HEADER TRANSFERASE 27-SEP-17 6B4Y TITLE SCHISTOSOMA MANSONI (BLOOD FLUKE) SULFOTRANSFERASE/OXAMNIQUINE TITLE 2 COMPLEX, F39Y MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SULFOTRANSFERASE OXAMNIQUINE RESISTANCE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SULFOTRANSFERASE; COMPND 5 EC: 2.8.2.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHISTOSOMA MANSONI; SOURCE 3 ORGANISM_COMMON: BLOOD FLUKE; SOURCE 4 ORGANISM_TAXID: 6183; SOURCE 5 GENE: SULT-OR, SMP_089320; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PAG8H KEYWDS SULFOTRANSFERASE, PARASITE, DRUG RESISTANCE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.B.TAYLOR REVDAT 4 04-OCT-23 6B4Y 1 REMARK REVDAT 3 22-APR-20 6B4Y 1 JRNL REVDAT 2 11-DEC-19 6B4Y 1 COMPND REVDAT 1 10-OCT-18 6B4Y 0 JRNL AUTH A.R.RUGEL,M.A.GUZMAN,A.B.TAYLOR,F.D.CHEVALIER,R.S.TARPLEY, JRNL AUTH 2 S.F.MCHARDY,X.CAO,S.P.HOLLOWAY,T.J.C.ANDERSON,P.J.HART, JRNL AUTH 3 P.T.LOVERDE JRNL TITL WHY DOES OXAMNIQUINE KILL SCHISTOSOMA MANSONI AND NOT S. JRNL TITL 2 HAEMATOBIUM AND S. JAPONICUM? JRNL REF INT.J.PARASITOL. 2020 JRNL REFN ESSN 1879-0135 JRNL DOI 10.1016/J.IJPDDR.2020.04.001 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 21951 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 70.1538 - 4.6994 0.93 1489 148 0.1658 0.1592 REMARK 3 2 4.6994 - 3.7301 0.97 1464 147 0.1466 0.1716 REMARK 3 3 3.7301 - 3.2586 0.95 1389 140 0.1717 0.2210 REMARK 3 4 3.2586 - 2.9607 0.97 1424 142 0.2018 0.2586 REMARK 3 5 2.9607 - 2.7485 0.99 1440 144 0.2063 0.2537 REMARK 3 6 2.7485 - 2.5864 0.99 1432 144 0.2032 0.2630 REMARK 3 7 2.5864 - 2.4569 0.99 1418 142 0.1940 0.2312 REMARK 3 8 2.4569 - 2.3499 0.97 1403 141 0.2033 0.2504 REMARK 3 9 2.3499 - 2.2594 0.98 1422 142 0.1977 0.2508 REMARK 3 10 2.2594 - 2.1815 0.98 1400 141 0.2257 0.2780 REMARK 3 11 2.1815 - 2.1133 1.00 1426 143 0.2381 0.2819 REMARK 3 12 2.1133 - 2.0528 0.99 1411 141 0.2444 0.3213 REMARK 3 13 2.0528 - 1.9988 1.00 1421 141 0.2820 0.2821 REMARK 3 14 1.9988 - 1.9500 1.00 1414 142 0.3276 0.3476 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.009 2163 REMARK 3 ANGLE : 1.189 2940 REMARK 3 CHIRALITY : 0.318 331 REMARK 3 PLANARITY : 0.004 363 REMARK 3 DIHEDRAL : 16.562 845 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 6B4Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000230273. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22010 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 140.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05100 REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.55700 REMARK 200 FOR SHELL : 2.100 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 5BYK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M SODIUM CITRATE, 0.1 M SODIUM REMARK 280 CACODYLATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 70.10850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.70500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 70.10850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.70500 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 507 LIES ON A SPECIAL POSITION. 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 ILE A 62 REMARK 465 THR A 63 REMARK 465 THR A 64 REMARK 465 PRO A 65 REMARK 465 PRO A 66 REMARK 465 PRO A 67 REMARK 465 LEU A 68 REMARK 465 ILE A 257 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 ASN A 44 -36.40 -137.77 REMARK 500 ASP A 91 172.36 70.24 REMARK 500 ASN A 150 -163.98 -107.56 REMARK 500 ASN A 228 30.63 75.