HEADER BIOSYNTHETIC PROTEIN 13-JUN-24 8ZWZ TITLE TERPENE SYNTHASES WITH FROM PARAMURICEA CLAVATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DITERPENE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARAMURICEA CLAVATA; SOURCE 3 ORGANISM_TAXID: 317549; SOURCE 4 GENE: PACLA_8A045082; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TERPENE SYNTHASES, CORAL, COMPLEX, MG, ALPHA HELIX, BIOSYNTHETIC KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.J.MAO,B.CHEN REVDAT 1 12-MAR-25 8ZWZ 0 JRNL AUTH B.CHEN,J.MAO,K.XU,L.LIU,W.LIN,Y.W.GUO,R.WU,C.WANG,B.XU JRNL TITL MINING CORAL-DERIVED TERPENE SYNTHASES AND MECHANISTIC JRNL TITL 2 STUDIES OF THE CORAL BIFLORANE SYNTHASE. JRNL REF SCI ADV V. 11 V0805 2025 JRNL REFN ESSN 2375-2548 JRNL PMID 40009671 JRNL DOI 10.1126/SCIADV.ADV0805 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 3.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 73.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 5925 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.260 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.490 REMARK 3 FREE R VALUE TEST SET COUNT : 266 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 73.8600 - 4.4100 1.00 2886 136 0.2454 0.2640 REMARK 3 2 4.4100 - 3.5000 1.00 2773 130 0.2802 0.3362 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.004 NULL REMARK 3 ANGLE : 0.690 NULL REMARK 3 CHIRALITY : 0.043 522 REMARK 3 PLANARITY : 0.005 578 REMARK 3 DIHEDRAL : 5.929 445 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 8ZWZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 18-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1300048682. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 80 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 : BL10U2 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 EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5948 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.500 REMARK 200 RESOLUTION RANGE LOW (A) : 73.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 17.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 2.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.63 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 <I/SIGMA(I)> 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M TRI-LITHIUM CITRATE 20% REMARK 280 POLYETHYLENE GLYCOL (PEG) 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.75800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.37900 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.37900 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 70.75800 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 ILE A 197 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 PHE A -4 -149.92 -143.48 REMARK 500 LEU A 41 -78.72 -61.07 REMARK 500 LYS A 191 3.49 -60.84 REMARK 500 VAL A 236 -51.11 68.70 REMARK 500 SER A 264 -144.34 54.27 REMARK 500 SER A 265 -154.61 54.37 REMARK 500 GLU A 275 -49.30 -132.96 REMARK 500 VAL A 278 -90.34 -93.22 REMARK 500 SER A 280 -78.89 -67.82 REMARK 500 TYR A 341 41.77 -76.60 REMARK 500 GLU A 343 -17.89 66.45 REMARK 500 GLU A 364 31.82 -90.77 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8ZWZ A 2 406 UNP A0A6S7HXL7_PARCT DBREF2 8ZWZ A A0A6S7HXL7 7 411 SEQADV 8ZWZ TYR A -5 UNP A0A6S7HXL EXPRESSION TAG SEQADV 8ZWZ PHE A -4 UNP A0A6S7HXL EXPRESSION TAG SEQADV 8ZWZ GLN A -3 UNP A0A6S7HXL EXPRESSION TAG SEQADV 8ZWZ GLY A -2 UNP A0A6S7HXL EXPRESSION TAG SEQADV 8ZWZ HIS A -1 UNP A0A6S7HXL EXPRESSION TAG SEQADV 8ZWZ MET