HEADER HYDROLASE 04-JAN-21 7BFT TITLE THERMOGUTTA TERRIFONTIS ESTERASE 2 PHOSPHORAMYLATED BY TABUN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ESTERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ESTERASE EST2; COMPND 5 EC: 3.1.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOGUTTA TERRIFONTIS; SOURCE 3 ORGANISM_TAXID: 1331910; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS NERVE AGENT, CONJUGATE, ESTERASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.B.BRAZZOLOTTO,J.BZDRENGA,F.NACHON REVDAT 2 31-JAN-24 7BFT 1 REMARK REVDAT 1 10-FEB-21 7BFT 0 JRNL AUTH J.BZDRENGA,E.TRENET,F.CHANTEGREIL,K.BERNAL,F.NACHON, JRNL AUTH 2 X.BRAZZOLOTTO JRNL TITL A THERMOPHILIC BACTERIAL ESTERASE FOR SCAVENGING NERVE JRNL TITL 2 AGENTS: A KINETIC, BIOPHYSICAL AND STRUCTURAL STUDY. JRNL REF MOLECULES V. 26 2021 JRNL REFN ESSN 1420-3049 JRNL PMID 33513869 JRNL DOI 10.3390/MOLECULES26030657 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 19233 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 962 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 43.6700 - 3.8100 1.00 2771 145 0.1458 0.1618 REMARK 3 2 3.8100 - 3.0300 1.00 2642 139 0.1577 0.1879 REMARK 3 3 3.0300 - 2.6400 1.00 2617 138 0.1741 0.2189 REMARK 3 4 2.6400 - 2.4000 1.00 2588 137 0.1669 0.2082 REMARK 3 5 2.4000 - 2.2300 1.00 2584 136 0.1644 0.2231 REMARK 3 6 2.2300 - 2.1000 1.00 2568 134 0.1692 0.2165 REMARK 3 7 2.1000 - 1.9900 0.98 2501 133 0.1791 0.2276 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.183 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.252 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.09 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 : 0.008 2141 REMARK 3 ANGLE : 1.054 2908 REMARK 3 CHIRALITY : 0.064 306 REMARK 3 PLANARITY : 0.009 384 REMARK 3 DIHEDRAL : 6.325 301 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 9.3275 11.7100 15.3418 REMARK 3 T TENSOR REMARK 3 T11: 0.1585 T22: 0.1579 REMARK 3 T33: 0.1572 T12: 0.0101 REMARK 3 T13: -0.0120 T23: -0.0074 REMARK 3 L TENSOR REMARK 3 L11: 0.9691 L22: 1.0495 REMARK 3 L33: 0.6598 L12: -0.0653 REMARK 3 L13: 0.0443 L23: 0.0236 REMARK 3 S TENSOR REMARK 3 S11: 0.0068 S12: 0.0770 S13: 0.0228 REMARK 3 S21: 0.1134 S22: 0.0272 S23: -0.1275 REMARK 3 S31: 0.0397 S32: 0.0627 S33: -0.0003 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 7BFT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1292113291. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-20 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9801 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19260 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 43.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 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: PHASER REMARK 200 STARTING MODEL: 7BFN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM HEPES PH 7.5, 25% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 26.87000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.47000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.93500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.47000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.87000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.93500 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 TOTAL BURIED SURFACE AREA: 220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 0 REMARK 465 ALA A 1 REMARK 465 GLU A 2 REMARK 465 VAL A 3 REMARK 465 GLY A 4 REMARK 465 ARG A 5 REMARK 465 LYS A 172 REMARK 465 ASP A 173 REMARK 465 HIS A 174 REMARK 465 VAL A 175 REMARK 465 PRO A 176 REMARK 465 ARG A 177 REMARK 465 GLN A 178 REMARK 465 ASP A 179 REMARK 465 TRP A 180 REMARK 465 GLU A 181 REMARK 465 GLU A 182 REMARK 465 ARG A 183 REMARK 465 GLY A 282 REMARK 465 GLU A 283 REMARK 465 SER A 284 REMARK 465 GLN A 285 REMARK 465 PRO A 286 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 OE1 GLU A 186 O HOH A 401 1.95 REMARK 500 NH1 ARG A 187 O HOH A 402 2.12 REMARK 500 OD2 ASP A 140 O HOH A 403 2.16 REMARK 500 O GLY A 256 O HOH A 404 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 TRP A 55 17.46 57.60 REMARK 500 SER A 57 -157.75 -148.22 REMARK 500 SUN A 126 -112.00 51.09 REMARK 500 ASP A 140 -149.98 64.73 REMARK 500 ASN A 161 71.63 16.