HEADER TRANSFERASE 13-JUL-14 4USS TITLE POPULUS TRICHOCARPA GLUTATHIONE TRANSFERASE X1-1 (GHR1), COMPLEXED TITLE 2 WITH GLUTATHIONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTATHIONYL HYDROQUINONE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 35-359; COMPND 5 EC: 2.5.1.18; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: THE EXPRESSED PROTEIN IS DEVOID OF THE FIRST 34 AMINO COMPND 8 ACIDS. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: POPULUS TRICHOCARPA; SOURCE 3 ORGANISM_COMMON: BLACK COTTONWOOD; SOURCE 4 ORGANISM_TAXID: 3694; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE, CLASS XI, POPLAR, PLASTIDS EXPDTA X-RAY DIFFRACTION AUTHOR P.A.LALLEMENT,E.MEUX,J.M.GUALBERTO,S.DUMARACAY,F.FAVIER,C.DIDIERJEAN, AUTHOR 2 F.SAUL,A.HAOUZ,M.MOREL-ROUHIER,E.GELHAYE,N.ROUHIER,A.HECKER REVDAT 5 10-JAN-24 4USS 1 REMARK REVDAT 4 23-OCT-19 4USS 1 ATOM REVDAT 3 31-DEC-14 4USS 1 JRNL REVDAT 2 17-DEC-14 4USS 1 JRNL REVDAT 1 03-DEC-14 4USS 0 JRNL AUTH P.LALLEMENT,E.MEUX,J.M.GUALBERTO,S.DUMARCAY,F.FAVIER, JRNL AUTH 2 C.DIDIERJEAN,F.SAUL,A.HAOUZ,M.MOREL-ROUHIER,E.GELHAYE, JRNL AUTH 3 N.ROUHIER,A.HECKER JRNL TITL GLUTATHIONYL-HYDROQUINONE REDUCTASES FROM POPLAR ARE JRNL TITL 2 PLASTIDIAL PROTEINS THAT DEGLUTATHIONYLATE BOTH REDUCED AND JRNL TITL 3 OXIDIZED GLUTATHIONYLATED QUINONES. JRNL REF FEBS LETT. V. 589 37 2015 JRNL REFN ISSN 0014-5793 JRNL PMID 25455804 JRNL DOI 10.1016/J.FEBSLET.2014.11.021 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 10702 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 548 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 19.5259 - 3.9604 1.00 2639 157 0.1478 0.1766 REMARK 3 2 3.9604 - 3.1478 1.00 2534 140 0.1818 0.2478 REMARK 3 3 3.1478 - 2.7511 1.00 2502 125 0.2362 0.3144 REMARK 3 4 2.7511 - 2.5001 1.00 2479 126 0.2346 0.3108 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.73 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 : 0.003 2574 REMARK 3 ANGLE : 0.668 3491 REMARK 3 CHIRALITY : 0.029 363 REMARK 3 PLANARITY : 0.002 454 REMARK 3 DIHEDRAL : 12.561 949 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 4USS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1290061226. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.826560 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : KIRKPATRICK-BAEZ PAIR OF BI REMARK 200 -MORPH MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10702 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.16000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.1 REMARK 200 DATA REDUNDANCY IN SHELL : 10.90 REMARK 200 R MERGE FOR SHELL (I) : 0.79000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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: PDB ENTRY 3PPU REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 18.26500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.20450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.26500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.20450 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: 4570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.4 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 ALA A 2 REMARK 465 ARG A 3 REMARK 465 SER A 4 REMARK 465 ALA A 5 REMARK 465 ILE A 6 REMARK 465 ASP A 7 REMARK 465 GLU A 8 REMARK 465 THR A 9 REMARK 465 SER A 10 REMARK 465 ASP A 11 REMARK 465 THR A 12 REMARK 465 GLY A 13 REMARK 465 ALA A 14 REMARK 465 PHE A 15 REMARK 465 LYS A 16 REMARK 465 ARG A 17 REMARK 465 SER A 324 REMARK 465 SER A 325 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 THR A 154 -35.68 -131.86 REMARK 500 VAL A 249 -66.64 -120.16 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 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 