HEADER PLANT PROTEIN 06-FEB-19 6NWB TITLE PYL10 BOUND TO THE SELECTIVE AGONIST HEXABACTIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABSCISIC ACID RECEPTOR PYL10; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ABI1-BINDING PROTEIN 8,PYR1-LIKE PROTEIN 10,REGULATORY COMPND 5 COMPONENTS OF ABA RECEPTOR 4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: PYL10, RCAR4, AT4G27920, T13J8.30; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PYR/PYL/RCAR, PYL10, HORMONE RECEPTOR, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.C.PETERSON,A.VAIDYA,D.R.JENSEN,B.F.VOLKMAN,S.R.CUTLER REVDAT 2 11-OCT-23 6NWB 1 REMARK REVDAT 1 12-FEB-20 6NWB 0 JRNL AUTH D.ELZINGA,A.S.VAIDYA,F.C.PETERSON,S.Y.PARK,B.F.VOLKMAN, JRNL AUTH 2 M.OKAMOTO,S.R.CUTLER JRNL TITL PYL10 BOUND TO THE SELECTIVE AGONIST HEXABACTIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 10999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1095 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 42.9083 - 4.0045 0.99 1356 150 0.1500 0.1961 REMARK 3 2 4.0045 - 3.1788 0.99 1274 143 0.1582 0.2184 REMARK 3 3 3.1788 - 2.7771 0.98 1254 138 0.2103 0.2286 REMARK 3 4 2.7771 - 2.5232 0.97 1227 133 0.2095 0.2667 REMARK 3 5 2.5232 - 2.3424 0.96 1214 136 0.1910 0.2377 REMARK 3 6 2.3424 - 2.2043 0.96 1198 132 0.1827 0.2294 REMARK 3 7 2.2043 - 2.0939 0.96 1202 136 0.1839 0.2782 REMARK 3 8 2.0939 - 2.0027 0.94 1179 127 0.1886 0.2608 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.19 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 : 0.007 1285 REMARK 3 ANGLE : 0.968 1740 REMARK 3 CHIRALITY : 0.060 203 REMARK 3 PLANARITY : 0.005 221 REMARK 3 DIHEDRAL : 17.243 807 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): 20.9158 20.6630 -10.5033 REMARK 3 T TENSOR REMARK 3 T11: 0.1646 T22: 0.2153 REMARK 3 T33: 0.1818 T12: 0.0241 REMARK 3 T13: 0.0180 T23: -0.0115 REMARK 3 L TENSOR REMARK 3 L11: 3.4399 L22: 3.2336 REMARK 3 L33: 2.9747 L12: 0.8759 REMARK 3 L13: -0.9930 L23: -1.0348 REMARK 3 S TENSOR REMARK 3 S11: 0.0487 S12: 0.1695 S13: 0.1770 REMARK 3 S21: -0.0899 S22: 0.0575 S23: -0.0598 REMARK 3 S31: -0.0952 S32: -0.0308 S33: -0.0910 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 6NWB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1000235563. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10999 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 20.80 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.25700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 16.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.6.0 REMARK 200 STARTING MODEL: 3RT0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WELL SOLUTION WAS COMPOSED OF 0.1 M REMARK 280 MMT BUFFER PH 6.0 PLUS 25% W/V PEG 1500. CRYSTALS WERE FLASH REMARK 280 FROZEN IN WELL SOLUTION PLUS 15% PEG 400, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 21.67667 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 43.35333 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 43.35333 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 21.67667 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 374 LIES ON A SPECIAL POSITION. 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 TYR A 55 -13.41 -145.32 REMARK 500 PRO A 144 170.70 -59.95 REMARK 500 GLU A 145 -71.86 -49.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue L6V A 201 DBREF 6NWB A 25 180 UNP Q8H1R0 PYL10_ARATH 25 180 SEQRES 1 A 156 SER GLN CYS SER SER THR LEU VAL LYS HIS ILE LYS ALA SEQRES 2 A 156 PRO LEU HIS LEU VAL TRP SER ILE VAL ARG ARG PHE ASP SEQRES 3 A 156 GLU PRO GLN LYS TYR LYS PRO PHE ILE SER ARG CYS VAL SEQRES 4 A 156 VAL GLN GLY LYS LYS LEU GLU VAL GLY SER VAL ARG GLU SEQRES 5 A 156 VAL ASP LEU LYS SER GLY LEU PRO ALA THR LYS SER THR SEQRES 6 A 156 GLU VAL LEU GLU ILE LEU ASP ASP ASN GLU HIS ILE LEU SEQRES 7 A 156 GLY ILE ARG ILE VAL GLY GLY ASP HIS ARG LEU LYS ASN SEQRES 8 A 156 TYR SER SER THR ILE SER LEU HIS SER GLU THR ILE ASP SEQRES 9 A 156 GLY LYS THR GLY THR LEU ALA ILE GLU SER PHE VAL VAL SEQRES 10 A 156 ASP VAL PRO GLU GLY ASN THR LYS GLU GLU THR CYS PHE SEQRES 11 A 156 PHE VAL GLU ALA LEU ILE GLN CYS ASN LEU ASN SER LEU SEQRES 12 A 156 ALA ASP VAL THR GLU ARG LEU GLN ALA GLU SER MET GLU HET L6V A 201 26 HETNAM L6V N-{[(4-CYANOPHENYL)METHYL]SULFONYL}-1-(THIOPHEN-3-YL) HETNAM 2 L6V CYCLOHEXANE-1-CARBOXAMIDE FORMUL 2 L6V C19 H20 N2 O3 S2 FORMUL 3 HOH *80(H2 O) HELIX 1 AA1 PRO A 38 ARG A 47 1 10 HELIX 2 AA2 GLU A 51 TYR A 55 5 5 HELIX 3 AA3 THR A 148 MET A 179 1 32 SHEET 1 AA1 7 GLN A 26 ILE A 35 0 SHEET 2 AA1 7 LYS A 130 ASP A 142 -1 O THR A 133 N ILE A 35 SHEET 3 AA1 7 SER A 117 ILE A 127 -1 N GLU A 125 O GLY A 132 SHEET 4 AA1 7 ILE A 101 GLY A 109 -1 N ILE A 104 O SER A 118 SHEET 5 AA1 7 LYS A 87 ASP A 96 -1 N ILE A 94 O GLY A 103 SHEET 6 AA1 7 VAL A 74 LEU A 79 -1 N ARG A 75 O GLU A 90 SHEET 7 AA1 7 ILE A 59 VAL A 63 -1 N SER A 60 O ASP A 78 SITE 1 AC1 11 LYS A 56 ILE A 59 LEU A 79 GLU A 90 SITE 2 AC1 11 ILE A 106 TYR A 116 SER A 118 LEU A 159 SITE 3 AC1 11 ASN A 163 HOH A 319 HOH A 338 CRYST1 65.910 65.910 65.030 90.00 90.00 120.00 P 31 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 0.015172 0.008760 0.000000 0.00000 SCALE2 0.000000 0.017519 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015378 0.00000