HEADER OXIDOREDUCTASE 29-AUG-07 2R37 TITLE CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE PEROXIDASE 3 (SELENOCYSTEINE TO TITLE 2 GLYCINE MUTANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTATHIONE PEROXIDASE 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 25-223; COMPND 5 SYNONYM: GSHPX-3, GPX-3, PLASMA GLUTATHIONE PEROXIDASE, GSHPX-P, COMPND 6 EXTRACELLULAR GLUTATHIONE PEROXIDASE, GPX-P; COMPND 7 EC: 1.11.1.9; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GPX3, GPXP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC-CTHF KEYWDS GLUTATHIONE, PEROXIDASE, PLASMA, STRUCTURAL GENOMICS CONSORTIUM, SGC, KEYWDS 2 OXIDOREDUCTASE, SECRETED, SELENIUM, SELENOCYSTEINE EXPDTA X-RAY DIFFRACTION AUTHOR E.S.PILKA,K.GUO,O.GILEADI,A.ROJKOWA,F.VON DELFT,A.C.W.PIKE, AUTHOR 2 K.L.KAVANAGH,C.JOHANNSON,M.SUNDSTROM,C.H.ARROWSMITH,J.WEIGELT, AUTHOR 3 A.M.EDWARDS,U.OPPERMANN,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 6 30-AUG-23 2R37 1 REMARK REVDAT 5 20-OCT-21 2R37 1 REMARK SEQADV LINK REVDAT 4 25-OCT-17 2R37 1 REMARK REVDAT 3 13-JUL-11 2R37 1 VERSN REVDAT 2 24-FEB-09 2R37 1 VERSN REVDAT 1 11-SEP-07 2R37 0 JRNL AUTH E.S.PILKA,K.GUO,O.GILEADI,A.ROJKOWA,F.VON DELFT,A.C.W.PIKE, JRNL AUTH 2 K.L.KAVANAGH,C.JOHANNSON,M.SUNDSTROM,C.H.ARROWSMITH, JRNL AUTH 3 J.WEIGELT,A.M.EDWARDS,U.OPPERMANN JRNL TITL CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE PEROXIDASE 3 JRNL TITL 2 (SELENOCYSTEINE TO GLYCINE MUTANT). JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0040 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 52544 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) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2807 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3803 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 215 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3013 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 406 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.75000 REMARK 3 B22 (A**2) : -0.27000 REMARK 3 B33 (A**2) : -0.49000 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): 0.085 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.906 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3140 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2169 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4258 ; 1.414 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5278 ; 1.200 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 377 ; 6.239 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 146 ;34.123 ;23.836 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 518 ;12.516 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;16.304 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 449 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3476 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 673 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 570 ; 0.210 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2187 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1533 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1529 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 263 ; 0.160 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 8 ; 0.094 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 10 ; 0.093 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 48 ; 0.256 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.151 ; 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): 1882 ; 2.520 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 772 ; 0.846 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3044 ; 3.834 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1307 ; 6.272 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1214 ; 8.750 ;11.000 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 38 A 228 REMARK 3 ORIGIN FOR THE GROUP (A): 10.9368 -13.8473 -14.5525 REMARK 3 T TENSOR REMARK 3 T11: -0.0681 T22: -0.0933 REMARK 3 T33: -0.0488 T12: -0.0037 REMARK 3 T13: 0.0032 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 1.2341 L22: 1.3257 REMARK 3 L33: 0.9296 L12: 0.1378 REMARK 3 L13: 0.1565 L23: -0.2303 REMARK 3 S TENSOR REMARK 3 S11: -0.0146 S12: 0.1120 S13: 0.0565 REMARK 3 S21: -0.0711 S22: -0.0079 S23: -0.0375 REMARK 3 S31: 0.0543 S32: 0.0632 S33: 0.0225 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 36 B 222 REMARK 3 ORIGIN FOR THE GROUP (A): 34.9963 10.5121 -23.4300 REMARK 3 T TENSOR REMARK 3 T11: -0.0334 T22: 0.0149 REMARK 3 T33: -0.0723 T12: -0.0590 REMARK 3 T13: -0.0279 T23: 0.0492 REMARK 3 L TENSOR REMARK 3 L11: 1.2659 L22: 1.1786 REMARK 3 L33: 0.9814 L12: 0.0483 REMARK 3 L13: 0.0868 L23: 0.4615 REMARK 3 S TENSOR REMARK 3 S11: -0.1201 S12: 0.2524 S13: 0.0859 REMARK 3 S21: -0.1250 S22: 0.0561 S23: 0.0607 REMARK 3 S31: -0.1336 S32: 0.0529 S33: 0.0639 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: THE BIJVOET DIFFERENCES WERE USED FOR REMARK 3 PHASING. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 2R37 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1000044367. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00721 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 226199 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 38.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : 0.09900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.66400 REMARK 200 R SYM FOR SHELL (I) : 0.76300 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2I3Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M PCB PH 8.0, 60% MPD, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 51.86000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.65400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 51.86000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.65400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 300 REMARK: POSSIBLY TETRAMER 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: 1890 ANGSTROM**2 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 -61.30800 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 1870 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 103.72000 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6010 ANGSTROM**2 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 -61.30800 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 51.86000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 -30.65400 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 -51.86000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 -30.65400 REMARK 350 BIOMT3 4 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 24 REMARK 465 GLN A 25 REMARK 465 GLU A 26 REMARK 465 LYS A 27 REMARK 465 SER A 28 REMARK 465 LYS A 29 REMARK 465 MET A 30 REMARK 465 ASP A 31 REMARK 465 CYS A 32 REMARK 465 HIS A 33 REMARK 465 GLY A 34 REMARK 465 GLY A 35 REMARK 465 ILE A 36 REMARK 465 SER A 37 REMARK 465 PHE A 229 REMARK 465 GLN A 230 REMARK 465 MET B 24 REMARK 465 GLN B 25 REMARK 465 GLU B 26 REMARK 465 LYS B 27 REMARK 465 SER B 28 REMARK 465 LYS B 29 REMARK 465 MET B 30 REMARK 465 ASP B 31 REMARK 465 CYS B 32 REMARK 465 HIS B 33 REMARK 465 GLY B 34 REMARK 465 GLY B 35 REMARK 465 ALA B 224 REMARK 465 GLU B 225 REMARK 465 ASN B 226 REMARK 465 LEU B 227 REMARK 465 TYR B 228 REMARK 465 PHE B 229 REMARK 465 GLN B 230 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 GLU A 51 OE1 OE2 REMARK 470 GLU A 87 CD OE1 OE2 REMARK 470 GLU A 88 CD OE1 OE2 REMARK 470 GLU A 143 CD OE1 OE2 REMARK 470 ARG A 201 CZ NH1 NH2 REMARK 470 LYS A 208 CE NZ REMARK 470 GLU A 225 CG CD OE1 OE2 REMARK 470 GLU B 87 CD OE1 OE2 REMARK 470 GLU B 143 CD OE1 OE2 REMARK 470 LYS B 147 CE NZ REMARK 470 LEU B 221 CG CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 81 O HOH A 383 2.03 REMARK 500 OE2 GLU A 81 O HOH A 405 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MET A 174 CG - SD - CE ANGL. DEV. = -14.