HEADER SIGNALING PROTEIN 07-JUL-22 8DLD TITLE CRYSTAL STRUCTURE OF CHALCONE-ISOMERASE LIKE PROTEIN FROM TITLE 2 PHYSCOMITRELLA PATENS (PPCHIL-A) 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: PHYSCOMITRIUM PATENS; SOURCE 3 ORGANISM_TAXID: 3218; SOURCE 4 GENE: PHYPA_030203, PHYPADRAFT_167842; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 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 8DLD 1 JRNL REVDAT 2 25-OCT-23 8DLD 1 REMARK REVDAT 1 10-MAY-23 8DLD 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. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 18647 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1863 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 37.3000 - 4.3500 0.99 1350 151 0.1589 0.1839 REMARK 3 2 4.3500 - 3.4500 0.99 1316 151 0.1482 0.1708 REMARK 3 3 3.4500 - 3.0200 0.99 1310 145 0.1752 0.2267 REMARK 3 4 3.0200 - 2.7400 0.99 1291 140 0.1986 0.2536 REMARK 3 5 2.7400 - 2.5400 0.99 1295 152 0.1978 0.2636 REMARK 3 6 2.5400 - 2.3900 0.98 1303 140 0.1963 0.2329 REMARK 3 7 2.3900 - 2.2700 0.98 1297 150 0.1961 0.2323 REMARK 3 8 2.2700 - 2.1800 0.97 1252 136 0.2192 0.2868 REMARK 3 9 2.1700 - 2.0900 0.98 1280 137 0.2054 0.2551 REMARK 3 10 2.0900 - 2.0200 0.98 1283 137 0.2314 0.2758 REMARK 3 11 2.0200 - 1.9600 0.98 1286 145 0.2156 0.2647 REMARK 3 12 1.9600 - 1.9000 0.96 1229 142 0.3076 0.3382 REMARK 3 13 1.9000 - 1.8500 0.97 1292 137 0.2784 0.3470 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.32 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 1677 REMARK 3 ANGLE : 1.098 2289 REMARK 3 CHIRALITY : 0.066 263 REMARK 3 PLANARITY : 0.008 300 REMARK 3 DIHEDRAL : 19.587 619 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): -4.8197 -2.3608 19.9799 REMARK 3 T TENSOR REMARK 3 T11: 0.1737 T22: 0.1528 REMARK 3 T33: 0.1670 T12: 0.0188 REMARK 3 T13: -0.0077 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 2.1819 L22: 1.6119 REMARK 3 L33: 2.7873 L12: 0.1617 REMARK 3 L13: -0.9499 L23: -0.1884 REMARK 3 S TENSOR REMARK 3 S11: -0.0482 S12: 0.2185 S13: -0.0200 REMARK 3 S21: -0.1914 S22: -0.0242 S23: -0.0825 REMARK 3 S31: 0.1824 S32: -0.0243 S33: 0.0493 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 8DLD 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_1000266870. 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 : 18703 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 37.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.66700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 (%): 49.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4K AND 0.2 M AMMONIUM SULFATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.15K 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 31.27500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.94000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 31.27500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.94000 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 HOH A 314 