HEADER SIGNALING PROTEIN 30-APR-16 5JNN TITLE CRYSTAL STRUCTURE OF ABSCISIC ACID RECEPTOR PYL2 IN COMPLEX WITH TITLE 2 PHASEIC ACID. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABSCISIC ACID RECEPTOR PYL2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYR1-LIKE PROTEIN 2,REGULATORY COMPONENTS OF ABA RECEPTOR COMPND 5 14; 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: PYL2, RCAR14, AT2G26040, T19L18.15; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ABA RECEPTOR, PHASEIC ACID, PYR/PYL, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.K.WENG,J.P.NOEL REVDAT 5 06-MAR-24 5JNN 1 REMARK REVDAT 4 20-NOV-19 5JNN 1 REMARK REVDAT 3 27-SEP-17 5JNN 1 REMARK REVDAT 2 07-SEP-16 5JNN 1 JRNL REVDAT 1 17-AUG-16 5JNN 0 JRNL AUTH J.K.WENG,M.YE,B.LI,J.P.NOEL JRNL TITL CO-EVOLUTION OF HORMONE METABOLISM AND SIGNALING NETWORKS JRNL TITL 2 EXPANDS PLANT ADAPTIVE PLASTICITY. JRNL REF CELL V. 166 881 2016 JRNL REFN ISSN 1097-4172 JRNL PMID 27518563 JRNL DOI 10.1016/J.CELL.2016.06.027 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 13405 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 672 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 52.7981 - 3.9326 1.00 2760 146 0.1777 0.2207 REMARK 3 2 3.9326 - 3.1215 1.00 2551 134 0.1811 0.2170 REMARK 3 3 3.1215 - 2.7270 1.00 2513 132 0.2153 0.2712 REMARK 3 4 2.7270 - 2.4776 1.00 2471 131 0.2125 0.2746 REMARK 3 5 2.4776 - 2.3001 0.99 2438 129 0.2119 0.2736 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 1438 REMARK 3 ANGLE : 1.107 1959 REMARK 3 CHIRALITY : 0.075 227 REMARK 3 PLANARITY : 0.004 251 REMARK 3 DIHEDRAL : 16.113 540 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): 0.5697 -24.6025 9.0723 REMARK 3 T TENSOR REMARK 3 T11: 0.2296 T22: 0.4402 REMARK 3 T33: 0.3235 T12: 0.0297 REMARK 3 T13: 0.0334 T23: 0.0932 REMARK 3 L TENSOR REMARK 3 L11: 2.0729 L22: 1.5751 REMARK 3 L33: 1.7263 L12: 0.0954 REMARK 3 L13: 0.3842 L23: 0.0955 REMARK 3 S TENSOR REMARK 3 S11: 0.0461 S12: 0.1293 S13: 0.0929 REMARK 3 S21: 0.1434 S22: 0.1114 S23: 0.1872 REMARK 3 S31: -0.0287 S32: -0.2121 S33: -0.1061 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 5JNN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000220916. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 80 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 : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13406 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 52.784 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 : 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4 M SODIUM FORMATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 85.27067 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 170.54133 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 127.90600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 213.17667 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 42.63533 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 85.27067 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 170.54133 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 213.17667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 