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HEADER HYDROLASE 29-AUG-17 6ATX
TITLE CRYSTAL STRUCTURE OF PHYSCOMITRELLA PATENS KAI2-LIKE C
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PPKAI2-LIKE C;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PHYSCOMITRELLA PATENS SUBSP. PATENS;
SOURCE 3 ORGANISM_COMMON: MOSS;
SOURCE 4 ORGANISM_TAXID: 3218;
SOURCE 5 GENE: PHYPADRAFT_213263;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T3
KEYWDS ALPHA/BETA HYDROLASE, STRIGOLACTONE BINDING, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.BURGER,H.J.LEE,J.CHORY
REVDAT 1 06-FEB-19 6ATX 0
JRNL AUTH M.BURGER,K.MASHIGUCHI,H.J.LEE,M.NAKANO,K.TAKEMOTO,Y.SETO,
JRNL AUTH 2 S.YAMAGUCHI,J.CHORY
JRNL TITL STRUCTURAL BASIS OF KARRIKIN AND NON-NATURAL STRIGOLACTONE
JRNL TITL 2 PERCEPTION IN PHYSCOMITRELLA PATENS.
JRNL REF CELL REP V. 26 855 2019
JRNL REFN ESSN 2211-1247
JRNL PMID 30673608
JRNL DOI 10.1016/J.CELREP.2019.01.003
REMARK 2
REMARK 2 RESOLUTION. 2.74 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX
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) : 2.74
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.63
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.351
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 7881
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.180
REMARK 3 R VALUE (WORKING SET) : 0.178
REMARK 3 FREE R VALUE : 0.219
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.063
REMARK 3 FREE R VALUE TEST SET COUNT : 399
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 46.6367 - 3.9517 1.00 2522 136 0.1442 0.1774
REMARK 3 2 3.9517 - 3.1368 1.00 2475 127 0.1831 0.2156
REMARK 3 3 3.1368 - 2.7403 1.00 2485 136 0.2467 0.3143
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) : 0.392
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.691
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 37.01
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.32
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 : 0.003 2111
REMARK 3 ANGLE : 0.596 2877
REMARK 3 CHIRALITY : 0.044 334
REMARK 3 PLANARITY : 0.004 369
REMARK 3 DIHEDRAL : 2.725 1244
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 6ATX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-17.
REMARK 100 THE DEPOSITION ID IS D_1000229824.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-AUG-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ALS
REMARK 200 BEAMLINE : 8.2.1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.000
REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111)
REMARK 200 OPTICS : MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7881
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.740
REMARK 200 RESOLUTION RANGE LOW (A) : 46.630
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 13.70
REMARK 200 R MERGE (I) : 0.22010
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 12.3500
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.74
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.84
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.83440
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: PDB ENTRY 4IH1
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.17
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M AMMONIUM SULFATE, 0.2 M BIS
REMARK 280 -TRIS, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43
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 -Y,X,Z+3/4
REMARK 290 4555 Y,-X,Z+1/4
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 70.44000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 105.66000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.22000
