HEADER TRANSFERASE 28-OCT-21 7VTA TITLE TALAROMYCES VERRUCULOSUS TALAROPENTAENE SYNTHASE APO COMPND MOL_ID: 1; COMPND 2 MOLECULE: TVTS CYCLASE DOMAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TALAROMYCES VERRUCULOSUS; SOURCE 3 ORGANISM_TAXID: 198730; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TALAROMYCES VERRUCULOSUS, TALAROPENTAENE SYNTHASE, TRITERPENE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.HUI,T.MORI,I.ABE REVDAT 4 29-NOV-23 7VTA 1 REMARK REVDAT 3 22-JUN-22 7VTA 1 JRNL REVDAT 2 15-JUN-22 7VTA 1 JRNL REVDAT 1 08-JUN-22 7VTA 0 JRNL AUTH H.TAO,L.LAUTERBACH,G.BIAN,R.CHEN,A.HOU,T.MORI,S.CHENG,B.HU, JRNL AUTH 2 L.LU,X.MU,M.LI,N.ADACHI,M.KAWASAKI,T.MORIYA,T.SENDA,X.WANG, JRNL AUTH 3 Z.DENG,I.ABE,J.S.DICKSCHAT,T.LIU JRNL TITL DISCOVERY OF NON-SQUALENE TRITERPENES. JRNL REF NATURE V. 606 414 2022 JRNL REFN ESSN 1476-4687 JRNL PMID 35650436 JRNL DOI 10.1038/S41586-022-04773-3 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 13269 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 634 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.0700 - 4.1000 0.99 2578 123 0.2267 0.2467 REMARK 3 2 4.1000 - 3.2600 1.00 2495 160 0.2179 0.2786 REMARK 3 3 3.2600 - 2.8500 1.00 2547 117 0.2564 0.2816 REMARK 3 4 2.8500 - 2.5900 0.99 2511 118 0.2271 0.2849 REMARK 3 5 2.5900 - 2.4000 0.98 2504 116 0.2523 0.3115 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.329 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.992 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2069 REMARK 3 ANGLE : 0.911 2794 REMARK 3 CHIRALITY : 0.053 306 REMARK 3 PLANARITY : 0.007 363 REMARK 3 DIHEDRAL : 16.835 752 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7VTA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1300025202. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13274 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 47.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.56800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5ER8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-CL (PH 8.5), 0.1 M MGCL2, REMARK 280 30% PEG 4000, 0.2 M NDSB-211, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 20.30217 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.88500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.34485 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 20.30217 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.88500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 36.34485 REMARK 290 REMARK 290 REMARK: NULL 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 1 REMARK 465 MET A 94 REMARK 465 THR A 95 REMARK 465 ASP A 96 REMARK 465 ALA A 97 REMARK 465 ALA A 98 REMARK 465 SER A 99 REMARK 465 LYS A 100 REMARK 465 ASP A 101 REMARK 465 GLN A 102 REMARK 465 VAL A 103 REMARK 465 ASN A 104 REMARK 465 GLY A 105 REMARK 465 LEU A 106 REMARK 465 ASN A 107 REMARK 465 ASP A 108 REMARK 465 ASP A 109 REMARK 465 LEU A 110 REMARK 465 LEU A 111 REMARK 465 GLY A 112 REMARK 465 GLY A 113 REMARK 465 LEU A 114 REMARK 465 ASP A 115 REMARK 465 PHE A 116 REMARK 465 THR A 117 REMARK 465 THR A 118 REMARK 465 GLU A 119 REMARK 465 ALA A 120 REMARK 465 ARG A 121 REMARK 465 SER A 122 REMARK 465 SER A 123 REMARK 465 MET A 157 REMARK 465 ARG A 158 REMARK 465 GLY A 159 REMARK 465 ALA A 160 REMARK 465 ALA A 161 REMARK 465 GLY A 162 REMARK 465 ARG A 163 REMARK 465 ASP A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 ARG A 167 REMARK 465 GLY A 168 REMARK 465 PHE A 169 REMARK 465 SER A 170 REMARK 465 SER A 171 REMARK 465 LEU A 172 REMARK 