HEADER TRANSFERASE 01-AUG-22 8ALS TITLE THE APO-CRYSTAL STRUCTURE OF THE 28-KDA SCHISTOSOMA BOVIS GLUTATHIONE TITLE 2 TRANSFERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTATHIONE S-TRANSFERASE CLASS-MU 28 KDA ISOZYME; COMPND 3 CHAIN: A, B; 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 BOVIS; SOURCE 3 ORGANISM_TAXID: 6184; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLUTATHIONE S-TRANSFERASES, SCHISTOSOMA BOVIS, SCHISTOSOMA, BOVIS, KEYWDS 2 28-KDA, SB28GST, GST, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.PANDIAN,H.H.MAKUMBE,Y.SAYED,I.A.ACHILONU REVDAT 2 25-DEC-24 8ALS 1 TITLE COMPND SOURCE KEYWDS REVDAT 2 2 1 JRNL REMARK DBREF SEQRES REVDAT 2 3 1 HELIX SHEET CRYST1 ATOM REVDAT 1 02-NOV-22 8ALS 0 JRNL AUTH H.H.MAKUMBE,R.PANDIAN,A.VALLI,Y.SAYED,I.ACHILONU JRNL TITL BIOPHYSICAL CHARACTERIZATION, CRYSTALLIZATION, AND SOLUTION JRNL TITL 2 OF THE FIRST CRYSTAL STRUCTURE OF THE 28 KDA-SCHISTOSOMA JRNL TITL 3 BOVIS GLUTATHIONE TRANSFERASE JRNL REF J.MOL.STRUCT. V.1298 36979 2024 JRNL REFN ISSN 0022-2860 JRNL DOI 10.1016/J.MOLSTRUC.2023.136979 REMARK 2 REMARK 2 RESOLUTION. 2.30 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 19582 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 1014 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 24.6780 - 4.3919 0.99 2705 159 0.1734 0.1912 REMARK 3 2 4.3919 - 3.4891 1.00 2630 206 0.1627 0.1902 REMARK 3 3 3.4891 - 3.0490 1.00 2691 126 0.2004 0.2852 REMARK 3 4 3.0490 - 2.7706 1.00 2703 114 0.2425 0.2530 REMARK 3 5 2.7706 - 2.5722 1.00 2684 123 0.2704 0.3805 REMARK 3 6 2.5722 - 2.4207 1.00 2682 139 0.2807 0.3553 REMARK 3 7 2.4207 - 2.3000 0.93 2473 147 0.3116 0.3005 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.21 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 : 0.002 3429 REMARK 3 ANGLE : 0.506 4636 REMARK 3 CHIRALITY : 0.040 519 REMARK 3 PLANARITY : 0.003 591 REMARK 3 DIHEDRAL : 1.678 2924 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 8ALS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1292124661. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : NULL 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 : 19612 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 24.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.60000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 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: 1OE8 REMARK 200 REMARK 200 REMARK: LONG NEEDLE-SHAPED CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5.3 MG/ML OF SB28GST IN 25MM OF SODIUM REMARK 280 PHOSPHATE BUFFER (NAH2PO4) AT 7.5 PH WITH THE CRYSTALLIZATION REMARK 280 CONDITION CONSISTING OF 2.1 M AMMONIUM SULFATE, 100 MM TRIS (PH REMARK 280 7.5), AND 5 MM B-MERCAPTOETHANOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 38.54300 REMARK 290 SMTRY3 2 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, B 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 3 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 GLU A 70 84.29 65.42 REMARK 500 LEU A 150 -168.81 -106.50 REMARK 500 ASP A 174 109.22 -163.19 REMARK 500 PHE B 11 -50.74 -130.15 REMARK 500 GLU B 70 91.83 62.86 REMARK 500 ASP B 174 109.53 -161.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 301 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 486 O REMARK 620 2 HOH A 554 O 62.