HEADER LYASE 01-SEP-22 8GR5 TITLE COP4 FROM ANTRODIA CINNAMOMEA IN APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACCOP4; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANTRODIA CINNAMOMEA; SOURCE 3 ORGANISM_TAXID: 279009; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TERPENOID, CUBEBOL, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR S.C.CHEN,C.H.HSU REVDAT 2 20-SEP-23 8GR5 1 JRNL REVDAT 1 06-SEP-23 8GR5 0 JRNL AUTH S.C.CHEN,B.C.JIANG,Y.J.LU,C.H.CHANG,T.H.WU,S.W.LIN,H.W.YIN, JRNL AUTH 2 T.H.LEE,C.H.HSU JRNL TITL CHARACTERIZATION AND CRYSTAL STRUCTURES OF A JRNL TITL 2 CUBEBOL-PRODUCING SESQUITERPENE SYNTHASE FROM ANTRODIA JRNL TITL 3 CINNAMOMEA . JRNL REF J.AGRIC.FOOD CHEM. V. 71 13014 2023 JRNL REFN ESSN 1520-5118 JRNL PMID 37566786 JRNL DOI 10.1021/ACS.JAFC.3C00570 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 33.950 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 17695 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.560 REMARK 3 FREE R VALUE TEST SET COUNT : 1868 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 2.1800 - 2.1000 0.62 897 103 0.2520 0.3140 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.43 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: 0.0300 REMARK 3 OPERATOR: H,-K,-H-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 8GR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1300031067. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : TPS 05A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9998 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18357 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 7OFL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES PH 7.5, 10% 2-PROPANOL, 20% PEG REMARK 280 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 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 REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 34.11950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.88400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 34.11950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.88400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SER A 2 REMARK 465 SER A 3 REMARK 465 ALA A 4 REMARK 465 ASN A 42 REMARK 465 ILE A 43 REMARK 465 LEU A 44 REMARK 465 SER A 45 REMARK 465 ASP A 46 REMARK 465 ARG A 47 REMARK 465 LYS A 48 REMARK 465 ARG A 49 REMARK 465 ALA A 50 REMARK 465 PHE A 51 REMARK 465 PHE A 52 REMARK 465 VAL A 53 REMARK 465 THR A 54 REMARK 465 GLU A 337 REMARK 465 HIS A 338 REMARK 465 HIS A 339 REMARK 465 HIS A 340 REMARK 465 HIS A 341 REMARK 465 HIS A 342 REMARK 465 HIS A 343 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 115 110.00 -179.58 REMARK 500 ASN A 238 51.59 -96.49 REMARK 500 TRP A 280 -66.25 -98.25 REMARK 500 REMARK 500 REMARK: NULL DBREF 8GR5 A 1 343 PDB 8GR5 8GR5 1 343 SEQRES 1 A 343 MET SER SER ALA THR LYS GLN PHE THR LEU PRO ASP LEU SEQRES 2 A 343 LEU