HEADER HYDROLASE 03-FEB-18 5Z9H TITLE CRYSTAL STRUCTURE OF KAI2_PLY2(A219V) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE ESTERASE KAI2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN DWARF-14-LIKE,PROTEIN D14-LIKE,PROTEIN HYPOSENSITIVE COMPND 5 TO LIGHT,PROTEIN KARRIKIN INSENSITIVE 2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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: KAI2, D14L, HTL, AT4G37470, F6G17.120; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALPHA/BETA HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.L.KIM,J.S.CHA,M.S.SOH,H.S.CHO REVDAT 2 22-NOV-23 5Z9H 1 REMARK REVDAT 1 22-AUG-18 5Z9H 0 JRNL AUTH I.LEE,K.KIM,S.LEE,S.LEE,E.HWANG,K.SHIN,D.KIM,J.CHOI,H.CHOI, JRNL AUTH 2 J.S.CHA,H.KIM,R.A.LEE,S.JEONG,J.KIM,Y.KIM,H.G.NAM,S.K.PARK, JRNL AUTH 3 H.S.CHO,M.S.SOH JRNL TITL A MISSENSE ALLELE OF KARRIKIN-INSENSITIVE2 IMPAIRS JRNL TITL 2 LIGAND-BINDING AND DOWNSTREAM SIGNALING IN ARABIDOPSIS JRNL TITL 3 THALIANA. JRNL REF J. EXP. BOT. V. 69 3609 2018 JRNL REFN ESSN 1460-2431 JRNL PMID 29722815 JRNL DOI 10.1093/JXB/ERY164 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.220 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 43059 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.136 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2170 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 27.7518 - 3.7517 0.99 2612 160 0.1539 0.1571 REMARK 3 2 3.7517 - 2.9790 1.00 2573 150 0.1591 0.1881 REMARK 3 3 2.9790 - 2.6027 1.00 2565 145 0.1677 0.1851 REMARK 3 4 2.6027 - 2.3649 1.00 2597 122 0.1465 0.1729 REMARK 3 5 2.3649 - 2.1955 1.00 2529 153 0.1373 0.1733 REMARK 3 6 2.1955 - 2.0661 1.00 2569 142 0.1281 0.1607 REMARK 3 7 2.0661 - 1.9626 1.00 2534 126 0.1195 0.1613 REMARK 3 8 1.9626 - 1.8772 1.00 2576 128 0.1163 0.1526 REMARK 3 9 1.8772 - 1.8050 1.00 2578 125 0.1138 0.1579 REMARK 3 10 1.8050 - 1.7427 1.00 2563 120 0.1096 0.1610 REMARK 3 11 1.7427 - 1.6882 0.99 2549 128 0.1030 0.1688 REMARK 3 12 1.6882 - 1.6399 1.00 2507 143 0.0941 0.1410 REMARK 3 13 1.6399 - 1.5968 0.99 2554 127 0.0944 0.1624 REMARK 3 14 1.5968 - 1.5578 0.99 2537 122 0.0940 0.1613 REMARK 3 15 1.5578 - 1.5224 0.99 2540 140 0.0976 0.1666 REMARK 3 16 1.5224 - 1.4900 0.99 2506 139 0.1099 0.1837 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.020 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 : 0.006 2120 REMARK 3 ANGLE : 1.028 2889 REMARK 3 CHIRALITY : 0.041 332 REMARK 3 PLANARITY : 0.005 377 REMARK 3 DIHEDRAL : 12.940 758 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 5Z9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1300006703. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 93.1 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 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 : 43147 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 48.