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 301 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 412 O REMARK 620 2 HOH B 514 O 126.6 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OE8 RELATED DB: PDB REMARK 900 RELATED ID: 1OE7 RELATED DB: PDB DBREF 8ALS A 3 207 UNP P30114 GST28_SCHBO 3 207 DBREF 8ALS B 3 207 UNP P30114 GST28_SCHBO 3 207 SEQRES 1 A 205 GLY ASP HIS ILE LYS VAL ILE TYR PHE ASN GLY ARG GLY SEQRES 2 A 205 ARG ALA GLU SER ILE ARG MET THR LEU VAL ALA ALA GLY SEQRES 3 A 205 VAL ASN TYR GLU ASP GLU ARG ILE SER PHE GLN ASP TRP SEQRES 4 A 205 PRO LYS ILE LYS PRO THR ILE PRO GLY GLY ARG LEU PRO SEQRES 5 A 205 ALA VAL LYS ILE THR ASP ASN HIS GLY HIS VAL LYS TRP SEQRES 6 A 205 MET LEU GLU SER LEU ALA ILE ALA ARG TYR MET ALA LYS SEQRES 7 A 205 LYS HIS HIS MET MET GLY GLU THR ASP GLU GLU TYR TYR SEQRES 8 A 205 ASN VAL GLU LYS LEU ILE GLY GLN VAL GLU ASP LEU GLU SEQRES 9 A 205 HIS GLU TYR HIS LYS THR LEU MET LYS PRO GLU GLU GLU SEQRES 10 A 205 LYS GLN LYS ILE THR LYS GLU ILE LEU ASN GLY LYS VAL SEQRES 11 A 205 PRO VAL LEU LEU ASP ILE ILE CYS GLU SER LEU LYS ALA SEQRES 12 A 205 SER THR GLY LYS LEU ALA VAL GLY ASP LYS VAL THR LEU SEQRES 13 A 205 ALA ASP LEU VAL LEU ILE ALA VAL ILE ASP HIS VAL THR SEQRES 14 A 205 ASP LEU ASP LYS GLU PHE LEU THR GLY LYS TYR PRO GLU SEQRES 15 A 205 ILE HIS LYS HIS ARG GLU ASN LEU LEU ALA SER SER PRO SEQRES 16 A 205 ARG LEU ALA LYS TYR LEU SER ASP ARG ALA SEQRES 1 B 205 GLY ASP HIS ILE LYS VAL ILE TYR PHE ASN GLY ARG GLY SEQRES 2 B 205 ARG ALA GLU SER ILE ARG MET THR LEU VAL ALA ALA GLY SEQRES 3 B 205 VAL ASN TYR GLU ASP GLU ARG ILE SER PHE GLN ASP TRP SEQRES 4 B 205 PRO LYS ILE LYS PRO THR ILE PRO GLY GLY ARG LEU PRO SEQRES 5 B 205 ALA VAL LYS ILE THR ASP ASN HIS GLY HIS VAL LYS TRP SEQRES 6 B 205 MET LEU GLU SER LEU ALA ILE ALA ARG TYR MET ALA LYS SEQRES 7 B 205 LYS HIS HIS MET MET GLY GLU THR ASP GLU GLU TYR TYR SEQRES 8 B 205 ASN VAL GLU LYS LEU ILE GLY GLN VAL GLU ASP LEU GLU SEQRES 9 B 205 HIS GLU TYR HIS LYS THR LEU MET LYS PRO GLU GLU GLU SEQRES 10 B 205 LYS GLN LYS ILE THR LYS GLU ILE LEU ASN GLY LYS VAL SEQRES 11 B 205 PRO VAL LEU LEU ASP ILE ILE CYS GLU SER LEU LYS ALA SEQRES 12 B 205 SER THR GLY LYS LEU ALA VAL GLY ASP LYS VAL THR LEU SEQRES 13 B 205 ALA ASP LEU VAL LEU ILE ALA VAL ILE ASP HIS VAL THR SEQRES 14 B 205 ASP LEU ASP LYS GLU PHE LEU THR GLY LYS TYR PRO GLU SEQRES 15 B 205 ILE HIS LYS HIS ARG GLU ASN LEU LEU ALA SER SER PRO SEQRES 16 B 205 ARG LEU ALA LYS TYR LEU SER ASP ARG ALA HET NA A 301 1 HET NA B 301 1 HETNAM NA SODIUM ION FORMUL 3 NA 2(NA 1+) FORMUL 5 HOH *448(H2 O) HELIX 1 AA1 ALA A 17 GLY A 28 1 12 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 HELIX 11 AB2 ALA B 17 ALA B 27 1 11 HELIX 12 AB3 ASP B 40 LYS B 45 1 6 HELIX 13 AB4 PRO B 46 ILE B 48 5 3 HELIX 14 AB5 GLU B 70 HIS B 82 1 13 HELIX 15 AB6 THR B 88 LYS B 111 1 24 HELIX 16 AB7 PRO B 116 ASN B 129 1 14 HELIX 17 AB8 GLY B 130 ALA B 145 1 16 HELIX 18 AB9 THR B 157 ASP B 174 1 18 HELIX 19 AC1 TYR B 182 SER B 196 1 15 HELIX 20 AC2 SER B 196 ALA B 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 ALA A 55 N ILE A 9 SHEET 4 AA1 4 VAL A 65 MET A 68 -1 O MET A 68 N VAL A 56 SHEET 1 AA2 4 GLU B 32 ARG B 35 0 SHEET 2 AA2 4 HIS B 5 TYR B 10 1 N VAL B 8 O GLU B 32 SHEET 3 AA2 4 ALA B 55 THR B 59 -1 O ALA B 55 N ILE B 9 SHEET 4 AA2 4 VAL B 65 MET B 68 -1 O LYS B 66 N ILE B 58 LINK NA NA A 301 O HOH A 486 1555 1555 3.20 LINK NA NA A 301 O HOH A 554 1555 1555 2.49 LINK NA NA B 301 O HOH B 412 1555 1555 2.72 LINK NA NA B 301 O HOH B 514 1555 1555 2.60 CISPEP 1 LEU A 53 PRO A 54 0 1.30 CISPEP 2 LEU B 53 PRO B 54 0 0.47 CRYST1 54.133 77.086 54.015 90.00 93.15 90.00 P 1 21 1 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 0.018473 0.000000 0.001016 0.00000 SCALE2 0.000000 0.012972 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018541 0.00000