HEADER HYDROLASE 11-SEP-17 6AZD TITLE CRYSTAL STRUCTURE OF PHYSCOMITRELLA PATENS KAI2-LIKE H COMPND MOL_ID: 1; COMPND 2 MOLECULE: PPKAI2-LIKE H; COMPND 3 CHAIN: A; COMPND 4 EC: 3.-.-.-; COMPND 5 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_184560; 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 6AZD 1 REMARK REVDAT 1 06-FEB-19 6AZD 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. 1.97 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.349 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 18741 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.962 REMARK 3 FREE R VALUE TEST SET COUNT : 930 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 37.0247 - 3.7675 0.97 2576 121 0.1697 0.1662 REMARK 3 2 3.7675 - 2.9908 0.98 2534 161 0.1807 0.2260 REMARK 3 3 2.9908 - 2.6129 0.99 2543 128 0.2116 0.2280 REMARK 3 4 2.6129 - 2.3740 0.99 2581 126 0.2227 0.2645 REMARK 3 5 2.3740 - 2.2039 0.98 2552 108 0.2306 0.3241 REMARK 3 6 2.2039 - 2.0740 0.99 2538 130 0.2429 0.2748 REMARK 3 7 2.0740 - 1.9701 0.98 2487 156 0.2807 0.3336 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) : 0.277 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.90 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 2108 REMARK 3 ANGLE : 0.605 2872 REMARK 3 CHIRALITY : 0.044 334 REMARK 3 PLANARITY : 0.003 371 REMARK 3 DIHEDRAL : 2.661 1247 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 6AZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000229832. 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 : MIRRORS 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18745 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 37.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.16740 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.44490 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.850 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 4JYP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M AMMONIUM SULFATE, 0.1 M MES 6.5, REMARK 280 5% PEG400, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.32500 REMARK 290 SMTRY3 2 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 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: 11000 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 PRO A 2 REMARK 465 SER A 269 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 ASP A 64 CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 268 O HOH A 301 2.09 REMARK 500 O HOH A 335 O HOH A 439 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 399 O HOH A 417 1565 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 30 -169.40 -116.99 REMARK 500 ASP A 64 63.25 -115.07 REMARK 500 SER A 98 -121.73 52.37 REMARK 500 ASN A 152 80.25 -154.55 REMARK 500 GLU A 172 -18.70 -147.27 REMARK 500 CYS A 255 59.24 -143.30 REMARK 500 REMARK 500 REMARK: NULL DBREF 6AZD A 1 269 UNP A9SG07 A9SG07_PHYPA 1 269 SEQADV 6AZD GLY A -1 UNP A9SG07 CLONING ARTIFACT SEQADV 6AZD PRO A 0 UNP A9SG07 CLONING ARTIFACT SEQRES 1 A 271 GLY PRO MET PRO SER PRO LEU LEU SER THR HIS ASN VAL SEQRES 2 A 271 THR VAL LEU GLY ASN ARG SER ASP PRO VAL VAL VAL LEU SEQRES 3 A 271 GLY HIS GLY LEU GLY THR ASP GLN SER VAL TRP LYS TYR SEQRES 4 A 271 THR VAL PRO SER LEU VAL ASN GLN ASN PHE GLN VAL VAL SEQRES 5 A 271 LEU TYR ASP THR MET GLY ALA GLY SER THR GLU THR SER SEQRES 6 A 271 ASP PHE ASN PHE LYS ARG TYR SER SER LEU GLN GLY HIS SEQRES 7 A 271 VAL ASP ASP LEU LEU ALA ILE LEU ASP GLU LEU GLU ILE SEQRES 8 A 271 GLU ASN CYS VAL TYR VAL GLY HIS SER MET SER GLY MET SEQRES 9 A 271 ILE GLY VAL LEU ALA SER LEU GLU ARG PRO ASP LEU PHE SEQRES 10 A 271 ARG LYS LEU ILE LEU LEU SER ALA SER PRO ARG TYR LEU SEQRES 11 A 271 ASN ASP SER SER TYR TYR GLY GLY PHE GLU GLN GLU ASP SEQRES 12 A 271 LEU ASP GLN LEU PHE SER SER MET ARG SER ASN PHE SER SEQRES 13 A 271 ALA TRP VAL SER GLY PHE ALA THR ALA ALA VAL GLY THR SEQRES 14 A 271 ASP ILE HIS ASP GLU ALA VAL GLN GLU PHE SER SER THR SEQRES 15 A 271 PHE ILE SER MET ARG PRO ASP VAL ALA LEU ARG THR SER SEQRES 16 A 271 GLN PHE VAL PHE GLN SER ASP PHE ARG SER ILE LEU SER SEQRES 17 A 271 GLU VAL THR VAL PRO CYS HIS ILE VAL GLN SER ARG LYS SEQRES 18 A 271 ASP ILE ALA VAL PRO ILE GLU VAL ALA GLU TYR LEU ARG SEQRES 19 A 271 CYS ASN LEU GLY GLY TRP THR SER VAL ASP ILE LEU GLN SEQRES 20 A 271 THR ASP GLY HIS LEU PRO GLN LEU SER CYS PRO GLU LEU SEQRES 21 A 271 VAL VAL PRO VAL LEU LEU HIS CYS ILE ASP SER FORMUL 2 HOH *155(H2 O) HELIX 1 AA1 SER A 3 HIS A 9 1 7 HELIX 2 AA2 ASP A 31 LYS A 36 5 6 HELIX 3 AA3 THR A 38 GLN A 45 1 8 HELIX 4 AA4 SER A 72 LEU A 87 1 16 HELIX 5 AA5 SER A 98 ARG A 111 1 14 HELIX 6 AA6 GLU A 138 ASN A 152 1 15 HELIX 7 AA7 ASN A 152 GLY A 166 1 15 HELIX 8 AA8 GLU A 172 SER A 183 1 12 HELIX 9 AA9 ARG A 185 GLN A 198 1 14 HELIX 10 AB1 PHE A 201 VAL A 208 5 8 HELIX 11 AB2 PRO A 224 LEU A 235 1 12 HELIX 12 AB3 LEU A 250 CYS A 255 1 6 HELIX 13 AB4 CYS A 255 ASP A 268 1 14 SHEET 1 AA1 7 THR A 12 LEU A 14 0 SHEET 2 AA1 7 GLN A 48 LEU A 51 -1 O VAL A 49 N LEU A 14 SHEET 3 AA1 7 VAL A 21 GLY A 25 1 N VAL A 22 O VAL A 50 SHEET 4 AA1 7 CYS A 92 HIS A 97 1 O VAL A 95 N VAL A 23 SHEET 5 AA1 7 PHE A 115 LEU A 121 1 O LEU A 121 N GLY A 96 SHEET 6 AA1 7 CYS A 212 LYS A 219 1 O VAL A 215 N LEU A 120 SHEET 7 AA1 7 THR A 239 ASP A 247 1 O SER A 240 N ILE A 214 CRYST1 49.410 52.650 52.300 90.00 95.51 90.00 P 1 21 1 2 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 0.020239 0.000000 0.001952 0.00000 SCALE2 0.000000 0.018993 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019209 0.00000