HEADER BIOSYNTHETIC PROTEIN 14-FEB-21 7E4O TITLE CLASS I PIMARANE-TYPE DITERPENE SYNTHASES FROM ACTINOMYCETES COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAT1646; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALINISPORA; SOURCE 3 ORGANISM_TAXID: 168694; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CLASS I DITERPENE SYNTHASES, PIMARANE-TYPE DITERPENOIDS, BIOSYNTHETIC KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.H.YU,B.Y.XING,M.MA REVDAT 4 29-NOV-23 7E4O 1 REMARK REVDAT 3 20-APR-22 7E4O 1 JRNL REVDAT 2 23-MAR-22 7E4O 1 SOURCE REVDAT 1 06-OCT-21 7E4O 0 JRNL AUTH B.XING,J.YU,C.CHI,X.MA,Q.XU,A.LI,Y.GE,Z.WANG,T.LIU,H.JIA, JRNL AUTH 2 F.YIN,J.GUO,L.HUANG,D.YANG,M.MA JRNL TITL FUNCTIONAL CHARACTERIZATION AND STRUCTURAL BASES OF TWO JRNL TITL 2 CLASS I DITERPENE SYNTHASES IN PIMARANE-TYPE DITERPENE JRNL TITL 3 BIOSYNTHESIS JRNL REF COMMUN CHEM V. 4 140 2021 JRNL REFN ESSN 2399-3669 JRNL DOI 10.1038/S42004-021-00578-Z REMARK 2 REMARK 2 RESOLUTION. 2.50 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 10145 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1016 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 27.3600 - 4.7800 0.99 1405 156 0.1932 0.2202 REMARK 3 2 4.7800 - 3.8000 1.00 1328 148 0.2062 0.2507 REMARK 3 3 3.8000 - 3.3200 1.00 1311 145 0.2245 0.3363 REMARK 3 4 3.3200 - 3.0200 1.00 1302 145 0.2685 0.3233 REMARK 3 5 3.0200 - 2.8000 0.99 1276 142 0.2771 0.3386 REMARK 3 6 2.8000 - 2.6400 0.98 1258 142 0.2734 0.3301 REMARK 3 7 2.6300 - 2.5000 0.97 1249 138 0.2865 0.3697 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.44 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 : 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -14.7481 -34.1284 -8.3305 REMARK 3 T TENSOR REMARK 3 T11: 0.5823 T22: 0.4825 REMARK 3 T33: 0.5230 T12: 0.0465 REMARK 3 T13: 0.0639 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 1.6928 L22: 0.6516 REMARK 3 L33: 1.1777 L12: -0.7568 REMARK 3 L13: 0.0339 L23: -0.0367 REMARK 3 S TENSOR REMARK 3 S11: 0.1604 S12: 0.1601 S13: 0.0720 REMARK 3 S21: -0.2568 S22: -0.1711 S23: -0.3317 REMARK 3 S31: -0.0682 S32: -0.1340 S33: 0.0002 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 7E4O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1300020040. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10288 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 25.80 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 45.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 25.90 REMARK 200 R MERGE FOR SHELL (I) : 0.51500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 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: 7E4N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% V/V TACSIMATE TM PH 7.0, 0.1M REMARK 280 HEPES PH 7.0, 2% W/V POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 44.50650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.50650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.31700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.50650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.50650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.31700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.50650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.50650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.31700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.50650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.50650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.31700 