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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 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
TER 2074 ILE A 268
MASTER 242 0 0 15 7 0 0 6 2271 1 0 21
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