HEADER TRANSFERASE 27-NOV-15 5F07 TITLE CRYSTAL STRUCTURE OF GLUTATHIONE TRANSFERASE F8 FROM POPULUS TITLE 2 TRICHOCARPA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE GLUTATHIONE S-TRANSFERASE FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLUTATHIONE TRANSFERASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: POPULUS TRICHOCARPA; SOURCE 3 ORGANISM_COMMON: WESTERN BALSAM POPLAR; SOURCE 4 ORGANISM_TAXID: 3694; SOURCE 5 GENE: POPTR_0017S02090G; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLUTATHIONE, TRANSFERASE, LIGANDIN EXPDTA X-RAY DIFFRACTION AUTHOR C.DIDIERJEAN,N.ROUHIER,H.PEGEOT,F.GENSE REVDAT 4 10-JAN-24 5F07 1 REMARK REVDAT 3 16-AUG-17 5F07 1 JRNL REVDAT 2 28-JUN-17 5F07 1 JRNL REVDAT 1 07-DEC-16 5F07 0 JRNL AUTH H.PEGEOT,S.MATHIOT,T.PERROT,F.GENSE,A.HECKER,C.DIDIERJEAN, JRNL AUTH 2 N.ROUHIER JRNL TITL STRUCTURAL PLASTICITY AMONG GLUTATHIONE TRANSFERASE PHI JRNL TITL 2 MEMBERS: NATURAL COMBINATION OF CATALYTIC RESIDUES CONFERS JRNL TITL 3 DUAL BIOCHEMICAL ACTIVITIES. JRNL REF FEBS J. V. 284 2442 2017 JRNL REFN ISSN 1742-4658 JRNL PMID 28622459 JRNL DOI 10.1111/FEBS.14138 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 37417 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1874 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 39.0302 - 3.5262 0.99 2777 156 0.1480 0.1713 REMARK 3 2 3.5262 - 2.7991 1.00 2767 152 0.1564 0.1507 REMARK 3 3 2.7991 - 2.4453 1.00 2779 140 0.1475 0.1842 REMARK 3 4 2.4453 - 2.2218 1.00 2707 152 0.1517 0.1899 REMARK 3 5 2.2218 - 2.0626 1.00 2729 167 0.1601 0.1940 REMARK 3 6 2.0626 - 1.9410 1.00 2750 139 0.1681 0.1771 REMARK 3 7 1.9410 - 1.8437 1.00 2713 149 0.1882 0.2249 REMARK 3 8 1.8437 - 1.7635 1.00 2760 131 0.1897 0.2382 REMARK 3 9 1.7635 - 1.6956 1.00 2738 135 0.1907 0.2241 REMARK 3 10 1.6956 - 1.6371 1.00 2738 133 0.1925 0.2334 REMARK 3 11 1.6371 - 1.5859 1.00 2733 147 0.1954 0.2094 REMARK 3 12 1.5859 - 1.5406 1.00 2725 136 0.2065 0.2381 REMARK 3 13 1.5406 - 1.5000 0.97 2627 137 0.2154 0.2524 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.008 1816 REMARK 3 ANGLE : 1.182 2464 REMARK 3 CHIRALITY : 0.049 271 REMARK 3 PLANARITY : 0.008 320 REMARK 3 DIHEDRAL : 12.764 686 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 5F07 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215743. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979769 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37437 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 47.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.29200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4RI6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 4000, NA MES PH6.5, 0.2 M MG REMARK 280 CHLORIDE, MICROBATCH, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 45.00500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.64500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.00500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.64500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -27.42296 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 47.70925 