HEADER OXIDOREDUCTASE 21-DEC-09 3L4N TITLE CRYSTAL STRUCTURE OF YEAST MONOTHIOL GLUTAREDOXIN GRX6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MONOTHIOL GLUTAREDOXIN-6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GRX6 C-TERMINAL GRX DOMAIN, UNP RESIDUES 113-231; COMPND 5 SYNONYM: MONOTHIOL GLUTAREDOXIN GRX6; COMPND 6 EC: 1.8.1.7; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: S288C; SOURCE 6 GENE: GRX6, YDL010W, D2890; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS C-TERMINAL DOMAIN OF GRX6, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.LUO,Y.-L.JIANG,X.-X.MA,Y.-X.HE,Y.-J.TANG,J.YU,R.-G.ZHANG,Y.CHEN,C.- AUTHOR 2 Z.ZHOU REVDAT 3 14-DEC-11 3L4N 1 HET HETATM HETNAM JRNL REVDAT 3 2 1 VERSN REVDAT 2 14-APR-10 3L4N 1 JRNL REVDAT 1 07-APR-10 3L4N 0 JRNL AUTH M.LUO,Y.-L.JIANG,X.-X.MA,Y.-J.TANG,Y.-X.HE,J.YU,R.-G.ZHANG, JRNL AUTH 2 Y.CHEN,C.-Z.ZHOU JRNL TITL STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF YEAST JRNL TITL 2 MONOTHIOL GLUTAREDOXIN GRX6 JRNL REF J.MOL.BIOL. V. 398 614 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20347849 JRNL DOI 10.1016/J.JMB.2010.03.029 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 25588 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1362 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1762 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 102 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 913 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 149 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.24000 REMARK 3 B22 (A**2) : 0.54000 REMARK 3 B33 (A**2) : -0.29000 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): 0.073 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.064 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.310 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 949 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1275 ; 1.230 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 112 ; 5.711 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 44 ;26.219 ;25.455 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 179 ;10.159 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ; 7.270 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 139 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 703 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 417 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 668 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 107 ; 0.098 ; 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): 21 ; 0.124 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.061 ; 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): 578 ; 1.089 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 900 ; 1.343 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 421 ; 2.442 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 375 ; 2.815 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 999 ; 2.307 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 149 ; 3.328 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 933 ; 2.776 ; 3.000 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3L4N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-DEC-09. REMARK 100 THE RCSB ID CODE IS RCSB056827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27154 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.67100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.260 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% POLYETHYLENE GLYCOL MONOMETHYL REMARK 280 ETHER 5000, 0.1M 2-(N-MORPHOLINO)-ETHANE SULFONIC ACID (MES), PH REMARK 280 6.5, 10MM REDUCED GLUTATHIONE (GSH), VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.27800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.54750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.56600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.54750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.27800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.56600 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: 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 GLU A 226 REMARK 465 LYS A 227 REMARK 465 PRO A 228 REMARK 465 SER A 229 REMARK 465 ASN A 230 REMARK 465 ASN A 231 REMARK 465 LEU A 232 REMARK 465 GLU A 233 REMARK 465 HIS A 234 REMARK 465 HIS A 235 REMARK 465 HIS A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 HIS A 239 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 1 DBREF 3L4N A 113 231 UNP Q12438 GLRX6_YEAST 113 231 SEQADV 3L4N LEU A 232 UNP Q12438 EXPRESSION TAG SEQADV 3L4N GLU A 233 UNP Q12438 EXPRESSION TAG SEQADV 3L4N HIS A 234 UNP Q12438 EXPRESSION TAG SEQADV 3L4N HIS A 235 UNP Q12438 EXPRESSION TAG SEQADV 3L4N HIS A 236 UNP Q12438 EXPRESSION TAG SEQADV 3L4N HIS A 237 UNP Q12438 EXPRESSION TAG SEQADV 3L4N HIS A 238 UNP Q12438 EXPRESSION TAG SEQADV 3L4N HIS A 239 UNP Q12438 EXPRESSION TAG SEQRES 1 A 127 PHE ASN VAL GLN LYS GLU TYR SER LEU ILE LEU ASP LEU SEQRES 2 A 127 SER PRO ILE ILE ILE PHE SER LYS SER THR CYS SER TYR SEQRES 3 A 127 SER LYS GLY MSE LYS GLU LEU LEU GLU ASN GLU TYR GLN SEQRES 4 A 127 PHE ILE PRO ASN TYR TYR ILE ILE GLU LEU ASP LYS HIS SEQRES 5 A 127 GLY HIS GLY GLU GLU LEU GLN GLU TYR ILE LYS LEU VAL SEQRES 6 A 127 THR GLY ARG GLY THR VAL PRO ASN LEU LEU VAL ASN GLY SEQRES 7 A 127 VAL SER ARG GLY GLY ASN GLU GLU ILE LYS LYS LEU HIS SEQRES 8 A 127 THR GLN GLY LYS LEU LEU GLU SER LEU GLN VAL TRP SER SEQRES 9 A 127 ASP GLY LYS PHE SER VAL GLU GLN ARG GLU LYS PRO SER SEQRES 10 A 127 ASN ASN LEU GLU HIS HIS HIS HIS HIS HIS MODRES 3L4N MSE A 142 MET SELENOMETHIONINE HET MSE A 142 8 HET GSH A 1 20 HETNAM MSE SELENOMETHIONINE HETNAM GSH GLUTATHIONE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 GSH C10 H17 N3 O6 S FORMUL 3 HOH *149(H2 O) HELIX 1 1 ASN A 114 ASP A 124 1 11 HELIX 2 2 CYS A 136 GLU A 149 1 14 HELIX 3 3 ASP A 162 HIS A 164 5 3 HELIX 4 4 HIS A 166 GLY A 179 1 14 HELIX 5 5 GLY A 195 GLN A 205 1 11 HELIX 6 6 LYS A 207 TRP A 215 1 9 SHEET 1 A 4 TYR A 157 GLU A 160 0 SHEET 2 A 4 ILE A 128 SER A 132 1 N SER A 132 O ILE A 159 SHEET 3 A 4 ASN A 185 VAL A 188 -1 O LEU A 187 N ILE A 129 SHEET 4 A 4 VAL A 191 SER A 192 -1 O VAL A 191 N VAL A 188 SHEET 1 B 2 TYR A 150 ILE A 153 0 SHEET 2 B 2 SER A 221 GLN A 224 -1 O SER A 221 N ILE A 153 LINK C GLY A 141 N MSE A 142 1555 1555 1.34 LINK C MSE A 142 N LYS A 143 1555 1555 1.34 CISPEP 1 ILE A 153 PRO A 154 0 -0.46 CISPEP 2 VAL A 183 PRO A 184 0 0.06 SITE 1 AC1 17 HOH A 8 LYS A 133 CYS A 136 TYR A 138 SITE 2 AC1 17 GLN A 171 THR A 182 VAL A 183 PRO A 184 SITE 3 AC1 17 GLY A 195 ASN A 196 GLU A 197 HOH A 252 SITE 4 AC1 17 HOH A 256 HOH A 277 HOH A 313 HOH A 322 SITE 5 AC1 17 HOH A 326 CRYST1 50.556 57.132 59.095 90.00 90.00 90.00 P 21 21 21 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 0.019780 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017503 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016922 0.00000