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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11250 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 GLY A -1
REMARK 465 PRO A 0
REMARK 465 MET A 1
REMARK 465 ASP A 2
REMARK 465 GLU A 3
REMARK 465 LEU A 4
REMARK 465 PRO A 5
REMARK 465 SER A 6
REMARK 465 GLU A 272
REMARK 465 SER A 273
REMARK 465 CYS A 274
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 LEU A 8 -54.51 71.75
REMARK 500 MET A 18 28.95 -141.47
REMARK 500 THR A 31 -167.76 -114.15
REMARK 500 GLU A 88 36.02 39.62
REMARK 500 SER A 98 -117.90 60.82
REMARK 500 LYS A 117 137.54 -177.26
REMARK 500 ALA A 167 179.49 66.60
REMARK 500 ILE A 169 13.98 -68.02
REMARK 500
REMARK 500 REMARK: NULL
DBREF 6ATX A 1 274 UNP A9SKF7 A9SKF7_PHYPA 1 274
SEQADV 6ATX GLY A -1 UNP A9SKF7 CLONING ARTIFACT
SEQADV 6ATX PRO A 0 UNP A9SKF7 CLONING ARTIFACT
SEQRES 1 A 276 GLY PRO MET ASP GLU LEU PRO SER LEU LEU GLU VAL HIS
SEQRES 2 A 276 ASN VAL ARG ILE VAL GLY MET GLY GLU GLU LEU VAL VAL
SEQRES 3 A 276 LEU ALA HIS GLY PHE GLY THR ASP GLN SER VAL TRP LYS
SEQRES 4 A 276 HIS VAL ILE PRO HIS LEU VAL ASP ASP TYR ARG VAL ILE
SEQRES 5 A 276 LEU PHE ASP ASN MET GLY ALA GLY THR THR ASP PRO GLU
SEQRES 6 A 276 TYR PHE SER PHE SER ARG TYR SER THR LEU TYR GLY TYR
SEQRES 7 A 276 ALA ASP ASP LEU LEU THR ILE LEU ASP GLU LEU GLU VAL
SEQRES 8 A 276 GLN SER CYS ILE PHE VAL GLY HIS SER VAL SER GLY MET
SEQRES 9 A 276 VAL GLY CYS LEU ALA SER LEU TYR ARG PRO GLU ILE PHE
SEQRES 10 A 276 SER LYS ILE ILE THR ILE SER ALA SER PRO ARG TYR LEU
SEQRES 11 A 276 ASN ASP MET ASP TYR PHE GLY GLY PHE GLU GLN GLU ASP
SEQRES 12 A 276 LEU ASN GLN LEU PHE GLU ALA MET GLN SER ASN PHE LYS
SEQRES 13 A 276 ALA TRP VAL SER GLY PHE ALA PRO LEU ALA VAL GLY ALA
SEQRES 14 A 276 ASP ILE ASP SER MET ALA VAL GLN GLU PHE GLY ARG THR
SEQRES 15 A 276 LEU PHE ASN ILE ARG PRO ASP ILE ALA PHE SER VAL ALA
SEQRES 16 A 276 LYS THR ILE PHE GLN SER ASP LEU ARG SER ILE LEU PRO
SEQRES 17 A 276 LYS VAL THR VAL PRO CYS HIS ILE LEU GLN SER SER LYS
SEQRES 18 A 276 ASP LEU ALA VAL PRO VAL VAL VAL ALA ASP TYR LEU HIS
SEQRES 19 A 276 LEU THR LEU GLY GLY PRO THR ILE VAL GLU VAL LEU PRO
SEQRES 20 A 276 THR GLU GLY HIS LEU PRO GLN LEU SER SER PRO ASP ILE
SEQRES 21 A 276 VAL ILE PRO VAL LEU LYS ARG HIS VAL ALA GLY ASN LEU
SEQRES 22 A 276 GLU SER CYS
FORMUL 2 HOH *42(H2 O)
HELIX 1 AA1 ASP A 32 LYS A 37 5 6
HELIX 2 AA2 VAL A 39 LEU A 43 5 5
HELIX 3 AA3 ASP A 61 PHE A 65 5 5
HELIX 4 AA4 SER A 68 THR A 72 5 5
HELIX 5 AA5 LEU A 73 LEU A 87 1 15
HELIX 6 AA6 SER A 98 ARG A 111 1 14
HELIX 7 AA7 GLU A 138 ASN A 152 1 15
HELIX 8 AA8 ASN A 152 VAL A 165 1 14
HELIX 9 AA9 SER A 171 ASN A 183 1 13
HELIX 10 AB1 ARG A 185 GLN A 198 1 14
HELIX 11 AB2 LEU A 201 VAL A 208 5 8
HELIX 12 AB3 PRO A 224 LEU A 235 1 12
HELIX 13 AB4 LEU A 250 SER A 255 1 6
HELIX 14 AB5 SER A 255 ALA A 268 1 14
SHEET 1 AA1 6 TYR A 47 LEU A 51 0
SHEET 2 AA1 6 GLU A 21 ALA A 26 1 N VAL A 23 O ILE A 50
SHEET 3 AA1 6 CYS A 92 HIS A 97 1 O VAL A 95 N VAL A 24
SHEET 4 AA1 6 PHE A 115 ILE A 121 1 O ILE A 119 N PHE A 94
SHEET 5 AA1 6 CYS A 212 LYS A 219 1 O HIS A 213 N ILE A 118
SHEET 6 AA1 6 THR A 239 GLU A 247 1 O LEU A 244 N GLN A 216
CRYST1 46.630 46.630 140.880 90.00 90.00 90.00 P 43 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 0.021445 0.000000 0.000000 0.00000
SCALE2 0.000000 0.021445 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007098 0.00000
TER 2062 LEU A 271
MASTER 237 0 0 14 6 0 0 6 2103 1 0 22
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