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 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: MOLREP REMARK 200 STARTING MODEL: 1WOM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M NA-CITRATE, 100 MM HEPES (PH 7.5), REMARK 280 5% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K 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 27.74700 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 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 ALA A 269 REMARK 465 MET A 270 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 MET A 166 CG SD CE 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 418 2.11 REMARK 500 O HOH A 399 O HOH A 423 2.13 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 28 -166.36 -120.12 REMARK 500 SER A 95 -122.90 56.47 REMARK 500 ARG A 123 121.75 -172.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 5Z9H A 1 270 UNP Q9SZU7 KAI2_ARATH 1 270 SEQADV 5Z9H VAL A 219 UNP Q9SZU7 ALA 219 ENGINEERED MUTATION SEQRES 1 A 270 MET GLY VAL VAL GLU GLU ALA HIS ASN VAL LYS VAL ILE SEQRES 2 A 270 GLY SER GLY GLU ALA THR ILE VAL LEU GLY HIS GLY PHE SEQRES 3 A 270 GLY THR ASP GLN SER VAL TRP LYS HIS LEU VAL PRO HIS SEQRES 4 A 270 LEU VAL ASP ASP TYR ARG VAL VAL LEU TYR ASP ASN MET SEQRES 5 A 270 GLY ALA GLY THR THR ASN PRO ASP TYR PHE ASP PHE ASP SEQRES 6 A 270 ARG TYR SER ASN LEU GLU GLY TYR SER PHE ASP LEU ILE SEQRES 7 A 270 ALA ILE LEU GLU ASP LEU LYS ILE GLU SER CYS ILE PHE SEQRES 8 A 270 VAL GLY HIS SER VAL SER ALA MET ILE GLY VAL LEU ALA SEQRES 9 A 270 SER LEU ASN ARG PRO ASP LEU PHE SER LYS ILE VAL MET SEQRES 10 A 270 ILE SER ALA SER PRO ARG TYR VAL ASN ASP VAL ASP TYR SEQRES 11 A 270 GLN GLY GLY PHE GLU GLN GLU ASP LEU ASN GLN LEU PHE SEQRES 12 A 270 GLU ALA ILE ARG SER ASN TYR LYS ALA TRP CYS LEU GLY SEQRES 13 A 270 PHE ALA PRO LEU ALA VAL GLY GLY ASP MET ASP SER ILE SEQRES 14 A 270 ALA VAL GLN GLU PHE SER ARG THR LEU PHE ASN MET ARG SEQRES 15 A 270 PRO ASP ILE ALA LEU SER VAL GLY GLN THR ILE PHE GLN SEQRES 16 A 270 SER ASP MET ARG GLN ILE LEU PRO PHE VAL THR VAL PRO SEQRES 17 A 270 CYS HIS ILE LEU GLN SER VAL LYS ASP LEU VAL VAL PRO SEQRES 18 A 270 VAL VAL VAL SER GLU TYR LEU HIS ALA ASN LEU GLY CYS SEQRES 19 A 270 GLU SER VAL VAL GLU VAL ILE PRO SER ASP GLY HIS LEU SEQRES 20 A 270 PRO GLN LEU SER SER PRO ASP SER VAL ILE PRO VAL ILE SEQRES 21 A 270 LEU ARG HIS ILE ARG ASN ASP ILE ALA MET FORMUL 2 HOH *198(H2 O) HELIX 1 AA1 GLY A 2 HIS A 8 1 7 HELIX 2 AA2 ASP A 29 LYS A 34 5 6 HELIX 3 AA3 LEU A 36 LEU A 40 5 5 HELIX 4 AA4 ASN A 58 PHE A 62 5 5 HELIX 5 AA5 ASP A 65 ASN A 69 5 5 HELIX 6 AA6 LEU A 70 LEU A 84 1 15 HELIX 7 AA7 SER A 95 ARG A 108 1 14 HELIX 8 AA8 GLU A 135 ASN A 149 1 15 HELIX 9 AA9 ASN A 149 GLY A 163 1 15 HELIX 10 AB1 SER A 168 MET A 181 1 14 HELIX 11 AB2 ARG A 182 GLN A 195 1 14 HELIX 12 AB3 MET A 198 VAL A 205 5 8 HELIX 13 AB4 PRO A 221 LEU A 232 1 12 HELIX 14 AB5 LEU A 247 SER A 252 1 6 HELIX 15 AB6 SER A 252 ASN A 266 1 15 SHEET 1 AA1 7 LYS A 11 ILE A 13 0 SHEET 2 AA1 7 ARG A 45 LEU A 48 -1 O VAL A 46 N ILE A 13 SHEET 3 AA1 7 THR A 19 GLY A 23 1 N ILE A 20 O VAL A 47 SHEET 4 AA1 7 CYS A 89 HIS A 94 1 O HIS A 94 N GLY A 23 SHEET 5 AA1 7 PHE A 112 ILE A 118 1 O VAL A 116 N PHE A 91 SHEET 6 AA1 7 CYS A 209 LYS A 216 1 O HIS A 210 N MET A 117 SHEET 7 AA1 7 SER A 236 ASP A 244 1 O VAL A 237 N ILE A 211 CRYST1 50.842 55.494 53.019 90.00 116.42 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 0.019669 0.000000 0.009771 0.00000 SCALE2 0.000000 0.018020 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021060 0.00000