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 VAL A 122 -66.34 -122.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 237 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 166 O REMARK 620 2 LEU A 169 O 93.3 REMARK 620 3 HOH A 300 O 99.6 84.1 REMARK 620 4 HOH A 412 O 174.2 89.3 75.5 REMARK 620 5 HOH A 413 O 86.6 89.8 171.5 98.6 REMARK 620 6 HOH A 417 O 91.6 173.4 90.8 85.4 94.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 237 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 166 O REMARK 620 2 LEU B 169 O 94.2 REMARK 620 3 HOH B 257 O 90.6 173.7 REMARK 620 4 HOH B 381 O 89.8 90.1 94.0 REMARK 620 5 HOH B 382 O 171.8 85.3 89.4 98.3 REMARK 620 6 HOH B 411 O 101.0 80.0 95.1 165.8 70.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 237 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 237 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2I3Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE PEROXIDASE 5 DBREF 2R37 A 25 223 UNP P22352 GPX3_HUMAN 25 223 DBREF 2R37 B 25 223 UNP P22352 GPX3_HUMAN 25 223 SEQADV 2R37 MET A 24 UNP P22352 INITIATING METHIONINE SEQADV 2R37 GLY A 73 UNP P22352 CYS 73 ENGINEERED MUTATION SEQADV 2R37 ALA A 224 UNP P22352 EXPRESSION TAG SEQADV 2R37 GLU A 225 UNP P22352 EXPRESSION TAG SEQADV 2R37 ASN A 226 UNP P22352 EXPRESSION TAG SEQADV 2R37 LEU A 227 UNP P22352 EXPRESSION TAG SEQADV 2R37 TYR A 228 UNP P22352 EXPRESSION TAG SEQADV 2R37 PHE A 229 UNP P22352 EXPRESSION TAG SEQADV 2R37 GLN A 230 UNP P22352 EXPRESSION TAG SEQADV 2R37 MET B 24 UNP P22352 INITIATING METHIONINE SEQADV 2R37 GLY B 73 UNP P22352 CYS 73 ENGINEERED MUTATION SEQADV 2R37 ALA B 224 UNP P22352 EXPRESSION TAG SEQADV 2R37 GLU B 225 UNP P22352 EXPRESSION TAG SEQADV 2R37 ASN B 226 UNP P22352 EXPRESSION TAG SEQADV 2R37 LEU B 227 UNP P22352 EXPRESSION TAG SEQADV 2R37 TYR B 228 UNP P22352 EXPRESSION TAG SEQADV 2R37 PHE B 229 UNP P22352 EXPRESSION TAG SEQADV 2R37 GLN B 230 UNP P22352 EXPRESSION TAG SEQRES 1 A 207 MET GLN GLU LYS SER LYS MET ASP CYS HIS GLY GLY ILE SEQRES 2 A 207 SER GLY THR ILE TYR GLU TYR GLY ALA LEU THR ILE ASP SEQRES 3 A 207 GLY GLU GLU TYR ILE PRO PHE LYS GLN TYR ALA GLY LYS SEQRES 4 A 207 TYR VAL LEU PHE VAL ASN VAL ALA SER TYR GLY GLY LEU SEQRES 5 A 207 THR GLY GLN TYR ILE GLU LEU ASN ALA LEU GLN GLU GLU SEQRES 6 A 207 LEU ALA PRO PHE GLY LEU VAL ILE LEU GLY PHE PRO CYS SEQRES 7 A 207 ASN GLN PHE GLY LYS GLN GLU PRO GLY GLU ASN SER GLU SEQRES 8 A 207 ILE LEU PRO THR LEU LYS TYR VAL ARG PRO GLY GLY GLY SEQRES 9 A 207 PHE VAL PRO ASN PHE GLN LEU PHE GLU LYS GLY ASP VAL SEQRES 10 A 207 ASN GLY GLU LYS GLU GLN LYS PHE TYR THR PHE LEU LYS SEQRES 11 A 207 ASN SER CYS PRO PRO THR SER GLU LEU LEU GLY THR SER SEQRES 12 A 207 ASP ARG LEU PHE TRP GLU PRO MET LYS VAL HIS ASP ILE SEQRES 13 A 207 ARG TRP ASN PHE GLU LYS PHE LEU VAL GLY PRO ASP GLY SEQRES 14 A 207 ILE PRO ILE MET ARG TRP HIS HIS ARG THR THR VAL SER SEQRES 15 A 207 ASN VAL LYS MET ASP ILE LEU SER TYR MET ARG ARG GLN SEQRES 16 A 207 ALA ALA LEU GLY VAL ALA GLU ASN LEU TYR PHE GLN SEQRES 1 B 207 MET GLN GLU LYS SER LYS MET ASP CYS HIS GLY GLY ILE SEQRES 2 B 207 SER GLY THR