HEADER OXIDOREDUCTASE 14-APR-08 3CTF TITLE CRYSTAL STRUCTURE OF OXIDIZED GRX2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAREDOXIN-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: THIOLTRANSFERASE, GLUTATHIONE-DEPENDENT OXIDOREDUCTASE 2; 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: GRX2, TTR, TTR1, YDR513W, D9719.17; 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: PET15B KEYWDS OXIDIZED FORM, ELECTRON TRANSPORT, MITOCHONDRION, REDOX-ACTIVE KEYWDS 2 CENTER, TRANSIT PEPTIDE, TRANSPORT, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.YU,Y.B.TENG,C.Z.ZHOU REVDAT 5 06-NOV-24 3CTF 1 REMARK REVDAT 4 01-NOV-23 3CTF 1 SEQADV REVDAT 3 01-SEP-10 3CTF 1 JRNL REVDAT 2 24-FEB-09 3CTF 1 VERSN REVDAT 1 11-NOV-08 3CTF 0 JRNL AUTH W.F.LI,J.YU,X.X.MA,Y.B.TENG,M.LUO,Y.J.TANG,C.Z.ZHOU JRNL TITL STRUCTURAL BASIS FOR THE DIFFERENT ACTIVITIES OF YEAST GRX1 JRNL TITL 2 AND GRX2. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1804 1542 2010 JRNL REFN ISSN 0006-3002 JRNL PMID 20417731 JRNL DOI 10.1016/J.BBAPAP.2010.04.010 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1136202.700 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 7063 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) : 0.222 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 364 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 642 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 27 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 831 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 105 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.60 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.500 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 : 46.49 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 3CTF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047189. 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 : 4.60 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) : 1.54179 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 : 12610 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 28.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.560 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.57 REMARK 200 R MERGE FOR SHELL (I) : 0.27400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 3C1R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.1M NAAC, 0.2M NH4AC, REMARK 280 VAPOR DIFFUSION, HANGING DROP, PH 4.60, TEMPERATURE 289K 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 48.22300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.38500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.38500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.11150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.38500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.38500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 72.33450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.38500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.38500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.11150 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.38500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.38500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 72.33450 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 48.22300 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 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 193 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 15 REMARK 465 GLY A 16 REMARK 465 SER A 17 REMARK 465 SER A 18 REMARK 465 HIS A 19 REMARK 465 HIS A 20 REMARK 465 HIS A 21 REMARK 465 HIS A 22 REMARK 465 HIS A 23 REMARK 465 HIS A 24 REMARK 465 SER A 25 REMARK 465 SER A 26 REMARK 465 GLY A 27 REMARK 465 LEU A 28 REMARK 465 VAL A 29 REMARK 465 PRO A 30 REMARK 465 ARG A 31 REMARK 465 GLY A 32 REMARK 465 SER A 33 REMARK 465 HIS A 34 REMARK 465 MET A 35 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CTG RELATED DB: PDB DBREF 3CTF A 35 143 UNP P17695 GLRX2_YEAST 35 143 SEQADV 3CTF MET A 15 UNP P17695 EXPRESSION TAG SEQADV 3CTF GLY A 16 UNP P17695 EXPRESSION TAG SEQADV 3CTF SER A 17 UNP P17695 EXPRESSION TAG SEQADV 3CTF SER A 18 UNP P17695 EXPRESSION TAG SEQADV 3CTF HIS A 19 UNP P17695 EXPRESSION TAG SEQADV 3CTF HIS A 20 UNP P17695 EXPRESSION TAG SEQADV 3CTF HIS A 21 UNP P17695 EXPRESSION TAG SEQADV 3CTF HIS A 22 UNP P17695 EXPRESSION TAG SEQADV 3CTF HIS A 23 UNP P17695 EXPRESSION TAG SEQADV 3CTF HIS A 24 UNP P17695 EXPRESSION TAG SEQADV 3CTF SER A 25 UNP P17695 EXPRESSION TAG SEQADV 3CTF SER A 26 UNP P17695 EXPRESSION TAG SEQADV 3CTF GLY A 27 UNP P17695 EXPRESSION TAG SEQADV 3CTF LEU A 28 UNP P17695 EXPRESSION TAG SEQADV 3CTF VAL A 29 UNP P17695 EXPRESSION TAG SEQADV 3CTF PRO A 30 UNP P17695 EXPRESSION TAG SEQADV 3CTF ARG A 31 UNP P17695 EXPRESSION TAG SEQADV 3CTF GLY A 32 UNP P17695 EXPRESSION TAG SEQADV 3CTF SER A 33 UNP P17695 EXPRESSION TAG SEQADV 3CTF HIS A 34 UNP P17695 EXPRESSION TAG SEQRES 1 A 129 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 129 LEU VAL PRO ARG GLY SER HIS MET VAL SER GLN GLU THR SEQRES 3 A 129 VAL ALA HIS VAL LYS ASP LEU ILE GLY GLN LYS GLU VAL SEQRES 4 A 129 PHE VAL ALA ALA LYS THR TYR CYS PRO TYR CYS LYS ALA SEQRES 5 A 129 THR LEU SER THR LEU PHE GLN GLU LEU ASN VAL PRO LYS SEQRES 6 A 129 SER LYS ALA LEU VAL LEU GLU LEU ASP GLU MET SER ASN SEQRES 7 A 129 GLY SER GLU ILE GLN ASP ALA LEU GLU GLU ILE SER GLY SEQRES 8 A 129 GLN LYS THR VAL PRO ASN VAL TYR ILE ASN GLY LYS HIS SEQRES 9 A 129 ILE GLY GLY ASN SER ASP LEU GLU THR LEU LYS LYS ASN SEQRES 10 A 129 GLY LYS LEU ALA GLU ILE LEU LYS PRO VAL PHE GLN FORMUL 2 HOH *105(H2 O) HELIX 1 1 SER A 37 GLY A 49 1 13 HELIX 2 2 CYS A 61 GLN A 73 1 13 HELIX 3 3 PRO A 78 SER A 80 5 3 HELIX 4 4 ASP A 88 MET A 90 5 3 HELIX 5 5 ASN A 92 GLY A 105 1 14 HELIX 6 6 GLY A 121 GLY A 132 1 12 HELIX 7 7 GLY A 132 LYS A 139 1 8 HELIX 8 8 PRO A 140 GLN A 143 5 4 SHEET 1 A 4 ALA A 82 GLU A 86 0 SHEET 2 A 4 VAL A 53 ALA A 57 1 N ALA A 57 O LEU A 85 SHEET 3 A 4 ASN A 111 ILE A 114 -1 O TYR A 113 N PHE A 54 SHEET 4 A 4 LYS A 117 GLY A 120 -1 O ILE A 119 N VAL A 112 SSBOND 1 CYS A 61 CYS A 64 1555 1555 2.06 CISPEP 1 VAL A 109 PRO A 110 0 3.81 CRYST1 48.770 48.770 96.446 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 0.020504 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020504 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010368 0.00000