502 REMARK 999 REMARK 999 SEQUENCE REMARK 999 DISCREPANCIES IN SEQUENCE ARE DUE TO POLYMORPHISM. REMARK 999 AUTHORS HAVE CLARIFIED THAT DISCREPANCIES IN SEQUENCE ARE DUE REMARK 999 TO POLYMORPHISM (RESIDUES 105, 175, 181, AND 185) DBREF 4USS A 1 325 UNP B9ICN7 B9ICN7_POPTR 35 359 SEQADV 4USS THR A 105 UNP B9ICN7 PRO 139 SEE REMARK 999 SEQADV 4USS GLN A 175 UNP B9ICN7 ARG 209 SEE REMARK 999 SEQADV 4USS GLY A 181 UNP B9ICN7 GLU 215 SEE REMARK 999 SEQADV 4USS ASP A 185 UNP B9ICN7 ASN 219 SEE REMARK 999 SEQRES 1 A 325 MET ALA ARG SER ALA ILE ASP GLU THR SER ASP THR GLY SEQRES 2 A 325 ALA PHE LYS ARG THR ALA SER THR PHE ARG ASN PHE ILE SEQRES 3 A 325 SER LYS GLU PRO ASN SER GLN PHE PRO PRO GLU SER GLY SEQRES 4 A 325 ARG TYR HIS LEU TYR VAL SER TYR ALA CYS PRO TRP ALA SEQRES 5 A 325 SER ARG CYS LEU ALA TYR LEU LYS ILE LYS GLY LEU GLU SEQRES 6 A 325 LYS ALA ILE ALA PHE THR SER VAL LYS PRO ILE TRP GLU SEQRES 7 A 325 ARG THR LYS GLU SER ASP GLU HIS MET GLY TRP VAL PHE SEQRES 8 A 325 PRO ALA SER GLU THR GLU GLU ALA GLY ALA GLU PRO ASP SEQRES 9 A 325 THR LEU ASN GLY ALA ARG SER ILE ARG GLU LEU TYR GLU SEQRES 10 A 325 LEU ALA SER THR ASN TYR ALA GLY LYS TYR THR VAL PRO SEQRES 11 A 325 VAL LEU TRP ASP LYS LYS LEU LYS THR ILE VAL ASN ASN SEQRES 12 A 325 GLU SER SER GLU ILE ILE ARG MET PHE ASN THR GLU PHE SEQRES 13 A 325 ASN ASP ILE ALA GLU ASN ALA ALA LEU ASP LEU TYR PRO SEQRES 14 A 325 SER HIS LEU GLN ALA GLN ILE ASP GLU THR ASN GLY TRP SEQRES 15 A 325 VAL TYR ASP GLY ILE ASN ASN GLY VAL TYR LYS CYS GLY SEQRES 16 A 325 PHE ALA ARG LYS GLN GLY PRO TYR GLU GLU ALA ALA ILE SEQRES 17 A 325 GLN LEU TYR GLU ALA LEU ASP LYS CYS GLU GLU ILE LEU SEQRES 18 A 325 GLY ARG GLN ARG TYR ILE CYS GLY ASN THR LEU SER GLU SEQRES 19 A 325 ALA ASP ILE LYS LEU PHE VAL THR LEU ILE ARG PHE ASP SEQRES 20 A 325 GLU VAL TYR ALA VAL HIS PHE LYS CYS ASN LYS LYS LEU SEQRES 21 A 325 LEU ARG ASP TYR PRO ASN MET PHE ASN TYR THR LYS ASP SEQRES 22 A 325 ILE PHE GLN ILE PRO GLY MET SER SER THR VAL ASN MET SEQRES 23 A 325 GLN HIS ILE LYS ARG HIS TYR TYR GLY SER HIS PRO THR SEQRES 24 A 325 VAL ASN PRO PHE GLY ILE ILE PRO LEU GLY PRO ASP ILE SEQRES 25 A 325 ASP TYR SER SER PRO HIS ASP ARG ASN ARG PHE SER SER HET GSH A 500 31 HET PO4 A 501 5 HET PO4 A 502 5 HETNAM GSH GLUTATHIONE HETNAM PO4 PHOSPHATE ION FORMUL 2 GSH C10 H17 N3 O6 S FORMUL 3 PO4 2(O4 P 3-) FORMUL 5 HOH *70(H2 O) HELIX 1 1 CYS A 49 LYS A 62 1 14 HELIX 2 2 SER A 111 SER A 120 1 10 HELIX 3 3 GLU A 144 GLU A 155 1 12 HELIX 4 4 PRO A 169 ILE A 187 1 19 HELIX 5 5 ASN A 189 ALA A 197 1 9 HELIX 6 6 LYS A 199 GLN A 224 1 26 HELIX 7 7 SER A 233 ILE A 244 1 12 HELIX 8 8 VAL A 249 PHE A 254 1 6 HELIX 9 9 LEU A 260 ASP A 263 5 4 HELIX 10 10 TYR A 264 GLN A 276 1 13 HELIX 11 11 MET A 280 VAL A 284 5 5 HELIX 12 12 ASN A 285 SER A 296 1 12 HELIX 13 13 ASP A 319 PHE A 323 5 5 SHEET 1 AA 4 ALA A 69 SER A 72 0 SHEET 2 AA 4 TYR A 41 VAL A 45 1 O TYR A 41 N ALA A 69 SHEET 3 AA 4 VAL A 131 ASP A 134 -1 O VAL A 131 N TYR A 44 SHEET 4 AA 4 THR A 139 ASN A 142 -1 O THR A 139 N ASP A 134 SHEET 1 AB 2 GLU A 78 ARG A 79 0 SHEET 2 AB 2 MET A 87 GLY A 88 -1 O GLY A 88 N GLU A 78 CISPEP 1 VAL A 129 PRO A 130 0 6.14 SITE 1 AC1 10 CYS A 49 TRP A 51 TRP A 89 THR A 128 SITE 2 AC1 10 VAL A 129 PRO A 130 ASN A 143 GLU A 144 SITE 3 AC1 10 SER A 145 HOH A2030 SITE 1 AC2 6 LYS A 81 GLU A 82 SER A 83 ALA A 124 SITE 2 AC2 6 GLY A 125 LYS A 126 SITE 1 AC3 3 HIS A 42 ALA A 69 LYS A 135 CRYST1 36.530 92.409 86.901 90.00 90.00 90.00 P 21 21 2 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 0.027375 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010821 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011507 0.00000