127.90600 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 42.63533 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 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 MET A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 PRO A 5 REMARK 465 ALA A 6 REMARK 465 VAL A 7 REMARK 465 LYS A 8 REMARK 465 GLY A 9 REMARK 465 LEU A 10 REMARK 465 THR A 11 REMARK 465 ASP A 12 REMARK 465 GLU A 13 REMARK 465 ASP A 189 REMARK 465 GLU A 190 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 O HOH A 941 O HOH A 951 2.08 REMARK 500 O GLY A 139 O HOH A 901 2.11 REMARK 500 O HIS A 119 NZ LYS A 122 2.17 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 SER A 89 24.05 -72.70 REMARK 500 SER A 138 -21.72 -154.14 REMARK 500 SER A 183 -5.43 -147.38 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 6LM A 800 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5JO1 RELATED DB: PDB REMARK 900 RELATED ID: 5JO2 RELATED DB: PDB DBREF 5JNN A 1 190 UNP O80992 PYL2_ARATH 1 190 SEQRES 1 A 190 MET SER SER SER PRO ALA VAL LYS GLY LEU THR ASP GLU SEQRES 2 A 190 GLU GLN LYS THR LEU GLU PRO VAL ILE LYS THR TYR HIS SEQRES 3 A 190 GLN PHE GLU PRO ASP PRO THR THR CYS THR SER LEU ILE SEQRES 4 A 190 THR GLN ARG ILE HIS ALA PRO ALA SER VAL VAL TRP PRO SEQRES 5 A 190 LEU ILE ARG ARG PHE ASP ASN PRO GLU ARG TYR LYS HIS SEQRES 6 A 190 PHE VAL LYS ARG CYS ARG LEU ILE SER GLY ASP GLY ASP SEQRES 7 A 190 VAL GLY SER VAL ARG GLU VAL THR VAL ILE SER GLY LEU SEQRES 8 A 190 PRO ALA SER THR SER THR GLU ARG LEU GLU PHE VAL ASP SEQRES 9 A 190 ASP ASP HIS ARG VAL LEU SER PHE ARG VAL VAL GLY GLY SEQRES 10 A 190 GLU HIS ARG LEU LYS ASN TYR LYS SER VAL THR SER VAL SEQRES 11 A 190 ASN GLU PHE LEU ASN GLN ASP SER GLY LYS VAL TYR THR SEQRES 12 A 190 VAL VAL LEU GLU SER TYR THR VAL ASP ILE PRO GLU GLY SEQRES 13 A 190 ASN THR GLU GLU ASP THR LYS MET PHE VAL ASP THR VAL SEQRES 14 A 190 VAL LYS LEU ASN LEU GLN LYS LEU GLY VAL ALA ALA THR SEQRES 15 A 190 SER ALA PRO MET HIS ASP ASP GLU HET 6LM A 800 20 HETNAM 6LM (3S,4E)-5-[(1R,5R,8S)-8-HYDROXY-1,5-DIMETHYL-3-OXO-6- HETNAM 2 6LM OXABICYCLO[3.2.1]OCTAN-8-YL]-3-METHYLPENT-4-ENOIC ACID FORMUL 2 6LM C15 H22 O5 FORMUL 3 HOH *52(H2 O) HELIX 1 AA1 GLU A 14 HIS A 26 1 13 HELIX 2 AA2 PRO A 46 ARG A 56 1 11 HELIX 3 AA3 ASN A 59 TYR A 63 5 5 HELIX 4 AA4 THR A 158 ALA A 184 1 27 SHEET 1 AA1 7 THR A 34 ILE A 43 0 SHEET 2 AA1 7 VAL A 141 ASP A 152 -1 O GLU A 147 N ILE A 39 SHEET 3 AA1 7 LYS A 125 LEU A 134 -1 N ASN A 131 O VAL A 144 SHEET 4 AA1 7 VAL A 109 GLY A 117 -1 N LEU A 110 O THR A 128 SHEET 5 AA1 7 THR A 95 ASP A 104 -1 N THR A 97 O VAL A 115 SHEET 6 AA1 7 VAL A 82 VAL A 87 -1 N VAL A 85 O SER A 96 SHEET 7 AA1 7 VAL A 67 SER A 74 -1 N ARG A 71 O GLU A 84 SITE 1 AC1 11 LYS A 64 VAL A 87 PHE A 112 HIS A 119 SITE 2 AC1 11 TYR A 124 PHE A 165 VAL A 166 ASN A 173 SITE 3 AC1 11 HOH A 903 HOH A 905 HOH A 920 CRYST1 60.950 60.950 255.812 90.00 90.00 120.00 P 61 2 2 12 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 0.016407 0.009473 0.000000 0.00000 SCALE2 0.000000 0.018945 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003909 0.00000