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HEADER HYDROLASE 04-JUN-24 8ZR6
TITLE ARABIDOPSIS CARBOXYL ESTERASE CXE15 E271Q MUTANT
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: STRIGOLACTONES HYDROLASE CXE15;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: CARBOXYLESTERASE 15,ATCXE15;
COMPND 5 EC: 3.1.1.-;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: 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-GOLD(DE3)PLYSS AG';
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768
KEYWDS STRIGOLACTONE, CATABOLIC ENZYME, CXE15, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.T.AROLD,U.F.S.HAMEED
REVDAT 1 04-JUN-25 8ZR6 0
JRNL AUTH S.T.AROLD,U.F.S.HAMEED
JRNL TITL ARABIDOPSIS CARBOXYL ESTERASE CXE15 E271Q MUTANT
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 2.55 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC V5.7
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.45
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 14462
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.204
REMARK 3 R VALUE (WORKING SET) : 0.202
REMARK 3 FREE R VALUE : 0.236
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.200
REMARK 3 FREE R VALUE TEST SET COUNT : 1046
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2529
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 6
REMARK 3 SOLVENT ATOMS : 19
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.28
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.35000
REMARK 3 B22 (A**2) : 0.35000
REMARK 3 B33 (A**2) : -0.69000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.471
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.269
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.196
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.336
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
REMARK 3 BOND LENGTH (A) : NULL ; NULL
REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL
REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL
REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
REMARK 3
REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL
REMARK 3
REMARK 3 NON-BONDED CONTACT RESTRAINTS.
REMARK 3 SINGLE TORSION (A) : NULL ; NULL
REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL
REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL
REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL
REMARK 3
REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL
REMARK 3 PLANAR (DEGREES) : NULL ; NULL
REMARK 3 STAGGERED (DEGREES) : NULL ; NULL
REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN
REMARK 3 THE INPUT
REMARK 4
REMARK 4 8ZR6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUN-24.
REMARK 100 THE DEPOSITION ID IS D_1300048394.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-OCT-22
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 : SOLEIL
REMARK 200 BEAMLINE : PROXIMA 1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.987
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 : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14468
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550
REMARK 200 RESOLUTION RANGE LOW (A) : 48.450
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 20.00
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 9.0300
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5
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 : 1.810
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: BALBES
REMARK 200 STARTING MODEL: AF-Q9FG13-F1
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 58.01
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.26 M SODIUM PHOSPHATE MONOBASIC
REMARK 280 MONOHYDRATE, 0.14 M POTASSIUM PHOSPHATE DIBASIC, PH 5.6, VAPOR
REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K
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 59.12650
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.13700
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.13700
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.56325
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.13700
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.13700