ILE TYR GLU TYR GLY ALA LEU THR ILE ASP SEQRES 3 B 207 GLY GLU GLU TYR ILE PRO PHE LYS GLN TYR ALA GLY LYS SEQRES 4 B 207 TYR VAL LEU PHE VAL ASN VAL ALA SER TYR GLY GLY LEU SEQRES 5 B 207 THR GLY GLN TYR ILE GLU LEU ASN ALA LEU GLN GLU GLU SEQRES 6 B 207 LEU ALA PRO PHE GLY LEU VAL ILE LEU GLY PHE PRO CYS SEQRES 7 B 207 ASN GLN PHE GLY LYS GLN GLU PRO GLY GLU ASN SER GLU SEQRES 8 B 207 ILE LEU PRO THR LEU LYS TYR VAL ARG PRO GLY GLY GLY SEQRES 9 B 207 PHE VAL PRO ASN PHE GLN LEU PHE GLU LYS GLY ASP VAL SEQRES 10 B 207 ASN GLY GLU LYS GLU GLN LYS PHE TYR THR PHE LEU LYS SEQRES 11 B 207 ASN SER CYS PRO PRO THR SER GLU LEU LEU GLY THR SER SEQRES 12 B 207 ASP ARG LEU PHE TRP GLU PRO MET LYS VAL HIS ASP ILE SEQRES 13 B 207 ARG TRP ASN PHE GLU LYS PHE LEU VAL GLY PRO ASP GLY SEQRES 14 B 207 ILE PRO ILE MET ARG TRP HIS HIS ARG THR THR VAL SER SEQRES 15 B 207 ASN VAL LYS MET ASP ILE LEU SER TYR MET ARG ARG GLN SEQRES 16 B 207 ALA ALA LEU GLY VAL ALA GLU ASN LEU TYR PHE GLN HET CL A 1 1 HET NA A 237 1 HET CL B 2 1 HET NA B 237 1 HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION FORMUL 3 CL 2(CL 1-) FORMUL 4 NA 2(NA 1+) FORMUL 7 HOH *406(H2 O) HELIX 1 1 THR A 39 GLU A 42 5 4 HELIX 2 2 LYS A 57 ALA A 60 5 4 HELIX 3 3 GLY A 77 ALA A 90 1 14 HELIX 4 4 GLU A 111 SER A 113 5 3 HELIX 5 5 GLU A 114 VAL A 122 1 9 HELIX 6 6 GLN A 146 CYS A 156 1 11 HELIX 7 7 THR A 165 LEU A 169 5 5 HELIX 8 8 THR A 203 TYR A 228 1 26 HELIX 9 9 THR B 39 GLU B 42 5 4 HELIX 10 10 LYS B 57 ALA B 60 5 4 HELIX 11 11 GLY B 77 ALA B 90 1 14 HELIX 12 12 GLU B 111 SER B 113 5 3 HELIX 13 13 GLU B 114 VAL B 122 1 9 HELIX 14 14 GLN B 146 CYS B 156 1 11 HELIX 15 15 THR B 165 LEU B 169 5 5 HELIX 16 16 THR B 203 GLY B 222 1 20 SHEET 1 A 2 GLY A 44 LEU A 46 0 SHEET 2 A 2 TYR A 53 PRO A 55 -1 O ILE A 54 N ALA A 45 SHEET 1 B 5 GLN A 133 LEU A 134 0 SHEET 2 B 5 LEU A 94 PRO A 100 1 N GLY A 98 O GLN A 133 SHEET 3 B 5 TYR A 63 VAL A 69 1 N LEU A 65 O VAL A 95 SHEET 4 B 5 LYS A 185 VAL A 188 -1 O VAL A 188 N VAL A 64 SHEET 5 B 5 PRO A 194 TRP A 198 -1 O ILE A 195 N LEU A 187 SHEET 1 C 2 GLY B 44 LEU B 46 0 SHEET 2 C 2 TYR B 53 PRO B 55 -1 O ILE B 54 N ALA B 45 SHEET 1 D 5 GLN B 133 LEU B 134 0 SHEET 2 D 5 LEU B 94 PRO B 100 1 N GLY B 98 O GLN B 133 SHEET 3 D 5 TYR B 63 VAL B 69 1 N LEU B 65 O LEU B 97 SHEET 4 D 5 LYS B 185 VAL B 188 -1 O VAL B 188 N VAL B 64 SHEET 5 D 5 PRO B 194 TRP B 198 -1 O MET B 196 N LEU B 187 LINK O SER A 166 NA NA A 237 1555 1555 2.28 LINK O LEU A 169 NA NA A 237 1555 1555 2.26 LINK NA NA A 237 O HOH A 300 1555 1555 2.59 LINK NA NA A 237 O HOH A 412 1555 1555 2.39 LINK NA NA A 237 O HOH A 413 1555 1555 2.29 LINK NA NA A 237 O HOH A 417 1555 1555 2.43 LINK O SER B 166 NA NA B 237 1555 1555 2.31 LINK O LEU B 169 NA NA B 237 1555 1555 2.33 LINK NA NA B 237 O HOH B 257 1555 1555 2.41 LINK NA NA B 237 O HOH B 381 1555 1555 2.40 LINK NA NA B 237 O HOH B 382 1555 1555 2.38 LINK NA NA B 237 O HOH B 411 1555 1555 2.70 CISPEP 1 ARG A 123 PRO A 124 0 -1.59 CISPEP 2 GLU A 172 PRO A 173 0 -6.45 CISPEP 3 ARG B 123 PRO B 124 0 -2.51 CISPEP 4 GLU B 172 PRO B 173 0 -5.09 SITE 1 AC1 5 GLY A 73 GLY A 74 LEU A 75 TRP A 181 SITE 2 AC1 5 ASN A 182 SITE 1 AC2 5 GLY B 73 GLY B 74 LEU B 75 TRP B 181 SITE 2 AC2 5 ASN B 182 SITE 1 AC3 6 SER A 166 LEU A 169 HOH A 300 HOH A 412 SITE 2 AC3 6 HOH A 413 HOH A 417 SITE 1 AC4 6 SER B 166 LEU B 169 HOH B 257 HOH B 381 SITE 2 AC4 6 HOH B 382 HOH B 411 CRYST1 103.720 61.308 100.400 90.00 90.00 90.00 P 21 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 0.009641 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016311 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009960 0.00000