HEADER TRANSFERASE 15-JAN-21 7DW4 TITLE CRYSTAL STRUCTURE OF A GLUTATHIONE S-TRANSFERASE MUTANT SBGSTU6(I55T) TITLE 2 FROM SALIX BABYLONICA IN COMPLEX WITH GLUTATHIONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTATHIONE S-TRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALIX BABYLONICA; SOURCE 3 ORGANISM_COMMON: BABYLON WEEPING WILLOW; SOURCE 4 ORGANISM_TAXID: 75706; SOURCE 5 GENE: GSTU6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENZYME, COMPLEX, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR X.L.ZHUGE,H.L.YANG REVDAT 2 29-NOV-23 7DW4 1 REMARK REVDAT 1 04-AUG-21 7DW4 0 JRNL AUTH X.L.ZHUGE,H.L.YANG JRNL TITL CRYSTAL STRUCTURE OF A GLUTATHIONE S-TRANSFERASE MUTANT JRNL TITL 2 SBGSTU6(I55T) FROM SALIX BABYLONICA IN COMPLEX WITH JRNL TITL 3 GLUTATHIONE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 46097 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.320 REMARK 3 FREE R VALUE TEST SET COUNT : 1990 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 34.4200 - 3.7900 1.00 3299 141 0.1981 0.1797 REMARK 3 2 3.7900 - 3.0100 1.00 3224 148 0.2115 0.2173 REMARK 3 3 3.0100 - 2.6300 1.00 3183 150 0.2248 0.2839 REMARK 3 4 2.6300 - 2.3900 1.00 3159 144 0.2275 0.1999 REMARK 3 5 2.3900 - 2.2200 1.00 3153 145 0.2191 0.2219 REMARK 3 6 2.2200 - 2.0900 1.00 3172 142 0.2290 0.2730 REMARK 3 7 2.0900 - 1.9800 1.00 3135 146 0.2303 0.2617 REMARK 3 8 1.9800 - 1.9000 1.00 3161 143 0.2395 0.2766 REMARK 3 9 1.9000 - 1.8200 1.00 3127 144 0.2375 0.2525 REMARK 3 10 1.8200 - 1.7600 1.00 3157 143 0.2524 0.2938 REMARK 3 11 1.7600 - 1.7100 1.00 3127 142 0.2517 0.2668 REMARK 3 12 1.7100 - 1.6600 1.00 3122 140 0.2755 0.3261 REMARK 3 13 1.6600 - 1.6100 1.00 3148 136 0.2788 0.2962 REMARK 3 14 1.6100 - 1.5700 0.93 2940 126 0.3241 0.3043 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) : 0.171 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.168 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.27 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 : 0.011 1797 REMARK 3 ANGLE : 1.174 2431 REMARK 3 CHIRALITY : 0.077 264 REMARK 3 PLANARITY : 0.007 309 REMARK 3 DIHEDRAL : 20.621 663 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 7DW4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300020308. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NFPSS REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46154 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 34.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 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: 7DW3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM ACETATE TETRAHYDRATE, SODIUM REMARK 280 CACODYLATE TRIHYDRATE, PEG8000, PH 7.4, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.70867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.41733 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.41733 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 17.70867 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: 590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 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 432 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 510 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 534 