HEADER SIGNALING PROTEIN 07-JUL-22 8DLC TITLE CRYSTAL STRUCTURE OF CHALCONE-ISOMERASE LIKE PROTEIN FROM VITIS TITLE 2 VINIFERA (VVCHIL) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHALCONE-FLAVONONE ISOMERASE FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VITIS VINIFERA; SOURCE 3 ORGANISM_COMMON: WINE GRAPE; SOURCE 4 ORGANISM_TAXID: 29760; SOURCE 5 GENE: CHI3_0, CK203_016634; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CHALCONE ISOMERASE-FOLD, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.WOLF SAXON,C.MOORMAN,A.CASTRO,A.RUIZ,J.P.MALLARI,J.R.BURKE REVDAT 3 22-NOV-23 8DLC 1 JRNL REVDAT 2 25-OCT-23 8DLC 1 REMARK REVDAT 1 10-MAY-23 8DLC 0 JRNL AUTH E.R.WOLF-SAXON,C.C.MOORMAN,A.CASTRO,A.RUIZ-RIVERA, JRNL AUTH 2 J.P.MALLARI,J.R.BURKE JRNL TITL REGULATORY LIGAND BINDING IN PLANT CHALCONE ISOMERASE-LIKE JRNL TITL 2 (CHIL) PROTEINS. JRNL REF J.BIOL.CHEM. V. 299 04804 2023 JRNL REFN ESSN 1083-351X JRNL PMID 37172720 JRNL DOI 10.1016/J.JBC.2023.104804 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 19800 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1982 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 42.8000 - 4.5800 1.00 1425 155 0.1944 0.2321 REMARK 3 2 4.5800 - 3.6300 1.00 1315 145 0.1526 0.1802 REMARK 3 3 3.6300 - 3.1800 1.00 1312 146 0.1716 0.2132 REMARK 3 4 3.1700 - 2.8800 1.00 1282 144 0.1840 0.2160 REMARK 3 5 2.8800 - 2.6800 1.00 1274 143 0.1964 0.2544 REMARK 3 6 2.6800 - 2.5200 1.00 1266 143 0.1978 0.2110 REMARK 3 7 2.5200 - 2.3900 1.00 1281 146 0.1937 0.2299 REMARK 3 8 2.3900 - 2.2900 1.00 1256 141 0.1800 0.2147 REMARK 3 9 2.2900 - 2.2000 0.94 1192 129 0.3082 0.4132 REMARK 3 10 2.2000 - 2.1300 1.00 1264 136 0.1921 0.2049 REMARK 3 11 2.1300 - 2.0600 1.00 1226 139 0.2323 0.2760 REMARK 3 12 2.0600 - 2.0000 1.00 1277 141 0.2106 0.2241 REMARK 3 13 2.0000 - 1.9500 1.00 1259 136 0.2528 0.2738 REMARK 3 14 1.9500 - 1.9000 0.97 1189 138 0.5025 0.4878 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) : 0.268 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.988 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.75 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 : 0.011 1700 REMARK 3 ANGLE : 1.104 2304 REMARK 3 CHIRALITY : 0.068 263 REMARK 3 PLANARITY : 0.008 294 REMARK 3 DIHEDRAL : 19.653 633 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 23.9153 -13.7143 12.5135 REMARK 3 T TENSOR REMARK 3 T11: 0.1561 T22: 0.1346 REMARK 3 T33: 0.1508 T12: 0.0032 REMARK 3 T13: 0.0058 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 1.0401 L22: 1.4195 REMARK 3 L33: 1.2663 L12: 0.2095 REMARK 3 L13: 0.3639 L23: -0.3585 REMARK 3 S TENSOR REMARK 3 S11: -0.0142 S12: -0.0200 S13: 0.0138 REMARK 3 S21: 0.0485 S22: 0.0162 S23: 0.0063 REMARK 3 S31: -0.0058 S32: 0.0160 S33: -0.0021 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 8DLC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000266869. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-13 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 : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19994 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 42.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 15.80 REMARK 200 R MERGE (I) : 0.19000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 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 : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4DOK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 3350 AND 200 MM REMARK 280 POTASSIUM NITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277.15K 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 113.90067 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 56.95033 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 56.95033 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 113.90067 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 300 REMARK: THE DIMER OBSERVED CRYSTALLOGRAPHICALLY HAS NOT BEEN PROVEN REMARK 300 TO REPRESENT THE TRUE BIOLOGICAL INTER-SUBUNIT INTERACTION; HOWEVER, REMARK 300 IT HAS BEEN SHOWN THAT THE PROTEIN IS DIMERIC. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 56.95033 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 HOH A 400 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 ARG A 32 REMARK 465 GLY A 33 REMARK 465 SER A 34 REMARK 465 HIS A 35 REMARK 465 GLY A 36 REMARK 465 GLY A 37 REMARK 465 SER A 38 REMARK 465 MET A 39 REMARK 465 GLY A 40 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 THR A 57 -115.75 -105.27 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8DLC A 40 247 UNP A0A438J2L0_VITVI DBREF2 8DLC A A0A438J2L0 48 255 SEQADV 8DLC ARG A 32 UNP A0A438J2L EXPRESSION TAG SEQADV 8DLC GLY A 33 UNP A0A438J2L EXPRESSION TAG SEQADV 8DLC SER A 34 UNP A0A438J2L EXPRESSION TAG SEQADV 8DLC HIS A 35 UNP A0A438J2L EXPRESSION TAG SEQADV 8DLC GLY A 36 UNP A0A438J2L EXPRESSION TAG SEQADV 8DLC GLY A 37 UNP A0A438J2L EXPRESSION TAG SEQADV 8DLC SER A 38 UNP A0A438J2L EXPRESSION TAG SEQADV 8DLC MET A 39 UNP A0A438J2L EXPRESSION TAG SEQRES 1 A 216 ARG GLY SER HIS GLY GLY SER MET GLY THR GLU MET VAL SEQRES 2 A 216 MET VAL ASP GLU ILE PRO PHE PRO PRO GLN ILE THR THR SEQRES 3 A 216 ALA LYS PRO LEU CYS LEU LEU GLY TYR GLY ILE THR ASP SEQRES 4 A 216 ILE GLU ILE HIS PHE LEU GLN ILE LYS PHE THR ALA ILE SEQRES 5 A 216 GLY VAL TYR LEU GLU PRO GLU ILE VAL GLY HIS LEU GLN SEQRES 6 A 216 PRO TRP LYS GLY LYS SER GLY LYS GLU LEU ALA GLU ASN SEQRES 7 A 216 ASP ASP PHE PHE GLU ALA LEU ILE SER ALA PRO GLY GLU SEQRES 8 A 216 LYS PHE LEU ARG ILE VAL VAL ILE LYS GLU ILE LYS GLY SEQRES 9 A 216 SER GLN TYR GLY VAL GLN LEU GLU SER ALA VAL ARG ASP SEQRES 10 A 216 ARG LEU ALA ALA ASP ASP LYS TYR GLU GLU GLU GLU GLU SEQRES 11 A 216 GLU ALA LEU GLU LYS VAL VAL GLU PHE PHE GLN SER LYS SEQRES 12 A 216 TYR PHE LYS LYS ASP SER ILE ILE THR PHE HIS PHE PRO SEQRES 13 A 216 ALA THR SER PHE THR ALA GLU ILE VAL PHE ALA THR GLU SEQRES 14 A 216 GLY LYS GLU GLU SER LYS ILE THR VAL GLU ASN ALA ASN SEQRES 15 A 216 VAL VAL GLU MET ILE LYS LYS TRP TYR LEU GLY GLY THR SEQRES 16 A 216 ARG GLY VAL SER PRO THR THR ILE SER ALA LEU ALA ASN SEQRES 17 A 216 THR LEU ALA THR GLU LEU SER LYS FORMUL 2 HOH *141(H2 O) HELIX 1 AA1 GLU A 90 LEU A 95 1 6 HELIX 2 AA2 GLN A 96 LYS A 99 5 4 HELIX 3 AA3 SER A 102 GLU A 108 1 7 HELIX 4 AA4 ASN A 109 ALA A 119 1 11 HELIX 5 AA5 GLY A 135 ASP A 153 1 19 HELIX 6 AA6 GLU A 157 SER A 173 1 17 HELIX 7 AA7 ASN A 211 GLY A 224 1 14 HELIX 8 AA8 GLY A 225 GLY A 228 5 4 HELIX 9 AA9 SER A 230 SER A 246 1 17 SHEET 1 AA1 2 VAL A 44 VAL A 46 0 SHEET 2 AA1 2 ILE A 49 PHE A 51 -1 O ILE A 49 N VAL A 46 SHEET 1 AA2 7 GLN A 54 THR A 56 0 SHEET 2 AA2 7 PRO A 60 ILE A 73 -1 O LEU A 61 N ILE A 55 SHEET 3 AA2 7 LEU A 76 LEU A 87 -1 O VAL A 85 N GLY A 65 SHEET 4 AA2 7 LYS A 123 VAL A 129 -1 O PHE A 124 N TYR A 86 SHEET 5 AA2 7 ILE A 181 PHE A 186 -1 O PHE A 186 N LYS A 123 SHEET 6 AA2 7 ALA A 193 ALA A 198 -1 O ALA A 198 N ILE A 181 SHEET 7 AA2 7 SER A 205 VAL A 209 -1 O VAL A 209 N ALA A 193 SHEET 1 AA3 2 ILE A 133 LYS A 134 0 SHEET 2 AA3 2 TYR A 175 PHE A 176 -1 O PHE A 176 N ILE A 133 CRYST1 49.420 49.420 170.851 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 0.020235 0.011683 0.000000 0.00000 SCALE2 0.000000 0.023365 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005853 0.00000