HEADER TRANSFERASE 01-NOV-22 8BHZ TITLE THE APO-CRYSTAL STRUCTURE OF A VARIANT FORM OF THE 28-KDA SCHISTOSOMA TITLE 2 HAEMATOBIUM GLUTATHIONE TRANSFERASE IN ORTHORHOMBIC FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTATHIONE S-TRANSFERASE CLASS-MU 28 KDA ISOZYME; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GST 28,SH28GST; COMPND 5 EC: 2.5.1.18; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHISTOSOMA HAEMATOBIUM; SOURCE 3 ORGANISM_TAXID: 6185; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLUTATHIONE S-TRANSFERASES, SCHISTOSOMA HAEMATOBIUM, SCHISTOSOMA, KEYWDS 2 HAEMATOBIUM, 28-KDA, SH28GST, GST, TRANSFERASE, ORTHORHOMBIC EXPDTA X-RAY DIFFRACTION AUTHOR R.PANDIAN,S.M.MFEKA,O.ONISURU,Y.SAYED,I.A.ACHILONU REVDAT 2 31-JAN-24 8BHZ 1 REMARK REVDAT 1 30-NOV-22 8BHZ 0 JRNL AUTH S.M.MFEKA,R.PANDIAN,O.ONISURU,Y.SAYED,I.A.ACHILONU JRNL TITL BIOPHYSICAL AND BIOCHEMICAL CHARACTERIZATION OF 28-KDA JRNL TITL 2 GLUTATHIONE TRANSFERASE FROM SCHISTOSOMA HAEMATOBIUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 8849 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT : 466 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 24.4000 - 3.4600 1.00 2860 195 0.1750 0.2364 REMARK 3 2 3.4600 - 2.7500 1.00 2814 128 0.2026 0.2547 REMARK 3 3 2.7500 - 2.4000 0.98 2709 143 0.2357 0.3284 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) : 0.297 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.802 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.71 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 : 0.001 1710 REMARK 3 ANGLE : 0.428 2312 REMARK 3 CHIRALITY : 0.038 259 REMARK 3 PLANARITY : 0.003 294 REMARK 3 DIHEDRAL : 1.281 1462 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 8BHZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126389. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER IMUS 3.0 MICROFOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : BRUKER PHOTON III 28 REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON III REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8867 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 24.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.32900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 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: 8ALS REMARK 200 REMARK 200 REMARK: LONG NEEDLE-SHAPED CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15 MG/ML OF SH28GST IN 100MM TRIS-HCL REMARK 280 AT 7.5 PH WITH THE CRYSTALLIZATION CONDITION CONSISTING OF 2.1 M REMARK 280 AMMONIUM SULFATE, 100 MM TRIS (PH 7.2), AND 5 MM B- REMARK 280 MERCAPTOETHANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 38.59250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.59250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 36.89800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.78500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.89800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.78500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.59250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.89800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.78500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.59250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.89800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.78500 REMARK 290 SMTRY3 8 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: DIMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -38.59250 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 MET A 1 REMARK 465 THR A 2 REMARK 465 GLY A 3 REMARK 465 ALA A 208 REMARK 465 THR A 209 REMARK 465 PRO A 210 REMARK 465 PHE A 211 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 PHE A 11 -49.67 -138.52 REMARK 500 GLU A 70 88.26 60.53 REMARK 500 LEU A 150 -168.65 -110.71 REMARK 500 TYR A 182 70.33 54.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8ALS RELATED DB: PDB REMARK 900 RELATED ID: 1OE7 RELATED DB: PDB REMARK 900 RELATED ID: 1OE8 RELATED DB: PDB DBREF 8BHZ A 1 211 UNP P30114 GST28_SCHHA 1 211 SEQRES 1 A 211 MET THR GLY ASP HIS ILE LYS VAL ILE TYR PHE ASN GLY SEQRES 2 A 211 ARG GLY ARG ALA GLU SER ILE ARG MET THR LEU VAL ALA SEQRES 3 A 211 ALA GLY VAL ASN TYR GLU ASP GLU ARG ILE SER PHE GLN SEQRES 4 A 211 ASP TRP PRO LYS ILE LYS PRO THR ILE PRO GLY GLY ARG SEQRES 5 A 211 LEU PRO ALA VAL LYS ILE THR ASP ASN HIS GLY HIS VAL SEQRES 6 A 211 LYS TRP MET LEU GLU SER LEU ALA ILE ALA ARG TYR MET SEQRES 7 A 211 ALA LYS LYS HIS HIS MET MET GLY GLU THR ASP GLU GLU SEQRES 8 A 211 TYR TYR ASN VAL GLU LYS LEU ILE GLY GLN VAL GLU ASP SEQRES 9 A 211 LEU GLU HIS GLU TYR HIS LYS THR LEU MET LYS PRO GLU SEQRES 10 A 211 GLU GLU LYS GLN LYS ILE THR LYS GLU ILE LEU ASN GLY SEQRES 11 A 211 LYS VAL PRO VAL LEU LEU ASP ILE ILE CYS GLU SER LEU SEQRES 12 A 211 LYS ALA SER THR GLY LYS LEU ALA VAL GLY ASP LYS VAL SEQRES 13 A 211 THR LEU ALA ASP LEU VAL LEU ILE ALA VAL ILE ASP HIS SEQRES 14 A 211 VAL THR ASP LEU ASP LYS GLU PHE LEU THR GLY LYS TYR SEQRES 15 A 211 PRO GLU ILE HIS LYS HIS ARG GLU ASN LEU LEU ALA SER SEQRES 16 A 211 SER PRO ARG LEU ALA LYS TYR LEU SER ASP ARG ALA ALA SEQRES 17 A 211 THR PRO PHE FORMUL 2 HOH *142(H2 O) HELIX 1 AA1 ALA A 17 ALA A 27 1 11 HELIX 2 AA2 ASP A 40 LYS A 45 1 6 HELIX 3 AA3 PRO A 46 ILE A 48 5 3 HELIX 4 AA4 GLU A 70 HIS A 82 1 13 HELIX 5 AA5 THR A 88 LYS A 111 1 24 HELIX 6 AA6 PRO A 116 ASN A 129 1 14 HELIX 7 AA7 GLY A 130 ALA A 145 1 16 HELIX 8 AA8 THR A 157 ASP A 174 1 18 HELIX 9 AA9 TYR A 182 SER A 196 1 15 HELIX 10 AB1 SER A 196 ALA A 207 1 12 SHEET 1 AA1 4 GLU A 32 ARG A 35 0 SHEET 2 AA1 4 HIS A 5 TYR A 10 1 N VAL A 8 O GLU A 32 SHEET 3 AA1 4 ALA A 55 THR A 59 -1 O LYS A 57 N LYS A 7 SHEET 4 AA1 4 VAL A 65 MET A 68 -1 O MET A 68 N VAL A 56 CISPEP 1 LEU A 53 PRO A 54 0 0.80 CRYST1 73.796 77.570 77.185 90.00 90.00 90.00 C 2 2 21 8 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 0.013551 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012892 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012956 0.00000