU CYS LEU HIS PRO ILE PRO VAL SER LEU GLU LEU ILE SEQRES 41 A 561 ARG ARG PRO LEU ASN LEU ALA ARG ALA ILE GLU PHE TYR SEQRES 42 A 561 TYR GLN CYS ARG ASP GLY TYR SER ASP SER ALA PHE GLU SEQRES 43 A 561 ILE LYS ASP TYR ILE THR MET LEU LEU VAL GLU PRO ALA SEQRES 44 A 561 VAL VAL HET FPS A 601 24 HET MG A 602 1 HET MG A 603 1 HET MG A 604 1 HETNAM FPS S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] HETNAM 2 FPS TRIHYDROGEN THIODIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN FPS FARNESYL THIOPYROPHOSPHATE FORMUL 2 FPS C15 H28 O6 P2 S FORMUL 3 MG 3(MG 2+) HELIX 1 AA1 SER A 55 VAL A 74 1 20 HELIX 2 AA2 SER A 77 LEU A 90 1 14 HELIX 3 AA3 VAL A 92 HIS A 95 5 4 HELIX 4 AA4 PHE A 96 ARG A 110 1 15 HELIX 5 AA5 ASP A 121 GLY A 136 1 16 HELIX 6 AA6 ASP A 142 LYS A 146 5 5 HELIX 7 AA7 GLU A 155 ARG A 159 5 5 HELIX 8 AA8 ASP A 161 TYR A 173 1 13 HELIX 9 AA9 ASP A 183 LEU A 197 1 15 HELIX 10 AB1 SER A 201 LEU A 214 1 14 HELIX 11 AB2 ILE A 220 GLN A 233 1 14 HELIX 12 AB3 ASN A 239 SER A 271 1 33 HELIX 13 AB4 LEU A 284 ILE A 289 1 6 HELIX 14 AB5 GLU A 297 GLN A 299 5 3 HELIX 15 AB6 TYR A 300 VAL A 323 1 24 HELIX 16 AB7 LYS A 326 TRP A 340 1 15 HELIX 17 AB8 GLU A 341 ASP A 346 5 6 HELIX 18 AB9 PRO A 349 GLY A 371 1 23 HELIX 19 AC1 LYS A 375 PHE A 377 5 3 HELIX 20 AC2 HIS A 378 GLU A 403 1 26 HELIX 21 AC3 ALA A 407 SER A 418 1 12 HELIX 22 AC4 ALA A 420 SER A 428 1 9 HELIX 23 AC5 LEU A 429 MET A 432 5 4 HELIX 24 AC6 THR A 437 SER A 446 1 10 HELIX 25 AC7 PRO A 448 ASN A 467 1 20 HELIX 26 AC8 SER A 469 ARG A 473 5 5 HELIX 27 AC9 SER A 478 GLU A 486 1 9 HELIX 28 AD1 THR A 490 CYS A 513 1 24 HELIX 29 AD2 SER A 520 TYR A 538 1 19 HELIX 30 AD3 LYS A 552 LEU A 559 1 8 LINK OD1 ASP A 318 MG MG A 603 1555 1555 2.23 LINK OE1 GLU A 470 MG MG A 604 1555 1555 2.73 LINK O2B FPS A 601 MG MG A 602 1555 1555 2.75 LINK O3B FPS A 601 MG MG A 603 1555 1555 2.43 LINK O1B FPS A 601 MG MG A 604 1555 1555 2.66 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