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -89.01300 REMARK 350 BIOMT3 2 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 ARG A 169 REMARK 465 ARG A 233 REMARK 465 ASP A 292 REMARK 465 TYR A 293 REMARK 465 TRP A 294 REMARK 465 GLY A 295 REMARK 465 ASP A 296 REMARK 465 SER A 297 REMARK 465 GLU A 298 REMARK 465 ARG A 299 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 ASN A 2 -63.84 -95.90 REMARK 500 ARG A 93 -52.00 -146.32 REMARK 500 THR A 96 -45.08 -130.89 REMARK 500 ASP A 98 -8.15 -57.83 REMARK 500 HIS A 166 52.14 -98.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 356 DISTANCE = 5.90 ANGSTROMS DBREF 7E4O A 1 299 PDB 7E4O 7E4O 1 299 SEQRES 1 A 299 SER ASN ALA MET VAL PRO THR HIS HIS ALA GLY ASN GLY SEQRES 2 A 299 PHE ALA VAL ALA SER GLU GLN GLY ARG ILE CYS ALA LEU SEQRES 3 A 299 ALA ALA ARG GLY GLN ARG ASP LEU ARG GLN CYS VAL ARG SEQRES 4 A 299 ALA TYR PRO SER LEU PHE PRO ASN PRO PRO VAL ASP ASP SEQRES 5 A 299 THR MET LEU SER ALA LEU ALA LEU SER THR ALA PHE ILE SEQRES 6 A 299 ALA PRO TRP CYS SER ALA GLU GLN LEU ARG VAL ALA ASN SEQRES 7 A 299 ARG ALA SER LEU TRP VAL THR ALA GLU ASP TRP GLN VAL SEQRES 8 A 299 ASP ARG VAL ALA THR SER ASP ASP ALA VAL ARG SER ILE SEQRES 9 A 299 VAL SER ALA CYS GLN ALA VAL ALA ASP GLY ALA ALA PRO SEQRES 10 A 299 ASP VAL ASP CYS ALA LEU GLY GLN LEU LEU ALA GLU ILE SEQRES 11 A 299 ARG ASP GLU LEU ALA THR GLY ALA GLY PHE THR GLU TRP SEQRES 12 A 299 GLN PRO VAL TRP ARG GLU GLU VAL ARG ARG MET LEU THR SEQRES 13 A 299 ALA ASP ILE ARG GLU TRP GLU TRP ARG HIS SER ALA ARG SEQRES 14 A 299 PRO PRO SER PHE ALA GLU TYR LEU ASP ASN ALA ASP ASN SEQRES 15 A 299 TYR GLY ALA SER PHE VAL ASN VAL SER HIS TRP ILE VAL SEQRES 16 A 299 THR GLY ASP ALA GLN THR ARG SER HIS LEU PRO GLU LEU SEQRES 17 A 299 ILE ALA ALA SER ARG GLU VAL GLN ARG ILE LEU ARG LEU SEQRES 18 A 299 SER ASN ASP LEU ALA SER TYR GLU ARG ASP ILE ARG SER SEQRES 19 A 299 GLY ASP LEU ASN ALA LEU LEU LEU VAL ASP ARG GLU GLU SEQRES 20 A 299 VAL SER ARG GLN LEU ARG ASP ARG ILE ARG ALA CYS GLN SEQRES 21 A 299 ASP HIS LEU HIS ALA LEU GLU VAL THR CYS PRO ARG GLU SEQRES 22 A 299 ALA LEU TYR LEU ALA ARG GLU ALA GLY PHE THR THR GLY SEQRES 23 A 299 PHE TYR HIS GLY ALA ASP TYR TRP GLY ASP SER GLU ARG FORMUL 2 HOH *56(H2 O) HELIX 1 AA1 HIS A 9 TYR A 41 1 33 HELIX 2 AA2 ASP A 51 ALA A 66 1 16 HELIX 3 AA3 LEU A 74 ASP A 92 1 19 HELIX 4 AA4 SER A 97 ASP A 113 1 17 HELIX 5 AA5 CYS A 121 ALA A 138 1 18 HELIX 6 AA6 TRP A 143 HIS A 166 1 24 HELIX 7 AA7 SER A 172 ASN A 179 1 8 HELIX 8 AA8 ALA A 180 TYR A 183 5 4 HELIX 9 AA9 GLY A 184 GLY A 197 1 14 HELIX 10 AB1 ASP A 198 ALA A 226 1 29 HELIX 11 AB2 SER A 227 ILE A 232 1 6 HELIX 12 AB3 ASP A 244 GLU A 267 1 24 HELIX 13 AB4 CYS A 270 GLY A 290 1 21 CRYST1 89.013 89.013 70.634 90.00 90.00 90.00 P 42 21 2 8 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 0.011234 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014157 0.00000