HEADER HYDROLASE INHIBITOR 02-MAY-11 3RT2 TITLE CRYSTAL STRUCTURE OF APO-PYL10 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: THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: PYL10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PYL10, ABA-INDEPENDENT PP2C INHIBITOR, PP2CS, ABSCISIC ACID, ABA KEYWDS 2 RECEPTOR, HYDROLASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR Q.HAO,P.YIN,W.LI,L.WANG,C.YAN,J.WANG,N.YAN REVDAT 3 16-OCT-24 3RT2 1 REMARK REVDAT 2 01-NOV-23 3RT2 1 REMARK REVDAT 1 22-JUN-11 3RT2 0 JRNL AUTH Q.HAO,P.YIN,W.LI,L.WANG,C.YAN,Z.LIN,J.Z.WU,J.WANG,S.F.YAN, JRNL AUTH 2 N.YAN JRNL TITL THE MOLECULAR BASIS OF ABA-INDEPENDENT INHIBITION OF PP2CS JRNL TITL 2 BY A SUBCLASS OF PYL PROTEINS JRNL REF MOL.CELL V. 42 662 2011 JRNL REFN ISSN 1097-2765 JRNL PMID 21658606 JRNL DOI 10.1016/J.MOLCEL.2011.05.011 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.3_473) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 28673 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1455 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 28.6031 - 3.2306 0.98 2901 145 0.1835 0.1832 REMARK 3 2 3.2306 - 2.5647 1.00 2850 148 0.1828 0.2129 REMARK 3 3 2.5647 - 2.2407 1.00 2798 160 0.1686 0.2115 REMARK 3 4 2.2407 - 2.0359 1.00 2773 152 0.1602 0.1922 REMARK 3 5 2.0359 - 1.8900 0.99 2749 142 0.1543 0.2373 REMARK 3 6 1.8900 - 1.7786 0.98 2756 133 0.1443 0.2224 REMARK 3 7 1.7786 - 1.6895 0.97 2666 168 0.1619 0.1907 REMARK 3 8 1.6895 - 1.6160 0.95 2639 131 0.1708 0.2608 REMARK 3 9 1.6160 - 1.5538 0.94 2578 148 0.1801 0.2462 REMARK 3 10 1.5538 - 1.5002 0.90 2508 128 0.2049 0.2722 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 60.79 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.19130 REMARK 3 B22 (A**2) : 0.13490 REMARK 3 B33 (A**2) : -0.32550 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1493 REMARK 3 ANGLE : 1.023 2033 REMARK 3 CHIRALITY : 0.064 234 REMARK 3 PLANARITY : 0.004 266 REMARK 3 DIHEDRAL : 14.853 564 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 3RT2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065341. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : ROTATED-INCLINED DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29479 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.37800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.480 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: 3KDH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MAGNESIUM ACETATE, 20% PEG3350, REMARK 280 PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 48.35900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.35900 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 19.00850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.21250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.00850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.21250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.35900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.00850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.21250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.35900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.00850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.21250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 38.01700 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -48.35900 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 345 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 347 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 MET A 1 REMARK 465 ASN A 2 REMARK 465 GLY A 3 REMARK 465 ASP A 4 REMARK 465 GLU A 5 REMARK 465 THR A 6 REMARK 465 LYS A 7 REMARK 465 LYS A 8 REMARK 465 VAL A 9 REMARK 465 LYS A 181 REMARK 465 LYS A 182 REMARK 465 ILE A 183 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 184 O HOH A 184 4555 1.98 REMARK 500 O HOH A 275 O HOH A 275 4555 2.19 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 11 114.84 -160.69 REMARK 500 TYR A 55 -15.75 -144.09 REMARK 500 SER A 178 40.59 -96.15 REMARK 500 MET A 179 -47.71 -136.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RT0 RELATED DB: PDB DBREF 3RT2 A 1 183 UNP Q8H1R0 PYL10_ARATH 1 183 SEQRES 1 A 183 MET ASN GLY ASP GLU THR LYS LYS VAL GLU SER GLU TYR SEQRES 2 A 183 ILE LYS LYS HIS HIS ARG HIS GLU LEU VAL GLU SER GLN SEQRES 3 A 183 CYS SER SER THR LEU VAL LYS HIS ILE LYS ALA PRO LEU SEQRES 4 A 183 HIS LEU VAL TRP SER ILE VAL ARG ARG PHE ASP GLU PRO SEQRES 5 A 183 GLN LYS TYR LYS PRO PHE ILE SER ARG CYS VAL VAL GLN SEQRES 6 A 183 GLY LYS LYS LEU GLU VAL GLY SER VAL ARG GLU VAL ASP SEQRES 7 A 183 LEU LYS SER GLY LEU PRO ALA THR LYS SER THR GLU VAL SEQRES 8 A 183 LEU GLU ILE LEU ASP ASP ASN GLU HIS ILE LEU GLY ILE SEQRES 9 A 183 ARG ILE VAL GLY GLY ASP HIS ARG LEU LYS ASN TYR SER SEQRES 10 A 183 SER THR ILE SER LEU HIS SER GLU THR ILE ASP GLY LYS SEQRES 11 A 183 THR GLY THR LEU ALA ILE GLU SER PHE VAL VAL ASP VAL SEQRES 12 A 183 PRO GLU GLY ASN THR LYS GLU GLU THR CYS PHE PHE VAL SEQRES 13 A 183 GLU ALA LEU ILE GLN CYS ASN LEU ASN SER LEU ALA ASP SEQRES 14 A 183 VAL THR GLU ARG LEU GLN ALA GLU SER MET GLU LYS LYS SEQRES 15 A 183 ILE FORMUL 2 HOH *175(H2 O) HELIX 1 1 SER A 11 HIS A 18 1 8 HELIX 2 2 PRO A 38 ARG A 47 1 10 HELIX 3 3 GLU A 51 TYR A 55 5 5 HELIX 4 4 THR A 148 SER A 178 1 31 SHEET 1 A 7 GLN A 26 ILE A 35 0 SHEET 2 A 7 LYS A 130 ASP A 142 -1 O THR A 133 N ILE A 35 SHEET 3 A 7 SER A 117 ILE A 127 -1 N GLU A 125 O GLY A 132 SHEET 4 A 7 ILE A 101 GLY A 109 -1 N LEU A 102 O ILE A 120 SHEET 5 A 7 LYS A 87 ASP A 96 -1 N THR A 89 O GLY A 108 SHEET 6 A 7 VAL A 74 LEU A 79 -1 N ARG A 75 O GLU A 90 SHEET 7 A 7 ILE A 59 VAL A 64 -1 N VAL A 63 O GLU A 76 SSBOND 1 CYS A 27 CYS A 153 1555 1555 2.02 CRYST1 38.017 98.425 96.718 90.00 90.00 90.00 C 2 2 21 8 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 0.026304 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010160 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010339 0.00000