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HEADER HYDROLASE 04-SEP-17 6AVW
TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA SOBER1 L63A
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CARBOXYLESTERASE SOBER1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: PHOSPHOLIPASE A2 SOBER1,PROTEIN SUPPRESSOR OF AVRBST-
COMPND 5 ELICITED RESISTANCE 1;
COMPND 6 EC: 3.1.1.-;
COMPND 7 ENGINEERED: YES;
COMPND 8 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: SOBER1, AT4G22305;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
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, PLANT DEACETYLASE, HYPERSENSITIVE RESPONSE,
KEYWDS 2 HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.BURGER,B.C.WILLIGE,J.CHORY
REVDAT 1 27-DEC-17 6AVW 0
JRNL AUTH M.BURGER,B.C.WILLIGE,J.CHORY
JRNL TITL A HYDROPHOBIC ANCHOR MECHANISM DEFINES A DEACETYLASE FAMILY
JRNL TITL 2 THAT SUPPRESSES HOST RESPONSE AGAINST YOPJ EFFECTORS.
JRNL REF NAT COMMUN V. 8 2201 2017
JRNL REFN ESSN 2041-1723
JRNL PMID 29259199
JRNL DOI 10.1038/S41467-017-02347-W
REMARK 2
REMARK 2 RESOLUTION. 2.14 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.10.1_2155)
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) : 2.14
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.66
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.338
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 10288
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.190
REMARK 3 R VALUE (WORKING SET) : 0.188
REMARK 3 FREE R VALUE : 0.226
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.006
REMARK 3 FREE R VALUE TEST SET COUNT : 515
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 42.6722 - 3.4037 1.00 2541 136 0.1812 0.1984
REMARK 3 2 3.4037 - 2.7018 1.00 2427 127 0.1912 0.2278
REMARK 3 3 2.7018 - 2.3603 1.00 2410 126 0.2024 0.2766
REMARK 3 4 2.3603 - 2.1445 1.00 2395 126 0.1867 0.2620
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) : 0.144
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.351
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 26.67
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.22
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 1655
REMARK 3 ANGLE : 0.580 2253
REMARK 3 CHIRALITY : 0.043 248
REMARK 3 PLANARITY : 0.005 290
REMARK 3 DIHEDRAL : 16.440 975
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 6AVW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-17.
REMARK 100 THE DEPOSITION ID IS D_1000229856.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 02-MAR-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
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 : NULL
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10296
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140
REMARK 200 RESOLUTION RANGE LOW (A) : 42.670
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 7.400
REMARK 200 R MERGE (I) : 0.14270
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 11.3100
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.14
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : 6.10
REMARK 200 R MERGE FOR SHELL (I) : 0.51330
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 5.900
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: 6AVV
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 31.20
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 2% (V/V) PEG 400,
REMARK 280 2 M AMMONIUM SULFATE., VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