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 536 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 PHE A 214 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 435 O HOH A 602 1.98 REMARK 500 O HOH A 598 O HOH A 599 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 545 O HOH A 621 2555 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 66 110.37 72.60 REMARK 500 HIS A 105 -73.49 -124.53 REMARK 500 ASN A 178 -86.77 -113.86 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 DBREF 5F07 A 2 214 UNP B9MWW0 B9MWW0_POPTR 2 214 SEQADV 5F07 VAL A 10 UNP B9MWW0 MET 10 CONFLICT SEQADV 5F07 LYS A 149 UNP B9MWW0 GLN 149 CONFLICT SEQADV 5F07 MET A 209 UNP B9MWW0 ILE 209 CONFLICT SEQRES 1 A 213 VAL VAL LYS VAL TYR GLY PRO ALA VAL ALA VAL CYS PRO SEQRES 2 A 213 GLN ARG VAL MET ALA CYS LEU LEU GLU LYS GLY VAL GLU SEQRES 3 A 213 PHE ASP LEU VAL HIS VAL ASP LEU ASP SER GLY GLU GLN SEQRES 4 A 213 LYS LEU PRO GLU PHE LEU LEU LYS GLN PRO PHE GLY GLN SEQRES 5 A 213 VAL PRO VAL VAL GLU ASP GLY ASP PHE LYS LEU PHE GLU SEQRES 6 A 213 SER ARG ALA ILE ILE ARG TYR TYR ALA ALA LYS TYR GLU SEQRES 7 A 213 ASP ARG GLY PRO ASN LEU LEU GLY ASN THR LEU GLU GLU SEQRES 8 A 213 LYS ALA LEU VAL ASP GLN TRP LEU GLU ILE GLU ALA HIS SEQRES 9 A 213 ASN PHE ASN ASP LEU VAL PHE ASN ILE VAL PHE GLN VAL SEQRES 10 A 213 VAL ILE LEU PRO ARG ILE GLY GLN GLN GLY ASP SER GLU SEQRES 11 A 213 LEU VAL ARG THR TYR GLU GLU LYS LEU GLU LYS VAL LEU SEQRES 12 A 213 ASP VAL TYR GLU LYS ARG LEU SER LYS SER LYS TYR LEU SEQRES 13 A 213 ALA GLY ASP SER PHE THR LEU ALA ASP LEU SER HIS LEU SEQRES 14 A 213 PRO ALA THR ARG TYR LEU VAL ASN GLU ALA GLY LEU GLY SEQRES 15 A 213 HIS LEU VAL LYS ASP ARG LYS LYS LEU ASN ALA TRP TRP SEQRES 16 A 213 GLU ASP ILE SER SER ARG PRO ALA TRP LYS LYS LEU MET SEQRES 17 A 213 ASN LEU ALA GLY PHE HET GSH A 301 20 HETNAM GSH GLUTATHIONE FORMUL 2 GSH C10 H17 N3 O6 S FORMUL 3 HOH *282(H2 O) HELIX 1 AA1 ALA A 11 LYS A 24 1 14 HELIX 2 AA2 GLY A 38 LYS A 41 5 4 HELIX 3 AA3 LEU A 42 LEU A 47 1 6 HELIX 4 AA4 GLU A 66 TYR A 78 1 13 HELIX 5 AA5 THR A 89 HIS A 105 1 17 HELIX 6 AA6 PHE A 107 VAL A 119 1 13 HELIX 7 AA7 VAL A 119 ILE A 124 1 6 HELIX 8 AA8 ASP A 129 SER A 154 1 26 HELIX 9 AA9 THR A 163 SER A 168 1 6 HELIX 10 AB1 HIS A 169 ASN A 178 1 10 HELIX 11 AB2 GLY A 183 ASP A 188 1 6 HELIX 12 AB3 ARG A 189 SER A 200 1 12 HELIX 13 AB4 ARG A 202 GLY A 213 1 12 SHEET 1 AA1 4 PHE A 28 VAL A 31 0 SHEET 2 AA1 4 VAL A 3 TYR A 6 1 N VAL A 5 O VAL A 31 SHEET 3 AA1 4 VAL A 56 ASP A 59 -1 O GLU A 58 N LYS A 4 SHEET 4 AA1 4 PHE A 62 PHE A 65 -1 O PHE A 62 N ASP A 59 LINK SG CYS A 13 SG2 GSH A 301 1555 1555 2.07 CISPEP 1 VAL A 54 PRO A 55 0 8.41 SITE 1 AC1 17 VAL A 12 CYS A 13 GLN A 40 LYS A 41 SITE 2 AC1 17 GLN A 53 VAL A 54 GLU A 66 SER A 67 SITE 3 AC1 17 ARG A 68 HOH A 427 HOH A 429 HOH A 435 SITE 4 AC1 17 HOH A 439 HOH A 448 HOH A 487 HOH A 532 SITE 5 AC1 17 HOH A 576 CRYST1 90.010 55.290 55.029 90.00 119.89 90.00 C 1 2 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 0.011110 0.000000 0.006387 0.00000 SCALE2 0.000000 0.018086 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020961 0.00000