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 88.68975
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.13700
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.13700
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.56325
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.13700
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.13700
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 88.68975
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 59.12650
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: 6520 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 25140 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 118.25300
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 GLN A 37 -168.19 -102.09
REMARK 500 ARG A 162 74.82 -119.53
REMARK 500 SER A 169 -120.76 59.78
REMARK 500 PRO A 253 155.55 -47.92
REMARK 500 LEU A 255 -18.50 78.77
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 ARG A 92 0.17 SIDE CHAIN
REMARK 500 ARG A 118 0.10 SIDE CHAIN
REMARK 500 ARG A 124 0.24 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
DBREF 8ZR6 A 9 329 UNP Q9FG13 CXE15_ARATH 9 329
SEQADV 8ZR6 GLN A 271 UNP Q9FG13 GLU 271 ENGINEERED MUTATION
SEQRES 1 A 321 GLN VAL ALA GLU ASP CYS MET GLY LEU LEU GLN LEU LEU
SEQRES 2 A 321 SER ASN GLY THR VAL LEU ARG SER GLU SER ILE ASP LEU
SEQRES 3 A 321 ILE THR GLN GLN ILE PRO PHE LYS ASN ASN GLN THR VAL
SEQRES 4 A 321 LEU PHE LYS ASP SER ILE TYR HIS LYS PRO ASN ASN LEU
SEQRES 5 A 321 HIS LEU ARG LEU TYR LYS PRO ILE SER ALA SER ASN ARG
SEQRES 6 A 321 THR ALA LEU PRO VAL VAL VAL PHE PHE HIS GLY GLY GLY
SEQRES 7 A 321 PHE CYS PHE GLY SER ARG SER TRP PRO HIS PHE HIS ASN
SEQRES 8 A 321 PHE CYS LEU THR LEU ALA SER SER LEU ASN ALA LEU VAL
SEQRES 9 A 321 VAL SER PRO ASP TYR ARG LEU ALA PRO GLU HIS ARG LEU
SEQRES 10 A 321 PRO ALA ALA PHE GLU ASP ALA GLU ALA VAL LEU THR TRP
SEQRES 11 A 321 LEU TRP ASP GLN ALA VAL SER ASP GLY VAL ASN HIS TRP
SEQRES 12 A 321 PHE GLU ASP GLY THR ASP VAL ASP PHE ASP ARG VAL PHE
SEQRES 13 A 321 VAL VAL GLY ASP SER SER GLY GLY ASN ILE ALA HIS GLN
SEQRES 14 A 321 LEU ALA VAL ARG PHE GLY SER GLY SER ILE GLU LEU THR
SEQRES 15 A 321 PRO VAL ARG VAL ARG GLY TYR VAL LEU MET GLY PRO PHE
SEQRES 16 A 321 PHE GLY GLY GLU GLU ARG THR ASN SER GLU ASN GLY PRO
SEQRES 17 A 321 SER GLU ALA LEU LEU SER LEU ASP LEU LEU ASP LYS PHE
SEQRES 18 A 321 TRP ARG LEU SER LEU PRO ASN GLY ALA THR ARG ASP HIS
SEQRES 19 A 321 HIS MET ALA ASN PRO PHE GLY PRO THR SER PRO THR LEU
SEQRES 20 A 321 GLU SER ILE SER LEU GLU PRO MET LEU VAL ILE VAL GLY
SEQRES 21 A 321 GLY SER GLN LEU LEU ARG ASP ARG ALA LYS GLU TYR ALA
SEQRES 22 A 321 TYR LYS LEU LYS LYS MET GLY GLY LYS ARG VAL ASP TYR
SEQRES 23 A 321 ILE GLU PHE GLU ASN LYS GLU HIS GLY PHE TYR SER ASN
SEQRES 24 A 321 TYR PRO SER SER GLU ALA ALA GLU GLN VAL LEU ARG ILE
SEQRES 25 A 321 ILE GLY ASP PHE MET ASN ASN LEU SER
HET GOL A 401 6
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 GOL C3 H8 O3
FORMUL 3 HOH *19(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 THR A 210 GLY A 215 1 6
HELIX 8 AA8 SER A 222 LEU A 234 1 13
HELIX 9 AA9 LEU A 273 LYS A 286 1 14
HELIX 10 AB1 GLY A 303 TYR A 308 1 6
HELIX 11 AB2 SER A 311 SER A 329 1 19
SHEET 1 AA1 8 VAL A 47 HIS A 55 0
SHEET 2 AA1 8 LEU A 60 PRO A 67 -1 O LYS A 66 N LEU A 48
SHEET 3 AA1 8 LEU A 111 PRO A 115 -1 O SER A 114 N ARG A 63
SHEET 4 AA1 8 LEU A 76 PHE A 82 1 N VAL A 79 O VAL A 113
SHEET 5 AA1 8 VAL A 158 ASP A 168 1 O PHE A 164 N VAL A 80
SHEET 6 AA1 8 VAL A 194 MET A 200 1 O VAL A 198 N GLY A 167
SHEET 7 AA1 8 MET A 263 GLY A 268 1 O LEU A 264 N LEU A 199
SHEET 8 AA1 8 VAL A 292 PHE A 297 1 O ASP A 293 N VAL A 265
SSBOND 1 CYS A 14 CYS A 14 1555 7556 2.37
CISPEP 1 ALA A 120 PRO A 121 0 12.07
CISPEP 2 LEU A 125 PRO A 126 0 28.10
CISPEP 3 THR A 190 PRO A 191 0 9.96
CRYST1 84.274 84.274 118.253 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 0.011866 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011866 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008456 0.00000
TER 2530 SER A 329
MASTER 254 0 1 11 8 0 0 6 2554 1 6 25
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