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 358 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 -6 REMARK 465 GLY A -5 REMARK 465 SER A -4 REMARK 465 HIS A -3 REMARK 465 GLY A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 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 40 -3.71 75.82 REMARK 500 ASP A 75 15.83 54.24 REMARK 500 REMARK 500 REMARK: NULL DBREF 8DLD A 1 209 UNP A9T3E4 A9T3E4_PHYPA 1 209 SEQADV 8DLD ARG A -6 UNP A9T3E4 EXPRESSION TAG SEQADV 8DLD GLY A -5 UNP A9T3E4 EXPRESSION TAG SEQADV 8DLD SER A -4 UNP A9T3E4 EXPRESSION TAG SEQADV 8DLD HIS A -3 UNP A9T3E4 EXPRESSION TAG SEQADV 8DLD GLY A -2 UNP A9T3E4 EXPRESSION TAG SEQADV 8DLD GLY A -1 UNP A9T3E4 EXPRESSION TAG SEQADV 8DLD SER A 0 UNP A9T3E4 EXPRESSION TAG SEQRES 1 A 216 ARG GLY SER HIS GLY GLY SER MET GLY PRO GLN VAL VAL SEQRES 2 A 216 LYS VAL GLU ASP ILE ASP PHE ALA THR LYS PHE THR PRO SEQRES 3 A 216 PRO THR GLY SER THR GLU LEU ASP LEU ILE GLY TYR GLY SEQRES 4 A 216 ASN THR GLY MET GLU ILE GLU THR VAL GLU ILE ARG PHE SEQRES 5 A 216 THR ALA ILE GLY PHE TYR ALA GLU PRO SER ILE SER GLU SEQRES 6 A 216 HIS LEU GLN LYS TRP LYS GLY THR PRO SER SER ASN LEU SEQRES 7 A 216 VAL GLU ASP ASP SER GLY PHE HIS LYS GLU LEU ILE GLN SEQRES 8 A 216 ALA PRO VAL GLU LYS ALA VAL ARG ILE SER ILE ILE LYS SEQRES 9 A 216 GLY ILE LYS GLY LEU PRO TYR GLY SER ALA LEU GLN SER SEQRES 10 A 216 SER LEU ARG ASP ARG LEU VAL ASN ASN ASP LEU PHE GLU SEQRES 11 A 216 GLU GLU GLU GLU GLU ALA LEU GLU LYS LEU ALA GLU PHE SEQRES 12 A 216 PHE GLN PRO HIS ASN LEU PRO LYS GLY THR ASN ILE ILE SEQRES 13 A 216 TYR HIS TRP ALA THR PRO SER SER VAL LYS VAL SER LEU SEQRES 14 A 216 SER GLU GLU GLY LYS MET PRO GLU ASP VAL ALA TYR THR SEQRES 15 A 216 ILE ASP ASP ALA HIS VAL ALA GLU ALA LEU LEU ASP LEU SEQRES 16 A 216 TYR LEU GLY GLU ASN THR ILE THR PRO SER THR LEU ALA SEQRES 17 A 216 SER VAL ALA GLU ALA ILE ALA ALA FORMUL 2 HOH *158(H2 O) HELIX 1 AA1 SER A 55 LEU A 60 1 6 HELIX 2 AA2 GLN A 61 LYS A 64 5 4 HELIX 3 AA3 PRO A 67 GLU A 73 1 7 HELIX 4 AA4 GLY A 77 ALA A 85 1 9 HELIX 5 AA5 GLY A 101 ASN A 119 1 19 HELIX 6 AA6 GLU A 123 GLN A 138 1 16 HELIX 7 AA7 ASP A 178 GLY A 191 1 14 HELIX 8 AA8 THR A 196 ALA A 209 1 14 SHEET 1 AA1 2 VAL A 5 VAL A 8 0 SHEET 2 AA1 2 ILE A 11 ALA A 14 -1 O PHE A 13 N VAL A 6 SHEET 1 AA2 7 LYS A 16 PHE A 17 0 SHEET 2 AA2 7 LEU A 26 ILE A 38 -1 O LEU A 26 N PHE A 17 SHEET 3 AA2 7 VAL A 41 ALA A 52 -1 O PHE A 50 N GLY A 30 SHEET 4 AA2 7 LYS A 89 ILE A 95 -1 O ALA A 90 N TYR A 51 SHEET 5 AA2 7 ASN A 147 TRP A 152 -1 O ILE A 148 N ILE A 93 SHEET 6 AA2 7 VAL A 158 SER A 163 -1 O SER A 163 N ASN A 147 SHEET 7 AA2 7 TYR A 174 ILE A 176 -1 O TYR A 174 N VAL A 160 SHEET 1 AA3 2 ILE A 99 LYS A 100 0 SHEET 2 AA3 2 ASN A 141 LEU A 142 -1 O LEU A 142 N ILE A 99 CRYST1 62.550 49.880 76.820 90.00 110.87 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 0.015987 0.000000 0.006095 0.00000 SCALE2 0.000000 0.020048 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013931 0.00000