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 223 REMARK 465 LYS A 224 REMARK 465 ALA A 225 REMARK 465 THR A 226 REMARK 465 PRO A 227 REMARK 465 PRO A 228 REMARK 465 LYS A 229 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 LYS A 63 117.11 -160.66 REMARK 500 GLU A 67 115.23 81.95 REMARK 500 TRP A 79 52.20 -91.71 REMARK 500 ALA A 221 88.80 -52.68 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 GSH A 301 DBREF1 7DW4 A 1 229 UNP A0A4Y5R032_SALBB DBREF2 7DW4 A A0A4Y5R032 1 229 SEQADV 7DW4 HIS A -5 UNP A0A4Y5R03 EXPRESSION TAG SEQADV 7DW4 HIS A -4 UNP A0A4Y5R03 EXPRESSION TAG SEQADV 7DW4 HIS A -3 UNP A0A4Y5R03 EXPRESSION TAG SEQADV 7DW4 HIS A -2 UNP A0A4Y5R03 EXPRESSION TAG SEQADV 7DW4 HIS A -1 UNP A0A4Y5R03 EXPRESSION TAG SEQADV 7DW4 HIS A 0 UNP A0A4Y5R03 EXPRESSION TAG SEQADV 7DW4 THR A 55 UNP A0A4Y5R03 ILE 55 ENGINEERED MUTATION SEQRES 1 A 235 HIS HIS HIS HIS HIS HIS MET ALA LYS SER ASP VAL LYS SEQRES 2 A 235 LEU LEU GLY ALA TRP PRO SER PRO PHE VAL MET ARG PRO SEQRES 3 A 235 ARG ILE ALA LEU ASN ILE LYS SER VAL GLU TYR GLU PHE SEQRES 4 A 235 LEU GLU GLU THR LEU GLY SER LYS SER GLN LEU LEU LEU SEQRES 5 A 235 GLU SER ASN PRO VAL HIS LYS LYS THR PRO VAL LEU ILE SEQRES 6 A 235 HIS GLY GLY LYS PRO ILE CYS GLU SER LEU VAL ILE VAL SEQRES 7 A 235 GLU TYR ILE ASP GLU VAL TRP SER PRO GLY PRO ALA ILE SEQRES 8 A 235 LEU PRO SER ASP PRO TYR ASP ARG ALA LEU ALA ARG PHE SEQRES 9 A 235 TRP ALA ALA TYR LEU ASP GLU LYS TRP PHE PRO THR MET SEQRES 10 A 235 ARG ASN ILE ALA ALA ALA LYS ASP GLU GLU ALA ARG LYS SEQRES 11 A 235 ALA LEU ILE ASP GLN VAL GLY GLU GLY LEU VAL LEU LEU SEQRES 12 A 235 GLU ASP ALA PHE SER LYS CYS SER LYS GLY LYS GLY PHE SEQRES 13 A 235 PHE GLY GLY ASP GLN ILE GLY TYR LEU ASP ILE ALA PHE SEQRES 14 A 235 GLY SER PHE LEU GLY TRP LEU ARG ALA ILE GLU LYS MET SEQRES 15 A 235 ASN GLY VAL LYS LEU MET ASP GLU THR ARG THR PRO GLY SEQRES 16 A 235 LEU LEU LYS TRP ALA ASN SER PHE SER SER HIS PRO ALA SEQRES 17 A 235 VAL LYS ASP VAL PHE PRO GLU THR GLU LYS LEU VAL GLU SEQRES 18 A 235 PHE ALA LYS VAL LEU ALA LYS LEU LYS ALA THR PRO PRO SEQRES 19 A 235 LYS HET GSH A 301 35 HETNAM GSH GLUTATHIONE FORMUL 2 GSH C10 H17 N3 O6 S FORMUL 3 HOH *159(H2 O) HELIX 1 AA1 SER A 14 LYS A 27 1 14 HELIX 2 AA2 SER A 42 ASN A 49 1 8 HELIX 3 AA3 GLU A 67 TRP A 79 1 13 HELIX 4 AA4 ASP A 89 LYS A 106 1 18 HELIX 5 AA5 LYS A 106 ALA A 115 1 10 HELIX 6 AA6 ASP A 119 LYS A 146 1 28 HELIX 7 AA7 GLY A 157 SER A 165 1 9 HELIX 8 AA8 PHE A 166 GLY A 178 1 13 HELIX 9 AA9 THR A 187 HIS A 200 1 14 HELIX 10 AB1 VAL A 203 PHE A 207 5 5 HELIX 11 AB2 GLU A 209 ALA A 221 1 13 SHEET 1 AA1 4 GLU A 32 GLU A 36 0 SHEET 2 AA1 4 VAL A 6 ALA A 11 1 N LEU A 8 O LEU A 34 SHEET 3 AA1 4 VAL A 57 HIS A 60 -1 O VAL A 57 N LEU A 9 SHEET 4 AA1 4 PRO A 64 CYS A 66 -1 O ILE A 65 N LEU A 58 CISPEP 1 TRP A 12 PRO A 13 0 -1.03 CISPEP 2 THR A 55 PRO A 56 0 3.40 SITE 1 AC1 11 ALA A 11 SER A 14 PHE A 16 LYS A 54 SITE 2 AC1 11 THR A 55 PRO A 56 GLU A 67 SER A 68 SITE 3 AC1 11 HOH A 403 HOH A 427 HOH A 459 CRYST1 104.379 104.379 53.126 90.00 90.00 120.00 P 31 2 1 6 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 0.009580 0.005531 0.000000 0.00000 SCALE2 0.000000 0.011063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018823 0.00000