465 ASP A 173 REMARK 465 GLU A 174 REMARK 465 TYR A 175 REMARK 465 ILE A 176 REMARK 465 PRO A 177 REMARK 465 TYR A 178 REMARK 465 ARG A 179 REMARK 465 CYS A 180 REMARK 465 ALA A 181 REMARK 465 ASP A 182 REMARK 465 ALA A 235 REMARK 465 GLU A 236 REMARK 465 ARG A 237 REMARK 465 SER A 238 REMARK 465 GLY A 239 REMARK 465 THR A 240 REMARK 465 GLY A 241 REMARK 465 GLN A 242 REMARK 465 VAL A 323 REMARK 465 ASP A 324 REMARK 465 PHE A 325 REMARK 465 LYS A 326 REMARK 465 THR A 327 REMARK 465 PRO A 328 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 LYS A 4 CE NZ REMARK 470 ARG A 59 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 144 CG CD OE1 OE2 REMARK 470 PHE A 156 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 203 CG CD OE1 NE2 REMARK 470 LYS A 230 CG CD CE NZ 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 GLU A 21 -138.74 52.27 REMARK 500 ASN A 30 48.94 -92.79 REMARK 500 ASN A 287 56.47 28.70 REMARK 500 REMARK 500 REMARK: NULL DBREF 7VTA A 1 328 PDB 7VTA 7VTA 1 328 SEQRES 1 A 328 MET ASP PHE LYS TYR SER ARG GLU LEU LYS LEU GLU SER SEQRES 2 A 328 LEU ASP ALA LEU ASN LEU THR GLU GLY ILE PRO LEU ARG SEQRES 3 A 328 VAL ASN GLU ASN ILE ASP LEU GLU PHE ARG GLY ILE GLU SEQRES 4 A 328 ARG ALA HIS SER ASP TRP GLU ARG TYR VAL GLY LYS LEU SEQRES 5 A 328 ASN GLY PHE HIS GLY GLY ARG GLY PRO GLN PHE GLY PHE SEQRES 6 A 328 VAL SER ALA CYS ILE PRO GLU CYS LEU PRO GLU ARG MET SEQRES 7 A 328 GLU THR VAL SER TYR ALA ASN GLU PHE ALA PHE LEU HIS SEQRES 8 A 328 ASP ASP MET THR ASP ALA ALA SER LYS ASP GLN VAL ASN SEQRES 9 A 328 GLY LEU ASN ASP ASP LEU LEU GLY GLY LEU ASP PHE THR SEQRES 10 A 328 THR GLU ALA ARG SER SER ALA SER GLY LYS GLN GLN MET SEQRES 11 A 328 GLN ALA LYS LEU LEU LEU GLU MET LEU SER ILE ASP ARG SEQRES 12 A 328 GLU ARG THR MET VAL THR ILE LYS ALA TRP ALA ASP PHE SEQRES 13 A 328 MET ARG GLY ALA ALA GLY ARG ASP HIS HIS ARG GLY PHE SEQRES 14 A 328 SER SER LEU ASP GLU TYR ILE PRO TYR ARG CYS ALA ASP SEQRES 15 A 328 CYS GLY GLU LYS PHE TRP PHE GLY LEU VAL THR PHE ALA SEQRES 16 A 328 MET ALA LEU SER ILE PRO GLU GLN GLU LEU GLU LEU VAL SEQRES 17 A 328 GLN ARG LEU ALA GLN ASN ALA TYR LEU ALA ALA GLY LEU SEQRES 18 A 328 THR ASN ASP LEU TYR SER TYR GLU LYS GLU GLN LEU VAL SEQRES 19 A 328 ALA GLU ARG SER GLY THR GLY GLN VAL PHE ASN ALA ILE SEQRES 20 A 328 ALA VAL ILE MET GLN GLU HIS SER VAL SER ILE SER GLU SEQRES 21 A 328 ALA GLU ASP ILE CYS ARG GLY ARG ILE ARG GLU TYR ALA SEQRES 22 A 328 ALA LYS TYR VAL ARG ASP VAL ALA ASP LEU ARG ALA LYS SEQRES 23 A 328 ASN GLU LEU SER ARG ASP SER LEU ALA TYR LEU GLU THR SEQRES 24 A 328 GLY LEU TYR GLY ILE SER GLY SER THR ALA TRP ASN LEU SEQRES 25 A 328 ASP CYS PRO ARG TYR GLN VAL SER THR PHE VAL ASP PHE SEQRES 26 A 328 LYS THR PRO FORMUL 2 HOH *29(H2 O) HELIX 1 AA1 GLU A 12 ASN A 18 1 7 HELIX 2 AA2 ASN A 30 VAL A 49 1 20 HELIX 3 AA3 GLY A 64 ILE A 70 1 7 HELIX 4 AA4 LEU A 74 GLU A 76 5 3 HELIX 5 AA5 ARG A 77 ASP A 93 1 17 HELIX 6 AA6 SER A 125 ASP A 142 1 18 HELIX 7 AA7 ASP A 142 PHE A 156 1 15 HELIX 8 AA8 GLY A 184 MET A 196 1 13 HELIX 9 AA9 PRO A 201 LEU A 233 1 33 HELIX 10 AB1 ASN A 245 HIS A 254 1 10 HELIX 11 AB2 SER A 257 ASN A 287 1 31 HELIX 12 AB3 SER A 290 CYS A 314 1 25 HELIX 13 AB4 PRO A 315 GLN A 318 5 4 SHEET 1 AA1 2 SER A 6 LEU A 9 0 SHEET 2 AA1 2 LEU A 25 ASN A 28 -1 O VAL A 27 N ARG A 7 CRYST1 76.503 61.770 81.071 90.00 116.28 90.00 I 1 2 1 4 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 0.013071 0.000000 0.006455 0.00000 SCALE2 0.000000 0.016189 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013757 0.00000