HEADER OXIDOREDUCTASE 14-MAY-08 3D4M TITLE GLUTAREDOXIN 2 OXIDIZED STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAREDOXIN-2, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: THIOLTRANSFERASE, GLUTATHIONE-DEPENDENT OXIDOREDUCTASE 2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: GRX2, TTR, TTR1, YDR513W, D9719.17; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS GRX2, CYTOPLASM, ELECTRON TRANSPORT, MITOCHONDRION, REDOX-ACTIVE KEYWDS 2 CENTER, TRANSIT PEPTIDE, TRANSPORT, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.F.DISCOLA,M.A.DE OLIVEIRA,J.A.BARCENA,P.PORRAS,B.G.GUIMARAES, AUTHOR 2 L.E.S.NETTO REVDAT 3 25-OCT-17 3D4M 1 REMARK REVDAT 2 17-FEB-09 3D4M 1 JRNL VERSN REVDAT 1 28-OCT-08 3D4M 0 JRNL AUTH K.F.DISCOLA,M.A.DE OLIVEIRA,J.R.ROSA CUSSIOL,G.MONTEIRO, JRNL AUTH 2 J.A.BARCENA,P.PORRAS,C.A.PADILLA,B.G.GUIMARAES,L.E.NETTO JRNL TITL STRUCTURAL ASPECTS OF THE DISTINCT BIOCHEMICAL PROPERTIES OF JRNL TITL 2 GLUTAREDOXIN 1 AND GLUTAREDOXIN 2 FROM SACCHAROMYCES JRNL TITL 3 CEREVISIAE. JRNL REF J.MOL.BIOL. V. 385 889 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 18992757 JRNL DOI 10.1016/J.JMB.2008.10.055 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 7295 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 340 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 505 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2010 REMARK 3 BIN FREE R VALUE SET COUNT : 15 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 806 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 83 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.68000 REMARK 3 B22 (A**2) : 0.68000 REMARK 3 B33 (A**2) : -1.36000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.194 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.165 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.108 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.903 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 818 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1111 ; 1.418 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 108 ; 5.714 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 30 ;35.283 ;27.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 141 ;12.891 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 136 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 593 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 465 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 585 ; 0.319 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 102 ; 0.161 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 59 ; 0.193 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.207 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 549 ; 0.906 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 867 ; 1.519 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 291 ; 2.704 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 244 ; 4.368 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3D4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047585. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : D03B-MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.431 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7295 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 42.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29400 REMARK 200 FOR SHELL : 7.800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, PH 4.2, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298.0K 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 47.29600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.81700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.81700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.64800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.81700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.81700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 70.94400 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.81700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.81700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.64800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.81700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.81700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 70.94400 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 47.29600 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 4 CG CD OE1 NE2 REMARK 470 GLU A 68 CG CD OE1 OE2 REMARK 470 LYS A 73 CG CD CE NZ REMARK 470 LYS A 96 CG CD CE NZ REMARK 470 LYS A 99 CG CD CE NZ REMARK 470 GLU A 102 CG CD OE1 OE2 REMARK 470 LYS A 105 CG CD CE NZ REMARK 470 GLN A 109 CG CD OE1 NE2 DBREF 3D4M A 1 109 UNP P17695 GLRX2_YEAST 35 143 SEQRES 1 A 109 MET VAL SER GLN GLU THR VAL ALA HIS VAL LYS ASP LEU SEQRES 2 A 109 ILE GLY GLN LYS GLU VAL PHE VAL ALA ALA LYS THR TYR SEQRES 3 A 109 CYS PRO TYR CYS LYS ALA THR LEU SER THR LEU PHE GLN SEQRES 4 A 109 GLU LEU ASN VAL PRO LYS SER LYS ALA LEU VAL LEU GLU SEQRES 5 A 109 LEU ASP GLU MET SER ASN GLY SER GLU ILE GLN ASP ALA SEQRES 6 A 109 LEU GLU GLU ILE SER GLY GLN LYS THR VAL PRO ASN VAL SEQRES 7 A 109 TYR ILE ASN GLY LYS HIS ILE GLY GLY ASN SER ASP LEU SEQRES 8 A 109 GLU THR LEU LYS LYS ASN GLY LYS LEU ALA GLU ILE LEU SEQRES 9 A 109 LYS PRO VAL PHE GLN FORMUL 2 HOH *83(H2 O) HELIX 1 1 SER A 3 LYS A 17 1 15 HELIX 2 2 CYS A 27 GLN A 39 1 13 HELIX 3 3 PRO A 44 SER A 46 5 3 HELIX 4 4 ASP A 54 MET A 56 5 3 HELIX 5 5 ASN A 58 GLY A 71 1 14 HELIX 6 6 GLY A 87 GLY A 98 1 12 HELIX 7 7 GLY A 98 GLN A 109 1 12 SHEET 1 A 4 ALA A 48 GLU A 52 0 SHEET 2 A 4 VAL A 19 ALA A 23 1 N VAL A 21 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 ILE A 85 N VAL A 78 SSBOND 1 CYS A 27 CYS A 30 1555 1555 2.08 CISPEP 1 VAL A 75 PRO A 76 0 5.00 CRYST1 47.634 47.634 94.592 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 0.020993 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020993 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010572 0.00000