A 0 UNP A0A6S7HXL EXPRESSION TAG SEQADV 8ZWZ MET A 1 UNP A0A6S7HXL EXPRESSION TAG SEQRES 1 A 412 TYR PHE GLN GLY HIS MET MET ILE HIS ALA PRO ARG ARG SEQRES 2 A 412 TRP VAL GLU ARG HIS LYS GLN VAL GLN VAL LEU PRO GLN SEQRES 3 A 412 ASN ALA VAL GLU LYS LEU ILE SER MET ASN GLU LEU ILE SEQRES 4 A 412 GLU LEU VAL ILE GLU CYS GLY LEU CYS ASP LYS THR SER SEQRES 5 A 412 ILE LYS LYS MET TYR ASP LYS ILE ASN THR TYR GLN PHE SEQRES 6 A 412 MET TRP CYS ILE VAL ASP THR ILE PRO ALA SER GLN TYR SEQRES 7 A 412 ALA GLU GLU ILE PHE LYS SER SER LEU HIS PHE LEU CYS SEQRES 8 A 412 ALA LEU PHE LEU VAL ASP ASP ALA VAL GLU SER TYR SER SEQRES 9 A 412 ALA ASN GLU MET GLN ASP LEU SER ARG SER TYR ASP ILE SEQRES 10 A 412 LEU GLU LYS GLU VAL CYS LYS THR PHE PRO ASN PHE PRO SEQRES 11 A 412 SER ILE ASN GLU MET LYS GLU SER LEU MET HIS LEU ARG SEQRES 12 A 412 ASN PRO PHE ASP ARG SER SER ILE THR PHE CYS MET GLN SEQRES 13 A 412 TYR VAL ASN LYS ILE THR ALA ILE LEU LEU GLU GLU GLY SEQRES 14 A 412 ASN THR PRO HIS HIS VAL VAL TYR ASN LEU ARG ARG ARG SEQRES 15 A 412 THR SER ASN ALA ILE SER ILE ALA PHE GLN ALA VAL LEU SEQRES 16 A 412 ILE LYS SER LYS CYS GLY SER ILE ILE THR SER HIS GLU SEQRES 17 A 412 MET LEU TRP ARG ARG VAL PHE ASP GLY LEU VAL ILE LEU SEQRES 18 A 412 PHE TYR GLN PHE GLY GLU LEU ILE SER GLY ALA THR GLU SEQRES 19 A 412 THR ALA GLN GLN HIS ILE THR VAL VAL THR GLU LEU ARG SEQRES 20 A 412 MET LEU GLY CYS LEU TYR CYS ILE VAL ILE ASN ASP LEU SEQRES 21 A 412 TYR SER TYR GLN ARG ASP LYS LEU ALA SER SER ASP ASN SEQRES 22 A 412 MET ILE LYS THR TRP LEU LEU GLU LYS THR VAL SER SER SEQRES 23 A 412 LEU SER GLU ALA THR ALA ARG CYS SER GLN ILE LEU ASP SEQRES 24 A 412 ALA ILE MET LYS TYR MET TYR GLN ARG VAL GLU GLN CYS SEQRES 25 A 412 MET GLN SER ASN PRO GLY CYS PRO GLN LEU GLU SER LEU SEQRES 26 A 412 LEU GLU THR THR ILE TYR THR THR VAL GLY TRP ILE ARG SEQRES 27 A 412 SER HIS THR THR VAL VAL PRO ARG TYR SER GLU SER GLN SEQRES 28 A 412 LEU LYS VAL ALA LEU VAL GLU VAL GLU GLU ARG GLU LEU SEQRES 29 A 412 PRO LYS TRP LEU ALA GLU LYS ASP GLU TYR GLY TRP ASN SEQRES 30 A 412 VAL VAL GLU LYS PHE VAL GLU THR LEU ASN ASP GLU LYS SEQRES 31 A 412 HIS LYS GLY ILE LEU ASP ALA LEU GLN GLY ILE ALA ASP SEQRES 32 A 412 GLY ARG ASP GLN LEU LEU LYS THR GLN HELIX 1 AA1 ARG A 6 GLU A 10 1 5 HELIX 2 AA2 PRO A 19 ILE A 27 1 9 HELIX 3 AA3 SER A 28 CYS A 39 1 12 HELIX 4 AA4 ASP A 43 ASN A 55 1 13 HELIX 5 AA5 ASN A 55 CYS A 62 1 8 HELIX 6 AA6 SER A 70 GLU A 95 1 26 HELIX 7 AA7 SER A 98 CYS A 117 1 20 HELIX 8 AA8 SER A 125 GLU A 131 1 7 HELIX 9 AA9 SER A 132 MET A 134 5 3 HELIX 10 AB1 ASN A 138 GLU A 162 1 25 HELIX 11 AB2 PRO A 166 LYS A 191 1 26 HELIX 12 AB3 HIS A 201 ASP A 210 1 10 HELIX 13 AB4 VAL A 213 SER A 224 1 12 HELIX 14 AB5 ALA A 226 GLN A 232 1 7 HELIX 15 AB6 HIS A 233 TYR A 257 1 25 HELIX 16 AB7 ASN A 267 LYS A 276 1 10 HELIX 17 AB8 SER A 279 ASN A 310 1 32 HELIX 18 AB9 CYS A 313 VAL A 337 1 25 HELIX 19 AC1 GLU A 354 ARG A 356 5 3 HELIX 20 AC2 GLU A 357 ALA A 363 1 7 HELIX 21 AC3 GLU A 367 ASN A 381 1 15 HELIX 22 AC4 ASP A 382 LYS A 384 5 3 HELIX 23 AC5 HIS A 385 GLN A 393 1 9 HELIX 24 AC6 ASP A 400 THR A 405 1 6 SHEET 1 AA1 2 MET A 0 PRO A 5 0 SHEET 2 AA1 2 VAL A 348 VAL A 353 1 O ALA A 349 N MET A 0 CISPEP 1 PHE A 120 PRO A 121 0 1.24 CRYST1 85.284 85.284 106.137 90.00 90.00 120.00 P 32 2 1 6 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 0.011726 0.006770 0.000000 0.00000 SCALE2 0.000000 0.013540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009422 0.00000