HEADER TRANSFERASE 17-JAN-21 7DWD TITLE CRYSTAL STRUCTURE OF A GLUTATHIONE S-TRANSFERASE SBGSTU7 FROM SALIX TITLE 2 BABYLONICA COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTATHIONE S-TRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: 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: GSTU7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENZYME, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR X.L.ZHUGE,H.L.YANG REVDAT 2 29-NOV-23 7DWD 1 REMARK REVDAT 1 04-AUG-21 7DWD 0 JRNL AUTH X.L.ZHUGE,H.L.YANG JRNL TITL CRYSTAL STRUCTURE OF A GLUTATHIONE S-TRANSFERASE SBGSTU7 JRNL TITL 2 FROM SALIX BABYLONICA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.58 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 39294 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 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 35.0400 - 3.8000 0.99 2912 156 0.2012 0.1915 REMARK 3 2 3.8000 - 3.0200 1.00 2754 148 0.2079 0.2185 REMARK 3 3 3.0200 - 2.6300 1.00 2705 145 0.2237 0.2133 REMARK 3 4 2.6300 - 2.3900 1.00 2695 144 0.2266 0.2371 REMARK 3 5 2.3900 - 2.2200 1.00 2667 143 0.2164 0.2386 REMARK 3 6 2.2200 - 2.0900 1.00 2650 142 0.2187 0.2521 REMARK 3 7 2.0900 - 1.9900 1.00 2672 143 0.2263 0.2540 REMARK 3 8 1.9900 - 1.9000 1.00 2629 140 0.2298 0.2710 REMARK 3 9 1.9000 - 1.8300 1.00 2636 142 0.2259 0.2460 REMARK 3 10 1.8300 - 1.7600 1.00 2621 140 0.2201 0.2496 REMARK 3 11 1.7600 - 1.7100 1.00 2621 141 0.2343 0.2232 REMARK 3 12 1.7100 - 1.6600 1.00 2621 140 0.2272 0.2337 REMARK 3 13 1.6600 - 1.6200 1.00 2590 138 0.2278 0.2449 REMARK 3 14 1.6200 - 1.5800 0.95 2523 136 0.2383 0.2322 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) : 0.137 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.339 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.81 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 1737 REMARK 3 ANGLE : 1.184 2359 REMARK 3 CHIRALITY : 0.070 257 REMARK 3 PLANARITY : 0.007 296 REMARK 3 DIHEDRAL : 19.379 643 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 7DWD 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_1300020335. 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 : 39294 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 35.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 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: 4TOP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES SODIUM, PEG400, AMMONIUM REMARK 280 SULFATE, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 91.00850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.45150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.45150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.50425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.45150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.45150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 136.51275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.45150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.45150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.50425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.45150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.45150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 136.51275 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 91.00850 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 376 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 464 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 467 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 ASN A 214 REMARK 465 ARG A 215 REMARK 465 PRO A 216 REMARK 465 ALA A 217 REMARK 465 LYS A 218 REMARK 465 ASN A 219 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 65 113.71 83.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 464 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A 465 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 466 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A 467 DISTANCE = 6.95 ANGSTROMS DBREF1 7DWD A 1 219 UNP A0A4Y5R087_SALBB DBREF2 7DWD A A0A4Y5R087 1 219 SEQADV 7DWD HIS A -5 UNP A0A4Y5R08 EXPRESSION TAG SEQADV 7DWD HIS A -4 UNP A0A4Y5R08 EXPRESSION TAG SEQADV 7DWD HIS A -3 UNP A0A4Y5R08 EXPRESSION TAG SEQADV 7DWD HIS A -2 UNP A0A4Y5R08 EXPRESSION TAG SEQADV 7DWD HIS A -1 UNP A0A4Y5R08 EXPRESSION TAG SEQADV 7DWD HIS A 0 UNP A0A4Y5R08 EXPRESSION TAG SEQRES 1 A 225 HIS HIS HIS HIS HIS HIS MET ALA GLU VAL LYS LEU TYR SEQRES 2 A 225 GLY PHE TRP PRO SER PRO PHE SER HIS ARG ILE ILE TRP SEQRES 3 A 225 ALA LEU LYS LEU LYS GLY VAL GLU TYR GLU TYR ILE GLU SEQRES 4 A 225 GLU ASP LEU SER ASN LYS SER GLU SER LEU LEU LYS TYR SEQRES 5 A 225 ASN PRO VAL TYR LYS LYS THR PRO VAL LEU VAL HIS GLY SEQRES 6 A 225 ASP LYS PRO ILE ALA GLU SER LEU VAL ILE LEU GLU TYR SEQRES 7 A 225 ILE GLU GLU THR TRP PRO GLU ASN PRO LEU LEU PRO LYS SEQRES 8 A 225 ASP PRO TYR GLU ARG ALA MET ALA ARG PHE TRP ILE GLN SEQRES 9 A 225 TYR GLY VAL ASP THR VAL ALA ALA LEU ARG ALA PHE TYR SEQRES 10 A 225 LEU GLY SER GLY GLU GLU LEU GLU LYS ALA ALA LYS GLU SEQRES 11 A 225 LEU SER GLU CYS LEU LYS ILE LEU GLU GLU GLN GLY LEU SEQRES 12 A 225 GLY ASP LYS LYS PHE PHE GLY GLY GLU SER MET ASN LEU SEQRES 13 A 225 VAL ASP ILE SER TYR GLY ALA LEU GLY TYR TRP LEU ALA SEQRES 14 A 225 ALA VAL GLU GLU ALA LYS GLY VAL THR VAL LEU LYS PRO SEQRES 15 A 225 SER THR LEU PRO ARG LEU HIS ALA TRP ALA LYS ASN LEU SEQRES 16 A 225 ASP GLU LEU PRO VAL VAL LYS GLU ASN ILE PRO ALA SER SEQRES 17 A 225 ASP LYS MET LEU ALA TYR VAL THR ALA ALA MET ASN ARG SEQRES 18 A 225 PRO ALA LYS ASN FORMUL 2 HOH *167(H2 O) HELIX 1 AA1 SER A 12 GLY A 26 1 15 HELIX 2 AA2 SER A 40 ASN A 47 1 8 HELIX 3 AA3 GLU A 65 TRP A 77 1 13 HELIX 4 AA4 ASP A 86 GLY A 113 1 28 HELIX 5 AA5 SER A 114 GLY A 136 1 23 HELIX 6 AA6 ASN A 149 GLY A 156 1 8 HELIX 7 AA7 GLY A 159 GLY A 170 1 12 HELIX 8 AA8 LEU A 179 LEU A 192 1 14 HELIX 9 AA9 LEU A 192 GLU A 197 1 6 HELIX 10 AB1 ALA A 201 ALA A 212 1 12 SHEET 1 AA1 4 GLU A 30 GLU A 33 0 SHEET 2 AA1 4 VAL A 4 GLY A 8 1 N LEU A 6 O ILE A 32 SHEET 3 AA1 4 VAL A 55 HIS A 58 -1 O VAL A 55 N TYR A 7 SHEET 4 AA1 4 LYS A 61 ALA A 64 -1 O ILE A 63 N LEU A 56 CISPEP 1 THR A 53 PRO A 54 0 -4.72 CRYST1 54.903 54.903 182.017 90.00 90.00 90.00 P 41 21 2 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 0.018214 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018214 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005494 0.00000