HEADER BIOSYNTHETIC PROTEIN 14-FEB-21 7E4M TITLE CLASS I PIMARANE-TYPE DITERPENE SYNTHASES STT4548 COMPND MOL_ID: 1; COMPND 2 MOLECULE: STT4548; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES SP.; SOURCE 3 ORGANISM_TAXID: 1931; 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 3 23-OCT-24 7E4M 1 REMARK REVDAT 2 20-APR-22 7E4M 1 JRNL REVDAT 1 06-OCT-21 7E4M 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. 1.57 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 77.4 REMARK 3 NUMBER OF REFLECTIONS : 29525 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1583 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 1.6080 - 1.5700 0.04 117 3 0.3040 0.1030 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.079 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 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 : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7E4M 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_1300020001. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-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 : BL17U1 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 : 31104 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 66.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CHLORIDE, 0.1M BIS-TRIS PH REMARK 280 6.5, 1.5M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K 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 33.43500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.45400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 33.43500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.45400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 66.87000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 GLY A 13 REMARK 465 LEU A 14 REMARK 465 VAL A 15 REMARK 465 PRO A 16 REMARK 465 ARG A 17 REMARK 465 GLY A 18 REMARK 465 SER A 19 REMARK 465 HIS A 20 REMARK 465 MET A 21 REMARK 465 MET A 22 REMARK 465 THR A 23 REMARK 465 THR A 24 REMARK 465 ASP A 25 REMARK 465 ASN A 26 REMARK 465 ALA A 27 REMARK 465 ASP A 28 REMARK 465 GLN A 29 REMARK 465 ARG A 245 REMARK 465 ARG A 246 REMARK 465 GLU A 247 REMARK 465 GLN A 248 REMARK 465 ALA A 249 REMARK 465 ALA A 250 REMARK 465 PRO A 306 REMARK 465 PRO A 307 REMARK 465 LEU A 308 REMARK 465 LEU A 309 REMARK 465 ASP A 310 REMARK 465 THR A 311 REMARK 465 ALA A 312 REMARK 465 GLY A 313 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 129 45.67 -99.89 REMARK 500 LEU A 200 -21.52 77.41 REMARK 500 ARG A 214 -101.43 38.65 REMARK 500 REMARK 500 REMARK: NULL DBREF 7E4M A 1 313 PDB 7E4M 7E4M 1 313 SEQRES 1 A 313 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 313 LEU VAL PRO ARG GLY SER HIS MET MET THR THR ASP ASN SEQRES 3 A 313 ALA ASP GLN LEU PRO ASP PRO GLU ALA CYS ALA PRO VAL SEQRES 4 A 313 CYS ALA HIS ALA VAL HIS LEU ILE SER ASP LEU ARG SER SEQRES 5 A 313 TRP ASN GLN ARG TYR GLY GLY VAL VAL SER ASP VAL ARG SEQRES 6 A 313 LEU ILE GLY ILE GLY VAL PHE THR ALA PHE ILE ALA PRO SEQRES 7 A 313 TRP LEU GLY PRO GLY GLN LEU VAL LEU PRO ALA ARG THR SEQRES 8 A 313 ALA ALA TRP CYS CYS ALA LEU ASP ASP CYS ALA ASP SER SEQRES 9 A 313 LYS GLU THR SER PRO GLU GLU VAL ALA ARG LEU ILE ASP SEQRES 10 A 313 ALA CYS ARG HIS VAL LEU THR GLY GLU ASP PRO ASP THR SEQRES 11 A 313 ALA ASN PRO ILE ALA CYS ALA LEU ALA ALA VAL ARG ALA SEQRES 12 A 313 ASP VAL ALA GLU ARG ARG LEU SER ALA ALA PHE ALA HIS SEQRES 13 A 313 ALA TRP ASN ARG SER LEU ASP ARG VAL LEU SER ALA THR SEQRES 14 A 313 LEU PHE GLU CYS GLN ALA ARG HIS ASP ILE ALA ALA GLY SEQRES 15 A 313 LEU PRO GLY PRO SER ILE GLU ASP TYR LEU ALA ARG SER SEQRES 16 A 313 THR GLY SER ILE LEU VAL GLU VAL PHE LEU LEU ASN LEU SEQRES 17 A 313 CYS VAL ALA GLU ALA ARG GLN ASN ALA VAL SER GLN LEU SEQRES 18 A 313 LYS ALA LEU ALA PRO ALA LEU SER HIS ALA GLU TYR ALA SEQRES 19 A 313 VAL ARG LEU GLY ASN ASP VAL ALA SER HIS ARG ARG GLU SEQRES 20 A 313 GLN ALA ALA GLY ASP ILE ASN VAL ILE MET LEU GLY MET SEQRES 21 A 313 ALA PRO GLU GLU ALA ARG ARG ARG THR ALA ASP HIS ALA SEQRES 22 A 313 ARG ARG CYS ARG ASP GLU LEU ARG PRO PHE LEU ASP ALA SEQRES 23 A 313 ASP PRO ARG GLY CYS ALA VAL MET LEU ASP ARG ALA THR SEQRES 24 A 313 ARG LEU PHE VAL GLY ILE PRO PRO LEU LEU ASP THR ALA SEQRES 25 A 313 GLY FORMUL 2 HOH *119(H2 O) HELIX 1 AA1 ASP A 32 TYR A 57 1 26 HELIX 2 AA2 SER A 62 ALA A 77 1 16 HELIX 3 AA3 GLY A 81 ASP A 103 1 23 HELIX 4 AA4 SER A 108 THR A 124 1 17 HELIX 5 AA5 ASN A 132 GLU A 147 1 16 HELIX 6 AA6 SER A 151 ALA A 181 1 31 HELIX 7 AA7 SER A 187 THR A 196 1 10 HELIX 8 AA8 GLY A 197 ILE A 199 5 3 HELIX 9 AA9 LEU A 200 ARG A 214 1 15 HELIX 10 AB1 ASN A 216 LEU A 224 1 9 HELIX 11 AB2 LEU A 224 HIS A 244 1 21 HELIX 12 AB3 ALA A 261 ASP A 287 1 27 HELIX 13 AB4 GLY A 290 GLY A 304 1 15 SSBOND 1 CYS A 209 CYS A 291 1555 1555 2.01 CRYST1 66.870 64.908 70.583 90.00 108.75 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 0.014954 0.000000 0.005077 0.00000 SCALE2 0.000000 0.015406 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014962 0.00000