HEADER HYDROLASE 13-DEC-23 8VCA TITLE CRYSTAL STRUCTURE OF PLANT CARBOXYLESTERASE 15 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBOXYLESTERASE 15; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ATCXE15,STRIGOLACTONES HYDROLASE CXE15; COMPND 5 EC: 3.1.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: CXE15, AT5G06570, F15M7.10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS CARBOXYLESTERASE 15, CXE15, STRIGOLACTONE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.PALAYAM,N.SHABEK REVDAT 2 14-AUG-24 8VCA 1 JRNL REVDAT 1 07-AUG-24 8VCA 0 JRNL AUTH M.PALAYAM,L.YAN,U.NAGALAKSHMI,A.K.GILIO,D.CORNU,F.D.BOYER, JRNL AUTH 2 S.P.DINESH-KUMAR,N.SHABEK JRNL TITL STRUCTURAL INSIGHTS INTO STRIGOLACTONE CATABOLISM BY JRNL TITL 2 CARBOXYLESTERASES REVEAL A CONSERVED CONFORMATIONAL JRNL TITL 3 REGULATION. JRNL REF NAT COMMUN V. 15 6500 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39090154 JRNL DOI 10.1038/S41467-024-50928-3 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 19196 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1920 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 48.0400 - 5.5500 1.00 1351 151 0.1898 0.2021 REMARK 3 2 5.5400 - 4.4000 1.00 1279 142 0.1677 0.2019 REMARK 3 3 4.4000 - 3.8500 1.00 1258 139 0.1652 0.2020 REMARK 3 4 3.8500 - 3.4900 1.00 1237 137 0.1826 0.2227 REMARK 3 5 3.4900 - 3.2400 1.00 1234 138 0.2113 0.2586 REMARK 3 6 3.2400 - 3.0500 1.00 1226 137 0.2168 0.2583 REMARK 3 7 3.0500 - 2.9000 1.00 1220 134 0.2261 0.2849 REMARK 3 8 2.9000 - 2.7700 1.00 1219 136 0.2304 0.2652 REMARK 3 9 2.7700 - 2.6700 1.00 1221 136 0.2402 0.2776 REMARK 3 10 2.6700 - 2.5700 1.00 1205 134 0.2331 0.2864 REMARK 3 11 2.5700 - 2.4900 1.00 1213 135 0.2221 0.2657 REMARK 3 12 2.4900 - 2.4200 1.00 1213 135 0.2255 0.2639 REMARK 3 13 2.4200 - 2.3600 1.00 1204 133 0.2299 0.2959 REMARK 3 14 2.3600 - 2.3000 1.00 1196 133 0.2510 0.3794 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.81 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 : 0.002 2612 REMARK 3 ANGLE : 0.524 3535 REMARK 3 CHIRALITY : 0.039 379 REMARK 3 PLANARITY : 0.004 461 REMARK 3 DIHEDRAL : 7.401 356 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 8VCA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1000279906. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7-7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19200 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 48.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 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 1.20.1-4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM/POTASSIUM PHOSPHATE PH7.5, REMARK 280 0.1M HEPES PH7.5, 22.5% /V PEG SMEAR MEDIUM, 10% GLYCEROL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 58.58850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.95750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.95750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.29425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.95750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.95750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 87.88275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.95750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.95750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.29425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.95750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.95750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 87.88275 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 58.58850 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 GLY A 2 REMARK 465 SER A 3 REMARK 465 LEU A 4 REMARK 465 GLY A 5 REMARK 465 GLU A 6 REMARK 465 GLU A 7 REMARK 465 ILE A 39 REMARK 465 PRO A 40 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 PHE A 41 CG CD1 CD2 CE1 CE2 CZ 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 PRO A 126 38.77 -91.63 REMARK 500 SER A 169 -112.45 54.78 REMARK 500 THR A 251 -57.40 -143.87 REMARK 500 THR A 254 49.79 -80.57 REMARK 500 LYS A 286 55.97 -103.06 REMARK 500 SER A 310 -0.63 68.