HEADER HYDROLASE 29-AUG-17 6ATX TITLE CRYSTAL STRUCTURE OF PHYSCOMITRELLA PATENS KAI2-LIKE C COMPND MOL_ID: 1; COMPND 2 MOLECULE: PPKAI2-LIKE C; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYSCOMITRELLA PATENS SUBSP. PATENS; SOURCE 3 ORGANISM_COMMON: MOSS; SOURCE 4 ORGANISM_TAXID: 3218; SOURCE 5 GENE: PHYPADRAFT_213263; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T3 KEYWDS ALPHA/BETA HYDROLASE, STRIGOLACTONE BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.BURGER,H.J.LEE,J.CHORY REVDAT 2 04-OCT-23 6ATX 1 REMARK REVDAT 1 06-FEB-19 6ATX 0 JRNL AUTH M.BURGER,K.MASHIGUCHI,H.J.LEE,M.NAKANO,K.TAKEMOTO,Y.SETO, JRNL AUTH 2 S.YAMAGUCHI,J.CHORY JRNL TITL STRUCTURAL BASIS OF KARRIKIN AND NON-NATURAL STRIGOLACTONE JRNL TITL 2 PERCEPTION IN PHYSCOMITRELLA PATENS. JRNL REF CELL REP V. 26 855 2019 JRNL REFN ESSN 2211-1247 JRNL PMID 30673608 JRNL DOI 10.1016/J.CELREP.2019.01.003 REMARK 2 REMARK 2 RESOLUTION. 2.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.351 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 7881 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.063 REMARK 3 FREE R VALUE TEST SET COUNT : 399 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 46.6367 - 3.9517 1.00 2522 136 0.1442 0.1774 REMARK 3 2 3.9517 - 3.1368 1.00 2475 127 0.1831 0.2156 REMARK 3 3 3.1368 - 2.7403 1.00 2485 136 0.2467 0.3143 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.392 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.691 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.32 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 : 0.003 2111 REMARK 3 ANGLE : 0.596 2877 REMARK 3 CHIRALITY : 0.044 334 REMARK 3 PLANARITY : 0.004 369 REMARK 3 DIHEDRAL : 2.725 1244 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 6ATX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1000229824. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7881 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.740 REMARK 200 RESOLUTION RANGE LOW (A) : 46.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : 0.22010 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.84 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.83440 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4IH1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M AMMONIUM SULFATE, 0.2 M BIS REMARK 280 -TRIS, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 70.44000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 105.66000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.22000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 GLY A -1 REMARK 465 PRO A 0 REMARK 465 MET A 1 REMARK 465 ASP A 2 REMARK 465 GLU A 3 REMARK 465 LEU A 4 REMARK 465 PRO A 5 REMARK 465 SER A 6 REMARK 465 GLU A 272 REMARK 465 SER A 273 REMARK 465 CYS A 274 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 LEU A 8 -54.51 71.75 REMARK 500 MET A 18 28.95 -141.47 REMARK 500 THR A 31 -167.76 -114.15 REMARK 500 GLU A 88 36.02 39.62 REMARK 500 SER A 98 -117.90 60.82 REMARK 500 LYS A 117 137.54 -177.26 REMARK 500 ALA A 167 179.49 66.60 REMARK 500 ILE A 169 13.98 -68.02 REMARK 500 REMARK 500 REMARK: NULL DBREF 6ATX A 1 274 UNP A9SKF7 A9SKF7_PHYPA 1 274 SEQADV 6ATX GLY A -1 UNP A9SKF7 CLONING ARTIFACT SEQADV 6ATX PRO A 0 UNP A9SKF7 CLONING ARTIFACT SEQRES 1 A 276 GLY PRO MET ASP GLU LEU PRO SER LEU LEU GLU VAL HIS SEQRES 2 A 276 ASN VAL ARG ILE VAL GLY MET GLY GLU GLU LEU VAL VAL SEQRES 3 A 276 LEU ALA HIS GLY PHE GLY THR ASP GLN SER VAL TRP LYS SEQRES 4 A 276 HIS VAL ILE PRO HIS LEU VAL ASP ASP TYR ARG VAL ILE SEQRES 5 A 276 LEU PHE ASP ASN MET GLY ALA GLY THR THR ASP PRO GLU SEQRES 6 A 276 TYR PHE SER PHE SER ARG TYR SER THR LEU TYR GLY TYR SEQRES 7 A 276 ALA ASP ASP LEU LEU THR ILE LEU ASP GLU LEU GLU VAL SEQRES 8 A 276 GLN SER CYS ILE PHE VAL GLY HIS SER VAL SER GLY MET SEQRES 9 A 276 VAL GLY CYS LEU ALA SER LEU TYR ARG PRO GLU ILE PHE SEQRES 10 A 276 SER LYS ILE ILE THR ILE SER ALA SER PRO ARG TYR LEU SEQRES 11 A 276 ASN ASP MET ASP TYR PHE GLY GLY PHE GLU GLN GLU ASP SEQRES 12 A 276 LEU ASN GLN LEU PHE GLU ALA MET GLN SER ASN PHE LYS SEQRES 13 A 276 ALA TRP VAL SER GLY PHE ALA PRO LEU ALA VAL GLY ALA SEQRES 14 A 276 ASP ILE ASP SER MET ALA VAL GLN GLU PHE GLY ARG THR SEQRES 15 A 276 LEU PHE ASN ILE ARG PRO ASP ILE ALA PHE SER VAL ALA SEQRES 16 A 276 LYS THR ILE PHE GLN SER ASP LEU ARG SER ILE LEU PRO SEQRES 17 A 276 LYS VAL THR VAL PRO CYS HIS ILE LEU GLN SER SER LYS SEQRES 18 A 276 ASP LEU ALA VAL PRO VAL VAL VAL ALA ASP TYR LEU HIS SEQRES 19 A 276 LEU THR LEU GLY GLY PRO THR ILE VAL GLU VAL LEU PRO SEQRES 20 A 276 THR GLU GLY HIS LEU PRO GLN LEU SER SER PRO ASP ILE SEQRES 21 A 276 VAL ILE PRO VAL LEU LYS ARG HIS VAL ALA GLY ASN LEU SEQRES 22 A 276 GLU SER CYS FORMUL 2 HOH *42(H2 O) HELIX 1 AA1 ASP A 32 LYS A 37 5 6 HELIX 2 AA2 VAL A 39 LEU A 43 5 5 HELIX 3 AA3 ASP A 61 PHE A 65 5 5 HELIX 4 AA4 SER A 68 THR A 72 5 5 HELIX 5 AA5 LEU A 73 LEU A 87 1 15 HELIX 6 AA6 SER A 98 ARG A 111 1 14 HELIX 7 AA7 GLU A 138 ASN A 152 1 15 HELIX 8 AA8 ASN A 152 VAL A 165 1 14 HELIX 9 AA9 SER A 171 ASN A 183 1 13 HELIX 10 AB1 ARG A 185 GLN A 198 1 14 HELIX 11 AB2 LEU A 201 VAL A 208 5 8 HELIX 12 AB3 PRO A 224 LEU A 235 1 12 HELIX 13 AB4 LEU A 250 SER A 255 1 6 HELIX 14 AB5 SER A 255 ALA A 268 1 14 SHEET 1 AA1 6 TYR A 47 LEU A 51 0 SHEET 2 AA1 6 GLU A 21 ALA A 26 1 N VAL A 23 O ILE A 50 SHEET 3 AA1 6 CYS A 92 HIS A 97 1 O VAL A 95 N VAL A 24 SHEET 4 AA1 6 PHE A 115 ILE A 121 1 O ILE A 119 N PHE A 94 SHEET 5 AA1 6 CYS A 212 LYS A 219 1 O HIS A 213 N ILE A 118 SHEET 6 AA1 6 THR A 239 GLU A 247 1 O LEU A 244 N GLN A 216 CRYST1 46.630 46.630 140.880 90.00 90.00 90.00 P 43 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 0.021445 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021445 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007098 0.00000