HEADER TRANSFERASE 16-MAY-22 7ZVP TITLE CRYSTAL STRUCTURE OF POPLAR GLUTATHIONE TRANSFERASE U19 IN COMPLEX TITLE 2 WITH GLUTATHIONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTATHIONE TRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.5.1.18; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: POPULUS TRICHOCARPA; SOURCE 3 ORGANISM_COMMON: BLACK COTTONWOOD; SOURCE 4 ORGANISM_TAXID: 3694; SOURCE 5 GENE: POPTR_008G174900; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS GLUTATHIONE, TAU, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.DIDIERJEAN,F.FAVIER REVDAT 3 31-JAN-24 7ZVP 1 REMARK REVDAT 2 07-SEP-22 7ZVP 1 JRNL REVDAT 1 20-JUL-22 7ZVP 0 JRNL AUTH E.SYLVESTRE-GONON,L.MORETTE,M.VILORIA,S.MATHIOT, JRNL AUTH 2 A.BOUTILLIAT,F.FAVIER,N.ROUHIER,C.DIDIERJEAN,A.HECKER JRNL TITL BIOCHEMICAL AND STRUCTURAL INSIGHTS ON THE POPLAR TAU JRNL TITL 2 GLUTATHIONE TRANSFERASE GSTU19 AND 20 PARALOGS BINDING JRNL TITL 3 FLAVONOIDS. JRNL REF FRONT MOL BIOSCI V. 9 58586 2022 JRNL REFN ESSN 2296-889X JRNL PMID 36032685 JRNL DOI 10.3389/FMOLB.2022.958586 REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.4 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 39549 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1895 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.62 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : 0.2557 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 33 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1746 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 257 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.69780 REMARK 3 B22 (A**2) : -2.69780 REMARK 3 B33 (A**2) : 5.39560 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.270 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.103 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.098 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.095 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.092 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1865 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2536 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 659 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 321 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1865 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 228 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 7 ; 1.000 ; HARMONIC REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1939 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.88 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.20 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.11 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7ZVP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1292123071. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98010 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39646 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 48.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: 7ZS3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CALCIUM ACETATE HYDRATE, 0.1 M REMARK 280 SODIUM CACODYLATE PH 6.5 AND 18 % W/V PEG 8000, MICROBATCH, REMARK 280 TEMPERATURE 277K 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 91.00750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.36350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.36350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.50375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.36350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.36350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 136.51125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.36350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.36350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.50375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.36350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.36350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 136.51125 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 91.00750 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: 3450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 489 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 MET A 1 REMARK 465 ASN A 218 REMARK 465 LYS 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 65 105.54 81.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7ZS3 RELATED DB: PDB DBREF 7ZVP A 1 219 UNP B9HKX9 B9HKX9_POPTR 1 219 SEQRES 1 A 219 MET ALA ASP VAL LYS LEU HIS GLY PHE TRP ALA SER PRO SEQRES 2 A 219 PHE SER TYR ARG VAL ILE TRP ALA LEU LYS LEU LYS GLY SEQRES 3 A 219 VAL GLU PHE GLU TYR ILE GLU GLU ASP LEU ALA ASN LYS SEQRES 4 A 219 SER GLU LEU LEU LEU LYS TYR ASN PRO VAL TYR LYS GLN SEQRES 5 A 219 ILE PRO VAL PHE VAL HIS GLY GLY LYS PRO ILE ALA GLU SEQRES 6 A 219 SER LEU VAL ILE LEU GLU TYR ILE GLU GLU THR TRP PRO SEQRES 7 A 219 GLU ASN PRO LEU LEU PRO THR ASP PRO TYR GLU ARG ALA SEQRES 8 A 219 MET ALA ARG PHE TRP ILE GLN TYR GLY ALA THR LYS SER SEQRES 9 A 219 ALA ALA PHE GLY ALA LEU PHE ARG ALA SER GLY GLU GLU SEQRES 10 A 219 LEU GLU LYS ALA ALA LYS GLU VAL VAL GLU VAL LEU ARG SEQRES 11 A 219 VAL LEU GLN GLU GLN GLY LEU GLY ASP LYS LYS PHE PHE SEQRES 12 A 219 GLY GLY ASP SER ILE ASN LEU VAL ASP ILE SER TYR GLY SEQRES 13 A 219 LEU PHE VAL TYR TRP LEU ALA ALA ILE GLU ASP ILE VAL SEQRES 14 A 219 GLY VAL LYS VAL LEU GLU PRO SER THR LEU PRO ARG LEU SEQRES 15 A 219 HIS ALA TRP ALA GLN ASN PHE ILE GLU VAL PRO LEU ILE SEQRES 16 A 219 LYS GLU ASN HIS PRO ASP ASN ASP LYS LEU LEU LEU HIS SEQRES 17 A 219 MET LYS GLY VAL ARG GLU LYS MET MET ASN LYS HET GS8 A 301 21 HET ACT A 302 4 HET ACT A 303 4 HETNAM GS8 S-HYDROXY-GLUTATHIONE HETNAM ACT ACETATE ION FORMUL 2 GS8 C10 H17 N3 O7 S FORMUL 3 ACT 2(C2 H3 O2 1-) FORMUL 5 HOH *257(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 SER A 104 1 19 HELIX 5 AA5 SER A 104 ALA A 113 1 10 HELIX 6 AA6 GLU A 117 GLY A 136 1 20 HELIX 7 AA7 ASN A 149 VAL A 169 1 21 HELIX 8 AA8 LEU A 179 VAL A 192 1 14 HELIX 9 AA9 VAL A 192 GLU A 197 1 6 HELIX 10 AB1 ASP A 201 MET A 216 1 16 SHEET 1 AA1 4 PHE A 29 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 HIS A 7 SHEET 4 AA1 4 LYS A 61 ALA A 64 -1 O ILE A 63 N PHE A 56 CISPEP 1 ILE A 53 PRO A 54 0 -4.25 CRYST1 56.727 56.727 182.015 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 0.017628 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017628 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005494 0.00000