| content |
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 1 07-AUG-24 8VCA 0
JRNL AUTH M.PALAYAM
JRNL TITL STRUCTURAL INSIGHTS INTO STRIGOLACTONE CATABOLISM BY
JRNL TITL 2 CARBOXYLESTERASES REVEAL A CONSERVED ALLOSTERIC REGULATION
JRNL REF NAT COMMUN 2024
JRNL REFN ESSN 2041-1723
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
TER 2516 SER A 329
MASTER 263 0 3 10 9 0 0 6 2581 1 18 26
END |