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7BFN RELATED DB: PDB REMARK 900 APO FORM OF THE SAME PROTEIN DBREF1 7BFT A 1 286 UNP A0A0X1KHD1_9BACT DBREF2 7BFT A A0A0X1KHD1 1 286 SEQADV 7BFT GLY A 0 UNP A0A0X1KHD EXPRESSION TAG SEQRES 1 A 287 GLY ALA GLU VAL GLY ARG LEU ARG TYR PRO PRO GLU MET SEQRES 2 A 287 PRO GLY ALA GLU VAL LYS VAL TYR LYS LYS VAL ASP ASN SEQRES 3 A 287 VAL ASP LEU LYS LEU TYR ILE TYR LYS PRO ALA ASP TRP SEQRES 4 A 287 LYS PRO ALA ASP ARG ARG SER ALA ILE VAL PHE PHE PHE SEQRES 5 A 287 GLY GLY GLY TRP GLN SER GLY SER PRO ALA GLN PHE ARG SEQRES 6 A 287 PRO GLN CYS GLU TYR PHE ALA GLY ARG GLY MET VAL ALA SEQRES 7 A 287 MET ALA ALA ASP TYR ARG VAL GLY SER ARG HIS ASN VAL SEQRES 8 A 287 LYS VAL ALA ASP CYS VAL ALA ASP ALA LYS SER ALA ILE SEQRES 9 A 287 ARG TRP VAL ARG GLN HIS ALA ALA GLU LEU GLY VAL ASP SEQRES 10 A 287 PRO GLN LYS ILE VAL ALA SER GLY GLY SUN ALA GLY GLY SEQRES 11 A 287 HIS LEU ALA ALA CYS THR VAL MET VAL PRO ASP LEU GLU SEQRES 12 A 287 ALA PRO GLU GLU ASP HIS THR ILE SER SER GLN ALA ASN SEQRES 13 A 287 ALA ALA ILE LEU PHE ASN PRO VAL LEU ILE LEU SER ARG SEQRES 14 A 287 GLU GLY LEU LYS ASP HIS VAL PRO ARG GLN ASP TRP GLU SEQRES 15 A 287 GLU ARG LEU ARG GLU ARG LEU GLY THR GLU PRO LYS ALA SEQRES 16 A 287 VAL SER PRO TYR HIS HIS ILE ARG ALA GLY LEU PRO PRO SEQRES 17 A 287 MET ILE ILE PHE HIS GLY THR ALA ASP ASN THR VAL PRO SEQRES 18 A 287 PHE GLU THR ILE ARG LEU PHE ALA GLU ALA MET LYS LYS SEQRES 19 A 287 ALA GLY ASN ARG CYS GLU LEU VAL PRO PHE GLU GLY ALA SEQRES 20 A 287 ALA HIS GLY PHE PHE ASN PHE GLY ARG GLY ASP ASN LEU SEQRES 21 A 287 ALA TYR GLN LYS THR LEU GLU LEU ALA ASP GLU PHE LEU SEQRES 22 A 287 VAL GLU ILE GLY PHE LEU ALA PRO LYS GLY GLU SER GLN SEQRES 23 A 287 PRO MODRES 7BFT SUN A 126 SER MODIFIED RESIDUE HET SUN A 126 14 HET PO4 A 301 5 HETNAM SUN O-[(R)-(DIMETHYLAMINO)(ETHOXY)PHOSPHORYL]-L-SERINE HETNAM PO4 PHOSPHATE ION HETSYN SUN TABUN CONJUGATED SERINE FORMUL 1 SUN C7 H17 N2 O5 P FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *231(H2 O) HELIX 1 AA1 SER A 59 GLN A 62 5 4 HELIX 2 AA2 PHE A 63 ARG A 73 1 11 HELIX 3 AA3 LYS A 91 HIS A 109 1 19 HELIX 4 AA4 HIS A 109 GLY A 114 1 6 HELIX 5 AA5 SUN A 126 VAL A 138 1 13 HELIX 6 AA6 LEU A 184 LEU A 188 5 5 HELIX 7 AA7 GLU A 191 ILE A 201 5 11 HELIX 8 AA8 PRO A 220 ALA A 234 1 15 HELIX 9 AA9 ASN A 258 ILE A 275 1 18 SHEET 1 AA1 8 GLU A 16 VAL A 23 0 SHEET 2 AA1 8 VAL A 26 TYR A 33 -1 O ILE A 32 N GLU A 16 SHEET 3 AA1 8 VAL A 76 ALA A 80 -1 O ALA A 77 N TYR A 33 SHEET 4 AA1 8 ARG A 44 PHE A 50 1 N PHE A 49 O MET A 78 SHEET 5 AA1 8 VAL A 115 GLY A 125 1 O VAL A 121 N ALA A 46 SHEET 6 AA1 8 ALA A 156 PHE A 160 1 O PHE A 160 N GLY A 124 SHEET 7 AA1 8 MET A 208 GLY A 213 1 O ILE A 209 N LEU A 159 SHEET 8 AA1 8 CYS A 238 PHE A 243 1 O VAL A 241 N ILE A 210 LINK C GLY A 125 N SUN A 126 1555 1555 1.34 LINK C SUN A 126 N ALA A 127 1555 1555 1.34 CISPEP 1 TYR A 8 PRO A 9 0 4.18 CRYST1 53.740 67.870 74.940 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 0.018608 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014734 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013344 0.00000