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HEADER HYDROLASE 04-JAN-21 7BFO
TITLE THERMOGUTTA TERRIFONTIS ESTERASE 2 PHOSPHONYLATED BY VX
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 1 10-FEB-21 7BFO 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) : 43.81
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 19410
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.162
REMARK 3 R VALUE (WORKING SET) : 0.160
REMARK 3 FREE R VALUE : 0.198
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 971
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 43.8100 - 3.8100 1.00 2788 146 0.1510 0.1592
REMARK 3 2 3.8100 - 3.0300 1.00 2663 140 0.1629 0.2001
REMARK 3 3 3.0300 - 2.6400 1.00 2641 139 0.1757 0.2430
REMARK 3 4 2.6400 - 2.4000 1.00 2608 138 0.1618 0.2132
REMARK 3 5 2.4000 - 2.2300 1.00 2614 137 0.1578 0.2250
REMARK 3 6 2.2300 - 2.1000 1.00 2598 138 0.1567 0.2213
REMARK 3 7 2.1000 - 1.9900 0.99 2527 133 0.1629 0.2200
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) : 0.158
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.942
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 26.79
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.47
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 : 0.004 2258
REMARK 3 ANGLE : 0.730 3063
REMARK 3 CHIRALITY : 0.051 319
REMARK 3 PLANARITY : 0.005 407
REMARK 3 DIHEDRAL : 5.993 315
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): 9.1570 10.9625 14.6088
REMARK 3 T TENSOR
REMARK 3 T11: 0.1381 T22: 0.1478
REMARK 3 T33: 0.1455 T12: 0.0138
REMARK 3 T13: -0.0095 T23: 0.0037
REMARK 3 L TENSOR
REMARK 3 L11: 1.3716 L22: 1.8244
REMARK 3 L33: 1.1799 L12: 0.0573
REMARK 3 L13: -0.1580 L23: -0.1667
REMARK 3 S TENSOR
REMARK 3 S11: 0.0362 S12: 0.1051 S13: -0.0662
REMARK 3 S21: 0.0851 S22: -0.0296 S23: -0.1550
REMARK 3 S31: 0.0753 S32: 0.0892 S33: 0.0019
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 7BFO 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_1292113285.
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 : 19423
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990
REMARK 200 RESOLUTION RANGE LOW (A) : 43.810
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 13.00
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 29.1500
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) : 2.07
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 (%): 43.64
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18
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 26.85000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.88000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.92000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.88000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.85000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.92000
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: 200 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 12100 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 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 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: 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 19.44 55.91
REMARK 500 SVX A 126 -112.35 54.85
REMARK 500 ASP A 140 -147.20 64.54
REMARK 500 ASN A 161 72.16 13.31
REMARK 500 GLU A 182 69.04 -42.63
REMARK 500 ARG A 183 47.93 39.34
REMARK 500 ASN A 258 17.79 58.05
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 7BFN RELATED DB: PDB
REMARK 900 APP FORME OF SAME PROTEIN
DBREF1 7BFO A 1 286 UNP A0A0X1KHD1_9BACT
DBREF2 7BFO A A0A0X1KHD1 1 286
SEQADV 7BFO 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 SVX 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 7BFO SVX A 126 SER MODIFIED RESIDUE
HET SVX A 126 12
HET EOH A 301 3
HETNAM SVX O-[(R)-ETHOXY(METHYL)PHOSPHORYL]-L-SERINE
HETNAM EOH ETHANOL
FORMUL 1 SVX C6 H14 N O5 P
FORMUL 2 EOH C2 H6 O
FORMUL 3 HOH *239(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 SVX A 126 VAL A 138 1 13
HELIX 6 AA6 ARG A 183 LEU A 188 5 6
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 PHE A 211 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 SVX A 126 1555 1555 1.33
LINK C SVX A 126 N ALA A 127 1555 1555 1.33
CISPEP 1 TYR A 8 PRO A 9 0 2.95
CRYST1 53.700 67.840 75.760 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 0.018622 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014741 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013200 0.00000
TER 2195 LYS A 281
MASTER 258 0 2 9 8 0 0 6 2411 1 17 23
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