ALA MET CYS PRO PHE THR GLY SER THR ASN PRO HIS SEQRES 3 A 343 TYR ALA LYS ALA ALA ALA GLU SER SER ALA TRP VAL ASN SEQRES 4 A 343 SER TYR ASN ILE LEU SER ASP ARG LYS ARG ALA PHE PHE SEQRES 5 A 343 VAL THR GLY SER ASN GLU LEU LEU VAL SER HIS THR TYR SEQRES 6 A 343 PRO TYR ALA GLY TYR GLU GLN PHE ARG THR CYS CYS ASP SEQRES 7 A 343 PHE VAL ASN LEU LEU PHE VAL VAL ASP GLU VAL SER ASP SEQRES 8 A 343 ASP GLN ASN GLY GLN ASP ALA ARG GLN THR GLY ASN VAL SEQRES 9 A 343 TYR LEU ASN ALA MET ARG ASP PRO ALA TRP ASP ASP GLY SEQRES 10 A 343 SER ALA LEU ALA LYS MET THR LYS GLU PHE ARG ALA ARG SEQRES 11 A 343 LEU LEU ARG TYR ALA GLY PRO GLY CYS TYR ARG ARG PHE SEQRES 12 A 343 LEU LYS HIS CYS GLU ASP TYR VAL ASP ALA VAL ALA ARG SEQRES 13 A 343 GLU ALA GLU TYR ARG GLU ARG GLY TYR VAL LEU ASP MET SEQRES 14 A 343 ALA SER PHE GLU THR LEU ARG ARG GLU ASN SER ALA ILE SEQRES 15 A 343 ARG LEU CYS PHE GLY LEU PHE GLU TYR VAL LEU GLY VAL SEQRES 16 A 343 ASP LEU PRO GLU GLY VAL PHE GLU ASP PRO VAL PHE MET SEQRES 17 A 343 THR LEU TYR TRP ALA ALA ALA ASP MET VAL CYS TRP SER SEQRES 18 A 343 ASN ASP VAL TYR SER TYR ASN MET GLU GLN ALA LYS GLY SEQRES 19 A 343 HIS SER GLY ASN ASN ILE VAL THR VAL LEU MET ARG GLN SEQRES 20 A 343 LYS ASN VAL ASP LEU GLN THR ALA SER ASP LEU VAL GLY SEQRES 21 A 343 GLU HIS PHE ALA THR LEU MET ASP ARG PHE VAL THR ALA SEQRES 22 A 343 LYS GLY GLY LEU PRO SER TRP SER PRO SER VAL ASP ALA SEQRES 23 A 343 ALA VAL SER ASP TYR VAL ARG ALA MET GLU TYR TRP VAL SEQRES 24 A 343 THR GLY ASN LEU GLU TRP SER PHE GLU THR GLN ARG TYR SEQRES 25 A 343 PHE GLY VAL MET HIS ALA GLU ILE LYS TYR THR ARG LEU SEQRES 26 A 343 ILE SER LEU ARG GLU ARG GLU GLU GLU GLU LEU GLU HIS SEQRES 27 A 343 HIS HIS HIS HIS HIS HET GOL A 401 6 HET GOL A 402 6 HET GOL A 403 6 HET GOL A 404 6 HET GOL A 405 6 HET P4G A 406 11 HETNAM GOL GLYCEROL HETNAM P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 5(C3 H8 O3) FORMUL 7 P4G C8 H18 O3 FORMUL 8 HOH *166(H2 O) HELIX 1 AA1 LEU A 13 CYS A 17 5 5 HELIX 2 AA2 HIS A 26 SER A 40 1 15 HELIX 3 AA3 SER A 56 TYR A 65 1 10 HELIX 4 AA4 GLY A 69 ASP A 92 1 24 HELIX 5 AA5 ASN A 94 ASP A 111 1 18 HELIX 6 AA6 SER A 118 ALA A 135 1 18 HELIX 7 AA7 GLY A 136 GLY A 164 1 29 HELIX 8 AA8 ASP A 168 SER A 180 1 13 HELIX 9 AA9 ALA A 181 GLY A 187 1 7 HELIX 10 AB1 LEU A 188 GLY A 194 1 7 HELIX 11 AB2 PRO A 198 GLU A 203 1 6 HELIX 12 AB3 ASP A 204 LYS A 233 1 30 HELIX 13 AB4 ASN A 239 ASN A 249 1 11 HELIX 14 AB5 ASP A 251 GLY A 275 1 25 HELIX 15 AB6 SER A 281 THR A 309 1 29 HELIX 16 AB7 MET A 316 ARG A 324 1 9 HELIX 17 AB8 LEU A 328 LEU A 336 1 9 SHEET 1 AA1 2 GLN A 7 THR A 9 0 SHEET 2 AA1 2 LEU A 325 SER A 327 -1 O ILE A 326 N PHE A 8 CRYST1 68.239 59.768 85.221 90.00 110.90 90.00 C 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 0.014654 0.000000 0.005595 0.00000 SCALE2 0.000000 0.016731 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012560 0.00000