HEADER BIOSYNTHETIC PROTEIN 10-SEP-21 7S5L TITLE CEMBRENE A SYNTHASE FROM ELEUTHEROBIA RUBRA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CEMBRENE A SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ELEUTHEROBIA RUBRA; SOURCE 3 ORGANISM_TAXID: 2508183; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TERPENE, DITERPENE SYNTHASE, OCTOCORAL, CEMBRENE A, ELEUTHEROBIA KEYWDS 2 RUBRA, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.Y.-T.CHEN,B.S.MOORE REVDAT 2 22-MAY-24 7S5L 1 REMARK REVDAT 1 08-JUN-22 7S5L 0 JRNL AUTH I.BURKHARDT,T.DE ROND,P.Y.CHEN,B.S.MOORE JRNL TITL ANCIENT PLANT-LIKE TERPENE BIOSYNTHESIS IN CORALS. JRNL REF NAT.CHEM.BIOL. V. 18 664 2022 JRNL REFN ESSN 1552-4469 JRNL PMID 35606558 JRNL DOI 10.1038/S41589-022-01026-2 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18_3845 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 52284 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2619 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 37.9700 - 4.2100 0.98 2712 143 0.1617 0.1742 REMARK 3 2 4.2100 - 3.3400 0.96 2614 140 0.1605 0.1792 REMARK 3 3 3.3400 - 2.9200 0.99 2708 137 0.1823 0.1891 REMARK 3 4 2.9200 - 2.6500 0.95 2590 141 0.1730 0.2103 REMARK 3 5 2.6500 - 2.4600 0.98 2650 139 0.1554 0.2001 REMARK 3 6 2.4600 - 2.3200 0.97 2650 138 0.1513 0.1866 REMARK 3 7 2.3200 - 2.2000 0.98 2668 137 0.1501 0.1875 REMARK 3 8 2.2000 - 2.1100 0.93 2554 134 0.1506 0.1793 REMARK 3 9 2.1100 - 2.0200 0.97 2616 141 0.1455 0.2165 REMARK 3 10 2.0200 - 1.9500 0.97 2629 137 0.1476 0.1914 REMARK 3 11 1.9500 - 1.8900 0.97 2637 142 0.1560 0.1898 REMARK 3 12 1.8900 - 1.8400 0.97 2633 134 0.1452 0.2106 REMARK 3 13 1.8400 - 1.7900 0.93 2525 140 0.1406 0.2143 REMARK 3 14 1.7900 - 1.7500 0.96 2593 139 0.1448 0.2190 REMARK 3 15 1.7500 - 1.7100 0.96 2622 134 0.1492 0.2031 REMARK 3 16 1.7100 - 1.6700 0.96 2612 138 0.1607 0.2073 REMARK 3 17 1.6700 - 1.6400 0.96 2604 137 0.1758 0.2506 REMARK 3 18 1.6400 - 1.6100 0.96 2603 131 0.1999 0.2639 REMARK 3 19 1.6100 - 1.5800 0.91 2445 137 0.2384 0.2702 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) : 0.184 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.661 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.35 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 : 0.005 3239 REMARK 3 ANGLE : 0.709 4384 REMARK 3 CHIRALITY : 0.044 490 REMARK 3 PLANARITY : 0.004 546 REMARK 3 DIHEDRAL : 21.275 1206 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 7S5L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000259626. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-20 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 : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52295 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 37.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 14.7000 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) : 1.67 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5, 28% (W/V) PEG 3350, REMARK 280 0.28 M MGCL2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 300K 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 42.84450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.82450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.84450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 50.82450 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CL CL A 401 LIES ON A SPECIAL POSITION. 