HEADER PLANT PROTEIN/ANTAGONIST 28-APR-21 7MLD TITLE PYL10 BOUND TO THE ABA PAN-ANTAGONIST ANTABACTIN 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 KEYWDS PYR/PYL/RCAR, PYL10, HORMONE RECEPTOR, PLANT PROTEIN, PLANT PROTEIN- KEYWDS 2 ANTAGONIST COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.C.PETERSON,A.S.VAIDYA,B.F.VOLKMAN,S.R.CUTLER REVDAT 2 18-OCT-23 7MLD 1 REMARK REVDAT 1 29-SEP-21 7MLD 0 JRNL AUTH A.S.VAIDYA,F.C.PETERSON,J.ECKHARDT,Z.XING,S.Y.PARK, JRNL AUTH 2 W.DEJONGHE,J.TAKEUCHI,O.PRI-TAL,J.FARIA,D.ELZINGA, JRNL AUTH 3 B.F.VOLKMAN,Y.TODOROKI,A.MOSQUNA,M.OKAMOTO,S.R.CUTLER JRNL TITL CLICK-TO-LEAD DESIGN OF A PICOMOLAR ABA RECEPTOR ANTAGONIST JRNL TITL 2 WITH POTENT ACTIVITY IN VIVO. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 34531324 JRNL DOI 10.1073/PNAS.2108281118 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 14462 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1446 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 42.4500 - 3.8700 1.00 1373 154 0.1433 0.1881 REMARK 3 2 3.8700 - 3.0700 1.00 1341 149 0.1502 0.1874 REMARK 3 3 3.0700 - 2.6900 0.99 1343 148 0.1620 0.1912 REMARK 3 4 2.6900 - 2.4400 0.99 1321 148 0.1765 0.2236 REMARK 3 5 2.4400 - 2.2700 0.99 1333 147 0.1589 0.2065 REMARK 3 6 2.2700 - 2.1300 0.98 1295 147 0.1562 0.1953 REMARK 3 7 2.1300 - 2.0300 0.98 1308 144 0.1579 0.2153 REMARK 3 8 2.0300 - 1.9400 0.97 1296 143 0.1620 0.2146 REMARK 3 9 1.9400 - 1.8600 0.94 1245 137 0.1806 0.2767 REMARK 3 10 1.8600 - 1.8000 0.87 1161 129 0.3144 0.3572 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.225 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.949 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.38 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 : 0.009 1285 REMARK 3 ANGLE : 0.938 1749 REMARK 3 CHIRALITY : 0.058 204 REMARK 3 PLANARITY : 0.005 220 REMARK 3 DIHEDRAL : 16.199 806 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 7MLD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1000256459. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : 14845 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 97.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 6NWB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM TRIBASIC AMMONIUM CITRATE AND REMARK 280 22% (W/V) PEG 3350, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 29.87650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.19500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.87650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.19500 REMARK 290 SMTRY3 4 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 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 463 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 500 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 LYS A 67 REMARK 465 LYS A 68 REMARK 465 GLU A 180 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 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 319 O HOH A 429 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 411 O HOH A 490 2555 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 TYR A 55 -7.40 -142.53 REMARK 500 ASP A 110 36.25 -97.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 501 DISTANCE = 6.12 ANGSTROMS DBREF 7MLD A 25 183 UNP Q8H1R0 PYL10_ARATH 25 183 SEQRES 1 A 159 SER GLN CYS SER SER THR LEU VAL LYS HIS ILE LYS ALA SEQRES 2 A 159 PRO LEU HIS LEU VAL TRP SER ILE VAL ARG ARG PHE ASP SEQRES 3 A 159 GLU PRO GLN LYS TYR LYS PRO PHE ILE SER ARG CYS VAL SEQRES 4 A 159 VAL GLN GLY LYS LYS LEU GLU VAL GLY SER VAL ARG GLU SEQRES 5 A 159 VAL ASP LEU LYS SER GLY LEU PRO ALA THR LYS SER THR SEQRES 6 A 159 GLU VAL LEU GLU ILE LEU ASP ASP ASN GLU HIS ILE LEU SEQRES 7 A 159 GLY ILE ARG ILE VAL GLY GLY ASP HIS ARG LEU LYS ASN SEQRES 8 A 159 TYR SER SER THR ILE SER LEU HIS SER GLU THR ILE ASP SEQRES 9 A 159 GLY LYS THR GLY THR LEU ALA ILE GLU SER PHE VAL VAL SEQRES 10 A 159 ASP VAL PRO GLU GLY ASN THR LYS GLU GLU THR CYS PHE SEQRES 11 A 159 PHE VAL GLU ALA LEU ILE GLN CYS ASN LEU ASN SER LEU SEQRES 12 A 159 ALA ASP VAL THR GLU ARG LEU GLN ALA GLU SER MET GLU SEQRES 13 A 159 LYS LYS ILE HET ZLG A 201 45 HET CIT A 202 13 HETNAM ZLG ANTABACTIN HETNAM CIT CITRIC ACID HETSYN ZLG 1-{2-[3,5-DICYCLOPROPYL-4-(4-{[(6-FLUOROQUINOLINE-2- HETSYN 2 ZLG CARBONYL)AMINO]METHYL}-1H-1,2,3-TRIAZOL-1-YL) HETSYN 3 ZLG PHENYL]ACETAMIDO}CYCLOHEXANE-1-CARBOXYLIC ACID FORMUL 2 ZLG C34 H35 F N6 O4 FORMUL 3 CIT C6 H8 O7 FORMUL 4 HOH *201(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 LEU A 102 O ILE A 120 SHEET 5 AA1 7 LYS A 87 ASP A 96 -1 N THR A 89 O VAL A 107 SHEET 6 AA1 7 VAL A 74 LEU A 79 -1 N VAL A 77 O SER A 88 SHEET 7 AA1 7 ILE A 59 VAL A 64 -1 N SER A 60 O ASP A 78 SSBOND 1 CYS A 27 CYS A 153 1555 1555 2.03 CRYST1 59.753 64.390 44.567 90.00 109.10 90.00 C 1 2 1 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 0.016736 0.000000 0.005795 0.00000 SCALE2 0.000000 0.015530 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023745 0.00000