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 22.79500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.00500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.77500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.00500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.79500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.77500
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 GLY A 212
REMARK 465 SER A 213
REMARK 465 SER A 214
REMARK 465 SER A 215
REMARK 465 THR A 216
REMARK 465 CYS A 217
REMARK 465 LEU A 218
REMARK 465 GLN A 219
REMARK 465 LEU A 220
REMARK 465 ASN A 221
REMARK 465 CYS A 222
REMARK 465 LEU A 223
REMARK 465 LYS A 224
REMARK 465 GLU A 225
REMARK 465 MET A 226
REMARK 465 PHE A 227
REMARK 465 HIS A 228
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 OE2 GLU A 183 OH TYR A 201 2.17
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 331 O HOH A 397 3555 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 106 -116.43 61.54
REMARK 500
REMARK 500 REMARK: NULL
DBREF 6AVW A 1 228 UNP Q84WK4 SOBR1_ARATH 1 228
SEQADV 6AVW GLY A -1 UNP Q84WK4 EXPRESSION TAG
SEQADV 6AVW PRO A 0 UNP Q84WK4 EXPRESSION TAG
SEQADV 6AVW ALA A 63 UNP Q84WK4 LEU 63 ENGINEERED MUTATION
SEQRES 1 A 230 GLY PRO MET ALA ARG THR PHE ILE LEU TRP LEU HIS GLY
SEQRES 2 A 230 LEU GLY ASP SER GLY PRO ALA ASN GLU PRO ILE GLN THR
SEQRES 3 A 230 GLN PHE LYS SER SER GLU LEU SER ASN ALA SER TRP LEU
SEQRES 4 A 230 PHE PRO SER ALA PRO PHE ASN PRO VAL THR CYS ASN ASN
SEQRES 5 A 230 GLY ALA VAL MET ARG SER TRP PHE ASP VAL PRO GLU ALA
SEQRES 6 A 230 PRO PHE LYS VAL GLY SER PRO ILE ASP GLU SER SER VAL
SEQRES 7 A 230 LEU GLU ALA VAL LYS ASN VAL HIS ALA ILE ILE ASP GLN
SEQRES 8 A 230 GLU ILE ALA GLU GLY THR ASN PRO GLU ASN VAL PHE ILE
SEQRES 9 A 230 CYS GLY LEU SER GLN GLY GLY ALA LEU THR LEU ALA SER
SEQRES 10 A 230 VAL LEU LEU TYR PRO LYS THR LEU GLY GLY GLY ALA VAL
SEQRES 11 A 230 LEU SER GLY TRP VAL PRO PHE THR SER SER ILE ILE SER
SEQRES 12 A 230 GLN PHE PRO GLU GLU ALA LYS LYS THR PRO ILE LEU TRP
SEQRES 13 A 230 SER HIS GLY THR ASP ASP ARG MET VAL LEU PHE GLU ALA
SEQRES 14 A 230 GLY GLN ALA ALA LEU PRO PHE LEU LYS GLU ALA GLY VAL
SEQRES 15 A 230 THR CYS GLU PHE LYS ALA TYR PRO GLY LEU GLY HIS SER
SEQRES 16 A 230 ILE SER ASN LYS GLU LEU LYS TYR ILE GLU SER TRP ILE
SEQRES 17 A 230 LYS ARG ARG LEU LYS GLY SER SER SER THR CYS LEU GLN
SEQRES 18 A 230 LEU ASN CYS LEU LYS GLU MET PHE HIS
FORMUL 2 HOH *104(H2 O)
HELIX 1 AA1 SER A 15 GLU A 20 1 6
HELIX 2 AA2 PRO A 21 PHE A 26 5 6
HELIX 3 AA3 THR A 47 ASN A 50 5 4
HELIX 4 AA4 ASP A 72 ALA A 92 1 21
HELIX 5 AA5 ASN A 96 GLU A 98 5 3
HELIX 6 AA6 SER A 106 LEU A 118 1 13
HELIX 7 AA7 THR A 136 PHE A 143 5 8
HELIX 8 AA8 GLU A 145 THR A 150 5 6
HELIX 9 AA9 LEU A 164 ALA A 170 1 7
HELIX 10 AB1 ALA A 170 GLY A 179 1 10
HELIX 11 AB2 SER A 195 LYS A 211 1 17
SHEET 1 AA1 6 SER A 35 LEU A 37 0
SHEET 2 AA1 6 PHE A 5 LEU A 9 1 N ILE A 6 O SER A 35
SHEET 3 AA1 6 VAL A 100 LEU A 105 1 O CYS A 103 N LEU A 7
SHEET 4 AA1 6 GLY A 125 LEU A 129 1 O ALA A 127 N ILE A 102
SHEET 5 AA1 6 ILE A 152 GLY A 157 1 O SER A 155 N VAL A 128
SHEET 6 AA1 6 CYS A 182 TYR A 187 1 O LYS A 185 N TRP A 154
SHEET 1 AA2 2 PHE A 43 PRO A 45 0
SHEET 2 AA2 2 VAL A 53 ARG A 55 -1 O MET A 54 N ASN A 44
CISPEP 1 ALA A 63 PRO A 64 0 3.91
CRYST1 45.590 51.550 76.010 90.00 90.00 90.00 P 21 21 21 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 0.021935 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019399 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013156 0.00000
TER 1611 LYS A 211
MASTER 267 0 0 11 8 0 0 6 1714 1 0 18
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