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 THR A 196 REMARK 465 GLY A 197 REMARK 465 CYS A 198 REMARK 465 GLU A 199 REMARK 465 ILE A 200 REMARK 465 ASP A 382 REMARK 465 PRO A 383 REMARK 465 GLN A 384 REMARK 465 LYS A 385 REMARK 465 LYS A 386 REMARK 465 ASN A 387 REMARK 465 ILE A 388 REMARK 465 ASP A 392 REMARK 465 GLU A 393 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 MET A 389 CG SD CE 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 122 129.75 -39.78 REMARK 500 ASN A 124 75.48 -105.32 REMARK 500 ASP A 266 -165.66 -123.00 REMARK 500 REMARK 500 REMARK: NULL DBREF 7S5L A 1 393 PDB 7S5L 7S5L 1 393 SEQRES 1 A 393 MET SER GLY LYS ILE VAL ARG ALA PRO SER ASN TRP THR SEQRES 2 A 393 THR PRO HIS LYS LYS MET LEU LYS GLU ASP GLU ASP GLN SEQRES 3 A 393 GLU LEU ILE ALA PHE ASP LYS LEU LEU SER TRP VAL SER SEQRES 4 A 393 GLU THR GLY VAL GLY THR GLU GLU GLN ALA LYS ILE VAL SEQRES 5 A 393 PHE LYS LYS ILE ASN ALA TYR PHE TYR LEU ARG CYS LEU SEQRES 6 A 393 TYR PRO VAL LEU PRO ARG ASP PRO LYS SER MET LYS ILE SEQRES 7 A 393 PHE GLN LEU ASN LEU HIS PHE LEU ILE LEU GLY TYR ILE SEQRES 8 A 393 ILE ASP ASP ALA ILE GLU LYS TYR ASN GLU ASN GLU MET SEQRES 9 A 393 LYS GLU LEU ILE ALA GLY TYR ASN LEU LEU GLN SER GLN SEQRES 10 A 393 VAL SER GLU THR PHE PRO ASN PHE PRO SER ILE PHE GLU SEQRES 11 A 393 MET LYS GLN LEU LEU GLY ASN MET LYS ASN ASP PHE SER SEQRES 12 A 393 LYS SER ALA ILE THR THR MET PHE ASP TYR VAL ASN LYS SEQRES 13 A 393 THR THR LEU ILE LEU LEU GLU GLU GLY GLU ILE ALA GLU SEQRES 14 A 393 HIS ASN VAL LEU ASN TYR ARG LYS ARG LEU SER ASN ALA SEQRES 15 A 393 VAL ALA VAL TYR PHE ASP ALA LEU LEU SER LYS THR LYS SEQRES 16 A 393 THR GLY CYS GLU ILE SER ASP GLY ALA MET LEU TRP ARG SEQRES 17 A 393 ARG CYS PHE ASP ALA LEU ALA ILE ALA VAL TYR MET LEU SEQRES 18 A 393 THR GLU VAL PHE SER LYS THR LEU VAL LYS ASN HIS THR SEQRES 19 A 393 LEU PRO VAL SER GLU PHE TYR LYS PHE TYR LEU LEU SER SEQRES 20 A 393 ILE LEU PHE CYS VAL VAL ILE ASN ASP LEU HIS SER TYR SEQRES 21 A 393 GLU ARG ASP LYS LEU ASP ASP THR ASP SER VAL VAL LYS SEQRES 22 A 393 VAL TRP PHE LYS GLU GLY SER VAL ALA ASN MET GLU ALA SEQRES 23 A 393 ALA THR SER LYS VAL SER LYS ILE LEU ASP ALA ILE ILE SEQRES 24 A 393 GLN GLN MET TYR LEU PHE VAL GLU GLU GLY LYS ALA ARG SEQRES 25 A 393 HIS PRO GLU LEU SER GLU TRP PHE GLU ARG ILE ALA TYR SEQRES 26 A 393 MET THR VAL GLY TRP ILE TYR ILE HIS LYS THR VAL VAL SEQRES 27 A 393 PRO ARG TYR VAL SER SER PRO PHE GLN ILE GLU VAL VAL SEQRES 28 A 393 GLU ILE HIS GLU ASN MET ILE SER ASN TRP LEU LEU LYS SEQRES 29 A 393 LYS ASP ALA TYR GLY GLN ARG VAL VAL GLN GLN PHE LEU SEQRES 30 A 393 LYS ASN LEU ASN ASP PRO GLN LYS LYS ASN ILE MET LEU SEQRES 31 A 393 TYR ASP GLU HET CL A 401 1 HET EDO A 402 4 HET EDO A 403 4 HET EDO A 404 4 HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 CL CL 1- FORMUL 3 EDO 3(C2 H6 O2) FORMUL 6 HOH *187(H2 O) HELIX 1 AA1 THR A 13 LEU A 20 1 8 HELIX 2 AA2 ASP A 25 ALA A 30 1 6 HELIX 3 AA3 ALA A 30 GLY A 42 1 13 HELIX 4 AA4 THR A 45 ASN A 57 1 13 HELIX 5 AA5 ASN A 57 TYR A 66 1 10 HELIX 6 AA6 ASP A 72 GLU A 97 1 26 HELIX 7 AA7 ASN A 100 GLU A 120 1 21 HELIX 8 AA8 SER A 127 LEU A 135 1 9 HELIX 9 AA9 ASP A 141 GLU A 163 1 23 HELIX 10 AB1 GLU A 164 GLU A 166 5 3 HELIX 11 AB2 ALA A 168 LYS A 195 1 28 HELIX 12 AB3 ASP A 202 CYS A 210 1 9 HELIX 13 AB4 LEU A 214 SER A 226 1 13 HELIX 14 AB5 PRO A 236 SER A 259 1 24 HELIX 15 AB6 SER A 259 LYS A 264 1 6 HELIX 16 AB7 SER A 270 GLU A 278 1 9 HELIX 17 AB8 ASN A 283 HIS A 313 1 31 HELIX 18 AB9 LEU A 316 THR A 336 1 21 HELIX 19 AC1 VAL A 338 SER A 343 1 6 HELIX 20 AC2 HIS A 354 ASN A 356 5 3 HELIX 21 AC3 MET A 357 LYS A 364 1 8 HELIX 22 AC4 ASP A 366 LYS A 378 1 13 HELIX 23 AC5 ASN A 379 ASN A 381 5 3 SHEET 1 AA1 2 ILE A 5 PRO A 9 0 SHEET 2 AA1 2 GLU A 349 ILE A 353 1 O GLU A 349 N VAL A 6 CISPEP 1 PHE A 122 PRO A 123 0 2.41 CRYST1 85.689 101.649 46.342 90.00 90.60 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 0.011670 0.000000 0.000121 0.00000 SCALE2 0.000000 0.009838 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021580 0.00000