HEADER OXIDOREDUCTASE 24-JAN-08 3C1S TITLE CRYSTAL STRUCTURE OF GRX1 IN GLUTATHIONYLATED FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAREDOXIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLUTATHIONE-DEPENDENT OXIDOREDUCTASE 1; COMPND 5 EC: 1.20.4.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 STRAIN: S288C; SOURCE 6 GENE: GRX1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS GLUTATHIONYLATED FORM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.YU,C.Z.ZHOU REVDAT 2 01-NOV-23 3C1S 1 REMARK SEQADV LINK REVDAT 1 09-DEC-08 3C1S 0 JRNL AUTH J.YU,N.N.ZHANG,P.D.YIN,P.X.CUI,C.Z.ZHOU JRNL TITL GLUTATHIONYLATION-TRIGGERED CONFORMATIONAL CHANGES OF JRNL TITL 2 GLUTAREDOXIN GRX1 FROM THE YEAST SACCHAROMYCES CEREVISIAE. JRNL REF PROTEINS V. 72 1077 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18473363 JRNL DOI 10.1002/PROT.22096 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 883820.030 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 4501 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 SET) : 0.221 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 228 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.017 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 418 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 228 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.075 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 847 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.25 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.33 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.600 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 41.92 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : GSH_PARA.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : GSH_TOPO.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3C1S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000046233. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.30 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOMAR REMARK 200 DATA SCALING SOFTWARE : AUTOMAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4547 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 29.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 2.790 REMARK 200 R MERGE (I) : 0.09180 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.3000 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) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.82 REMARK 200 R MERGE FOR SHELL (I) : 0.17870 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 3C1R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 0.1M SODIUM ACETATE, REMARK 280 0.2M AMMONIUM DIHYDROGEN PHOSPHATE, PH 5.30, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 289K 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 50.14500 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 50.14500 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 16.09750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.78550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 16.09750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.78550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 50.14500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 16.09750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.78550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 50.14500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 16.09750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.78550 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 -7 REMARK 465 GLY A -6 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 ALA A 109 REMARK 465 ASN A 110 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 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3C1R RELATED DB: PDB DBREF 3C1S A 1 110 UNP P25373 GLRX1_YEAST 1 110 SEQADV 3C1S MET A -7 UNP P25373 EXPRESSION TAG SEQADV 3C1S GLY A -6 UNP P25373 EXPRESSION TAG SEQADV 3C1S HIS A -5 UNP P25373 EXPRESSION TAG SEQADV 3C1S HIS A -4 UNP P25373 EXPRESSION TAG SEQADV 3C1S HIS A -3 UNP P25373 EXPRESSION TAG SEQADV 3C1S HIS A -2 UNP P25373 EXPRESSION TAG SEQADV 3C1S HIS A -1 UNP P25373 EXPRESSION TAG SEQADV 3C1S HIS A 0 UNP P25373 EXPRESSION TAG SEQRES 1 A 118 MET GLY HIS HIS HIS HIS HIS HIS MET VAL SER GLN GLU SEQRES 2 A 118 THR ILE LYS HIS VAL LYS ASP LEU ILE ALA GLU ASN GLU SEQRES 3 A 118 ILE PHE VAL ALA SER LYS THR TYR CYS PRO TYR CYS HIS SEQRES 4 A 118 ALA ALA LEU ASN THR LEU PHE GLU LYS LEU LYS VAL PRO SEQRES 5 A 118 ARG SER LYS VAL LEU VAL LEU GLN LEU ASN ASP MET LYS SEQRES 6 A 118 GLU GLY ALA ASP ILE GLN ALA ALA LEU TYR GLU ILE ASN SEQRES 7 A 118 GLY GLN ARG THR VAL PRO ASN ILE TYR ILE ASN GLY LYS SEQRES 8 A 118 HIS ILE GLY GLY ASN ASP ASP LEU GLN GLU LEU ARG GLU SEQRES 9 A 118 THR GLY GLU LEU GLU GLU LEU LEU GLU PRO ILE LEU ALA SEQRES 10 A 118 ASN HET GSH A2001 20 HETNAM GSH GLUTATHIONE FORMUL 2 GSH C10 H17 N3 O6 S FORMUL 3 HOH *73(H2 O) HELIX 1 1 SER A 3 GLU A 16 1 14 HELIX 2 2 CYS A 27 GLU A 39 1 13 HELIX 3 3 PRO A 44 SER A 46 5 3 HELIX 4 4 ASN A 54 MET A 56 5 3 HELIX 5 5 GLU A 58 GLY A 71 1 14 HELIX 6 6 GLY A 87 THR A 97 1 11 HELIX 7 7 GLU A 99 GLU A 105 1 7 SHEET 1 A 4 VAL A 48 GLN A 52 0 SHEET 2 A 4 ILE A 19 SER A 23 1 N SER A 23 O LEU A 51 SHEET 3 A 4 ASN A 77 ILE A 80 -1 O TYR A 79 N PHE A 20 SHEET 4 A 4 LYS A 83 GLY A 86 -1 O LYS A 83 N ILE A 80 LINK SG CYS A 27 SG2 GSH A2001 1555 1555 2.10 CISPEP 1 VAL A 75 PRO A 76 0 3.14 SITE 1 AC1 16 LYS A 24 TYR A 26 CYS A 27 TYR A 29 SITE 2 AC1 16 GLN A 63 THR A 74 PRO A 76 GLY A 87 SITE 3 AC1 16 ASN A 88 ASP A 89 HOH A2013 HOH A2019 SITE 4 AC1 16 HOH A2036 HOH A2037 HOH A2039 HOH A2041 CRYST1 32.195 77.571 100.290 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 0.031061 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012891 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009971 0.00000