HEADER TRANSFERASE/PEPTIDE 14-OCT-98 1BX9 TITLE GLUTATHIONE S-TRANSFERASE IN COMPLEX WITH HERBICIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTATHIONE S-TRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: FOE-4053-GLUTATHIONE CONJUGATE GGL-FOE-GLY; COMPND 6 CHAIN: B; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES KEYWDS HERBICIDE, FOE-4053-GLUTATHIONE CONJUGATE, PRODUCT OF THE DETOXIFYING KEYWDS 2 REACTION, TRANSFERASE, TRANSFERASE-PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.PRADE,R.HUBER,B.BIESELER REVDAT 6 30-OCT-24 1BX9 1 LINK REVDAT 5 13-JUL-11 1BX9 1 VERSN REVDAT 4 24-FEB-09 1BX9 1 VERSN REVDAT 3 01-APR-03 1BX9 1 JRNL REVDAT 2 22-DEC-99 1BX9 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 21-OCT-98 1BX9 0 JRNL AUTH L.PRADE,R.HUBER,B.BIESELER JRNL TITL STRUCTURES OF HERBICIDES IN COMPLEX WITH THEIR DETOXIFYING JRNL TITL 2 ENZYME GLUTATHIONE S-TRANSFERASE - EXPLANATIONS FOR THE JRNL TITL 3 SELECTIVITY OF THE ENZYME IN PLANTS. JRNL REF STRUCTURE V. 6 1445 1998 JRNL REFN ISSN 0969-2126 JRNL PMID 9817846 JRNL DOI 10.1016/S0969-2126(98)00143-9 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 7598 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1727 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 70 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.50 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 2.660 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BX9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008143. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 287.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7598 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 44.92500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.92500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 29.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.41500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.41500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 44.92500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.50000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.41500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 44.92500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.50000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.41500 REMARK 290 SMTRY3 8 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: TETRAMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 59.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 44.92500 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 ALA A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 191 C - N - CA ANGL. DEV. = 9.3 DEGREES 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 65 105.53 78.08 REMARK 500 ASN A 79 39.21 -76.57 REMARK 500 ILE A 121 -25.95 -141.25 REMARK 500 TYR A 126 32.66 -95.40 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 CHAIN B OF FOE-4053-GLUTATHIONE REMARK 800 CONJUGATE GGL-FOE-GLY DBREF 1BX9 A 0 210 UNP P46422 GTH4_ARATH 2 212 DBREF 1BX9 B 101 103 PDB 1BX9 1BX9 101 103 SEQRES 1 A 211 ALA GLY ILE LYS VAL PHE GLY HIS PRO ALA SER ILE ALA SEQRES 2 A 211 THR ARG ARG VAL LEU ILE ALA LEU HIS GLU LYS ASN LEU SEQRES 3 A 211 ASP PHE GLU LEU VAL HIS VAL GLU LEU LYS ASP GLY GLU SEQRES 4 A 211 HIS LYS LYS GLU PRO PHE LEU SER ARG ASN PRO PHE GLY SEQRES 5 A 211 GLN VAL PRO ALA PHE GLU ASP GLY ASP LEU LYS LEU PHE SEQRES 6 A 211 GLU SER ARG ALA ILE THR GLN TYR ILE ALA HIS ARG TYR SEQRES 7 A 211 GLU ASN GLN GLY THR ASN LEU LEU GLN THR ASP SER LYS SEQRES 8 A 211 ASN ILE SER GLN TYR ALA ILE MET ALA ILE GLY MET GLN SEQRES 9 A 211 VAL GLU ASP HIS GLN PHE ASP PRO VAL ALA SER LYS LEU SEQRES 10 A 211 ALA PHE GLU GLN ILE PHE LYS SER ILE TYR GLY LEU THR SEQRES 11 A 211 THR ASP GLU ALA VAL VAL ALA GLU GLU GLU ALA LYS LEU SEQRES 12 A 211 ALA LYS VAL LEU ASP VAL TYR GLU ALA ARG LEU LYS GLU SEQRES 13 A 211 PHE LYS TYR LEU ALA GLY GLU THR PHE THR LEU THR ASP SEQRES 14 A 211 LEU HIS HIS ILE PRO ALA ILE GLN TYR LEU LEU GLY THR SEQRES 15 A 211 PRO THR LYS LYS LEU PHE THR GLU ARG PRO ARG VAL ASN SEQRES 16 A 211 GLU TRP VAL ALA GLU ILE THR LYS ARG PRO ALA SER GLU SEQRES 17 A 211 LYS VAL GLN SEQRES 1 B 3 GGL FOE GLY MODRES 1BX9 FOE B 102 CYS HET GGL B 101 9 HET FOE B 102 20 HETNAM GGL GAMMA-L-GLUTAMIC ACID HETNAM FOE 2-(2-AMINO-3-OXO-PROPYLSULFANYL)-N-(4-FLUORO-PHENYL)-N- HETNAM 2 FOE ISOPROPYL-ACETAMIDE HETSYN GGL L-GLUTAMIC ACID FORMUL 2 GGL C5 H9 N O4 FORMUL 2 FOE C14 H19 F N2 O3 S FORMUL 3 HOH *70(H2 O) HELIX 1 1 ILE A 11 GLU A 22 1 12 HELIX 2 2 GLU A 38 LYS A 40 5 3 HELIX 3 3 PHE A 44 SER A 46 5 3 HELIX 4 4 SER A 66 ARG A 76 1 11 HELIX 5 5 ILE A 92 HIS A 107 1 16 HELIX 6 6 ASP A 110 ILE A 121 1 12 HELIX 7 7 SER A 124 TYR A 126 5 3 HELIX 8 8 GLU A 132 GLU A 155 1 24 HELIX 9 9 LEU A 166 GLY A 180 1 15 HELIX 10 10 PRO A 182 THR A 188 5 7 HELIX 11 11 PRO A 191 ILE A 200 1 10 HELIX 12 12 PRO A 204 GLU A 207 1 4 SHEET 1 A 4 GLU A 28 HIS A 31 0 SHEET 2 A 4 ILE A 2 GLY A 6 1 N VAL A 4 O GLU A 28 SHEET 3 A 4 ALA A 55 ASP A 58 -1 N GLU A 57 O LYS A 3 SHEET 4 A 4 LEU A 61 PHE A 64 -1 N LEU A 63 O PHE A 56 LINK CD GGL B 101 N FOE B 102 1555 1555 1.33 LINK C FOE B 102 N GLY B 103 1555 1555 1.33 CISPEP 1 GLU A 42 PRO A 43 0 0.21 CISPEP 2 VAL A 53 PRO A 54 0 0.38 SITE 1 AC1 13 SER A 10 ILE A 11 HIS A 39 LYS A 40 SITE 2 AC1 13 GLN A 52 VAL A 53 GLU A 65 SER A 66 SITE 3 AC1 13 ARG A 67 PHE A 122 HOH A 253 HOH A 279 SITE 4 AC1 13 HOH B 41 CRYST1 59.000 88.830 89.850 90.00 90.00 90.00 C 2 2 21 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 0.016949 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011257 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011130 0.00000