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 2 04-OCT-23 6AVW 1 REMARK 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