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 8VCA A 1 329 UNP Q9FG13 CXE15_ARATH 1 329 SEQRES 1 A 329 MET GLY SER LEU GLY GLU GLU PRO GLN VAL ALA GLU ASP SEQRES 2 A 329 CYS MET GLY LEU LEU GLN LEU LEU SER ASN GLY THR VAL SEQRES 3 A 329 LEU ARG SER GLU SER ILE ASP LEU ILE THR GLN GLN ILE SEQRES 4 A 329 PRO PHE LYS ASN ASN GLN THR VAL LEU PHE LYS ASP SER SEQRES 5 A 329 ILE TYR HIS LYS PRO ASN ASN LEU HIS LEU ARG LEU TYR SEQRES 6 A 329 LYS PRO ILE SER ALA SER ASN ARG THR ALA LEU PRO VAL SEQRES 7 A 329 VAL VAL PHE PHE HIS GLY GLY GLY PHE CYS PHE GLY SER SEQRES 8 A 329 ARG SER TRP PRO HIS PHE HIS ASN PHE CYS LEU THR LEU SEQRES 9 A 329 ALA SER SER LEU ASN ALA LEU VAL VAL SER PRO ASP TYR SEQRES 10 A 329 ARG LEU ALA PRO GLU HIS ARG LEU PRO ALA ALA PHE GLU SEQRES 11 A 329 ASP ALA GLU ALA VAL LEU THR TRP LEU TRP ASP GLN ALA SEQRES 12 A 329 VAL SER ASP GLY VAL ASN HIS TRP PHE GLU ASP GLY THR SEQRES 13 A 329 ASP VAL ASP PHE ASP ARG VAL PHE VAL VAL GLY ASP SER SEQRES 14 A 329 SER GLY GLY ASN ILE ALA HIS GLN LEU ALA VAL ARG PHE SEQRES 15 A 329 GLY SER GLY SER ILE GLU LEU THR PRO VAL ARG VAL ARG SEQRES 16 A 329 GLY TYR VAL LEU MET GLY PRO PHE PHE GLY GLY GLU GLU SEQRES 17 A 329 ARG THR ASN SER GLU ASN GLY PRO SER GLU ALA LEU LEU SEQRES 18 A 329 SER LEU ASP LEU LEU ASP LYS PHE TRP ARG LEU SER LEU SEQRES 19 A 329 PRO ASN GLY ALA THR ARG ASP HIS HIS MET ALA ASN PRO SEQRES 20 A 329 PHE GLY PRO THR SER PRO THR LEU GLU SER ILE SER LEU SEQRES 21 A 329 GLU PRO MET LEU VAL ILE VAL GLY GLY SER GLU LEU LEU SEQRES 22 A 329 ARG ASP ARG ALA LYS GLU TYR ALA TYR LYS LEU LYS LYS SEQRES 23 A 329 MET GLY GLY LYS ARG VAL ASP TYR ILE GLU PHE GLU ASN SEQRES 24 A 329 LYS GLU HIS GLY PHE TYR SER ASN TYR PRO SER SER GLU SEQRES 25 A 329 ALA ALA GLU GLN VAL LEU ARG ILE ILE GLY ASP PHE MET SEQRES 26 A 329 ASN ASN LEU SER HET GOL A 401 6 HET GOL A 402 6 HET GOL A 403 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 HOH *48(H2 O) HELIX 1 AA1 GLN A 9 SER A 22 1 14 HELIX 2 AA2 ILE A 68 ASN A 72 1 5 HELIX 3 AA3 TRP A 94 ASN A 109 1 16 HELIX 4 AA4 PRO A 126 SER A 145 1 20 HELIX 5 AA5 ASP A 146 TRP A 151 5 6 HELIX 6 AA6 SER A 169 SER A 184 1 16 HELIX 7 AA7 SER A 222 LEU A 234 1 13 HELIX 8 AA8 LEU A 273 LYS A 286 1 14 HELIX 9 AA9 GLY A 303 TYR A 308 1 6 HELIX 10 AB1 SER A 311 LEU A 328 1 18 SHEET 1 AA1 9 SER A 31 THR A 36 0 SHEET 2 AA1 9 ASN A 44 HIS A 55 -1 O PHE A 49 N SER A 31 SHEET 3 AA1 9 LEU A 60 PRO A 67 -1 O LYS A 66 N LEU A 48 SHEET 4 AA1 9 LEU A 111 PRO A 115 -1 O SER A 114 N ARG A 63 SHEET 5 AA1 9 LEU A 76 PHE A 82 1 N VAL A 79 O VAL A 113 SHEET 6 AA1 9 VAL A 158 ASP A 168 1 O VAL A 166 N VAL A 80 SHEET 7 AA1 9 VAL A 194 MET A 200 1 O VAL A 198 N GLY A 167 SHEET 8 AA1 9 MET A 263 GLY A 268 1 O LEU A 264 N LEU A 199 SHEET 9 AA1 9 VAL A 292 PHE A 297 1 O ILE A 295 N VAL A 265 CISPEP 1 ALA A 120 PRO A 121 0 1.37 CISPEP 2 LEU A 125 PRO A 126 0 5.37 CISPEP 3 THR A 190 PRO A 191 0 7.77 CRYST1 83.915 83.915 117.177 90.00 90.00 90.00 P 41 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 0.011917 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011917 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008534 0.00000