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue A3P A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OAQ A 302 DBREF 6B4Y A 1 257 UNP G4VLE5 G4VLE5_SCHMA 1 257 SEQADV 6B4Y GLY A -1 UNP G4VLE5 EXPRESSION TAG SEQADV 6B4Y ALA A 0 UNP G4VLE5 EXPRESSION TAG SEQADV 6B4Y TYR A 39 UNP G4VLE5 PHE 39 ENGINEERED MUTATION SEQRES 1 A 259 GLY ALA MET ILE GLU SER SER THR THR ILE GLN VAL ILE SEQRES 2 A 259 SER ALA GLY LEU PRO ARG THR GLY THR LYS SER LEU LYS SEQRES 3 A 259 ASN ALA LEU GLU ILE ILE TYR HIS LYS PRO CYS TYR HIS SEQRES 4 A 259 MET TYR GLU ILE ILE PHE ASN LYS GLN SER ASP ILE ILE SEQRES 5 A 259 LYS TRP GLN ASN LEU ILE HIS ASP SER HIS MET ILE THR SEQRES 6 A 259 THR PRO PRO PRO LEU THR THR LYS THR ILE ALA ILE TYR SEQRES 7 A 259 ASP LYS LEU LYS GLU LEU LEU ASP GLY TYR ILE ALA THR SEQRES 8 A 259 THR ASP LEU PRO THR CYS GLY PHE TYR LYS ASP LEU MET SEQRES 9 A 259 ASN ILE TYR PRO ASN ALA LYS VAL LEU LEU THR ILE ARG SEQRES 10 A 259 ASP LYS TYR ASP TRP LEU HIS SER LEU ARG LYS VAL VAL SEQRES 11 A 259 LEU PRO LYS SER ASN ASP PRO TRP LYS LEU LYS ILE GLU SEQRES 12 A 259 GLU GLY ASP LYS VAL LEU GLY LEU ASN SER ASP PHE TYR SEQRES 13 A 259 LYS LEU THR GLU ASP SER LEU LYS PHE ALA PHE GLN LYS SEQRES 14 A 259 ASP ASP LEU ASN PHE ASP ASP ASP GLN VAL LEU LEU GLU SEQRES 15 A 259 CYS TYR ASP GLU TYR ASN ARG LEU VAL GLN GLU THR VAL SEQRES 16 A 259 PRO SER ASP ARG LEU LEU VAL LEU ARG LEU GLY ASP GLY SEQRES 17 A 259 TRP GLU PRO LEU CYS LYS PHE LEU ASN VAL GLU ILE PRO SEQRES 18 A 259 ASN GLY ILE ASP TYR PRO CYS VAL ASN SER HIS HIS GLN SEQRES 19 A 259 MET THR GLN LEU THR GLU GLN LEU ILE LYS TYR LYS SER SEQRES 20 A 259 LEU ASP ALA ILE ILE HIS MET PHE PRO ASP LEU ILE HET A3P A 301 27 HET OAQ A 302 20 HETNAM A3P ADENOSINE-3'-5'-DIPHOSPHATE HETNAM OAQ {(2S)-7-NITRO-2-[(PROPAN-2-YLAMINO)METHYL]-1,2,3,4- HETNAM 2 OAQ TETRAHYDROQUINOLIN-6-YL}METHANOL HETSYN OAQ OXAMNIQUINE FORMUL 2 A3P C10 H15 N5 O10 P2 FORMUL 3 OAQ C14 H21 N3 O3 FORMUL 4 HOH *109(H2 O) HELIX 1 AA1 GLY A 19 HIS A 32 1 14 HELIX 2 AA2 HIS A 37 ASN A 44 1 8 HELIX 3 AA3 SER A 47 SER A 59 1 13 HELIX 4 AA4 THR A 70 LEU A 83 1 14 HELIX 5 AA5 PRO A 93 GLY A 96 5 4 HELIX 6 AA6 PHE A 97 TYR A 105 1 9 HELIX 7 AA7 ASP A 116 VAL A 128 1 13 HELIX 8 AA8 PRO A 135 LEU A 147 1 13 HELIX 9 AA9 ASN A 150 GLN A 166 1 17 HELIX 10 AB1 ASP A 174 VAL A 193 1 20 HELIX 11 AB2 GLY A 206 ASN A 215 1 10 HELIX 12 AB3 SER A 229 LYS A 244 1 16 HELIX 13 AB4 ILE A 249 PHE A 253 5 5 SHEET 1 AA1 5 CYS A 35 TYR A 36 0 SHEET 2 AA1 5 ALA A 88 THR A 89 1 O ALA A 88 N TYR A 36 SHEET 3 AA1 5 VAL A 10 SER A 12 1 N SER A 12 O THR A 89 SHEET 4 AA1 5 LYS A 109 ILE A 114 1 O LYS A 109 N ILE A 11 SHEET 5 AA1 5 LEU A 198 ARG A 202 1 O LEU A 201 N LEU A 112 CISPEP 1 LEU A 92 PRO A 93 0 -1.75 SITE 1 AC1 19 ARG A 17 THR A 18 GLY A 19 THR A 20 SITE 2 AC1 19 LYS A 21 SER A 22 ARG A 115 SER A 123 SITE 3 AC1 19 LEU A 203 PRO A 225 CYS A 226 VAL A 227 SITE 4 AC1 19 ASN A 228 SER A 229 HIS A 230 HOH A 444 SITE 5 AC1 19 HOH A 454 HOH A 456 HOH A 485 SITE 1 AC2 11 MET A 38 TYR A 39 ASP A 91 VAL A 128 SITE 2 AC2 11 ILE A 140 ASP A 144 THR A 157 MET A 233 SITE 3 AC2 11 THR A 237 HOH A 411 HOH A 473 CRYST1 140.217 39.410 53.504 90.00 90.00 90.00 P 21 21 2 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 0.007132 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025374 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018690 0.00000