HEADER TRANSCRIPTION 02-MAR-01 1I6A TITLE CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF OXYR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROGEN PEROXIDE-INDUCIBLE GENES ACTIVATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: REGULATORY DOMAIN; COMPND 5 SYNONYM: OXYR; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS OXYR REGULATORY DOMAIN, OXIDIZED FORM, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR H.CHOI,S.KIM,S.RYU REVDAT 7 13-NOV-24 1I6A 1 REMARK REVDAT 6 03-APR-24 1I6A 1 REMARK REVDAT 5 27-OCT-21 1I6A 1 SEQADV SHEET REVDAT 4 04-OCT-17 1I6A 1 REMARK REVDAT 3 01-FEB-17 1I6A 1 TITLE VERSN REVDAT 2 24-FEB-09 1I6A 1 VERSN REVDAT 1 02-SEP-01 1I6A 0 JRNL AUTH H.CHOI,S.KIM,P.MUKHOPADHYAY,S.CHO,J.WOO,G.STORZ,S.RYU JRNL TITL STRUCTURAL BASIS OF THE REDOX SWITCH IN THE OXYR JRNL TITL 2 TRANSCRIPTION FACTOR. JRNL REF CELL(CAMBRIDGE,MASS.) V. 105 103 2001 JRNL REFN ISSN 0092-8674 JRNL PMID 11301006 JRNL DOI 10.1016/S0092-8674(01)00300-2 REMARK 2 REMARK 2 RESOLUTION. 2.30 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 9049 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1657 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.440 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.930 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 1I6A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-01. REMARK 100 THE DEPOSITION ID IS D_1000012957. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : NULL 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9049 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: REDUCED FORM OF OXYR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 48.41500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.92500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 48.41500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.92500 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 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 360 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 LYS A 299 REMARK 465 VAL A 300 REMARK 465 LEU A 301 REMARK 465 LYS A 302 REMARK 465 GLN A 303 REMARK 465 ALA A 304 REMARK 465 VAL A 305 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 LEU A 97 CA - CB - CG ANGL. DEV. = 16.6 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 MET A 89 59.33 -110.59 REMARK 500 VAL A 101 -56.04 -122.28 REMARK 500 HIS A 198 -58.95 -121.25 REMARK 500 THR A 222 -114.66 -103.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1I69 RELATED DB: PDB REMARK 900 1I69 IS THE REDUCED FORM OF OXYR DBREF 1I6A A 87 305 UNP P0ACQ4 OXYR_ECOLI 87 305 SEQADV 1I6A ALA A 143 UNP P0ACQ4 CYS 143 ENGINEERED MUTATION SEQADV 1I6A ALA A 180 UNP P0ACQ4 CYS 180 ENGINEERED MUTATION SEQADV 1I6A ALA A 259 UNP P0ACQ4 CYS 259 ENGINEERED MUTATION SEQRES 1 A 219 GLU THR MET SER GLY PRO LEU HIS ILE GLY LEU ILE PRO SEQRES 2 A 219 THR VAL GLY PRO TYR LEU LEU PRO HIS ILE ILE PRO MET SEQRES 3 A 219 LEU HIS GLN THR PHE PRO LYS LEU GLU MET TYR LEU HIS SEQRES 4 A 219 GLU ALA GLN THR HIS GLN LEU LEU ALA GLN LEU ASP SER SEQRES 5 A 219 GLY LYS LEU ASP ALA VAL ILE LEU ALA LEU VAL LYS GLU SEQRES 6 A 219 SER GLU ALA PHE ILE GLU VAL PRO LEU PHE ASP GLU PRO SEQRES 7 A 219 MET LEU LEU ALA ILE TYR GLU ASP HIS PRO TRP ALA ASN SEQRES 8 A 219 ARG GLU ALA VAL PRO MET ALA ASP LEU ALA GLY GLU LYS SEQRES 9 A 219 LEU LEU MET LEU GLU ASP GLY HIS CYS LEU ARG ASP GLN SEQRES 10 A 219 ALA MET GLY PHE CYS PHE GLU ALA GLY ALA ASP GLU ASP SEQRES 11 A 219 THR HIS PHE ARG ALA THR SER LEU GLU THR LEU ARG ASN SEQRES 12 A 219 MET VAL ALA ALA GLY SER GLY ILE THR LEU LEU PRO ALA SEQRES 13 A 219 LEU ALA VAL PRO PRO GLU ARG LYS ARG ASP GLY VAL VAL SEQRES 14 A 219 TYR LEU PRO ALA ILE LYS PRO GLU PRO ARG ARG THR ILE SEQRES 15 A 219 GLY LEU VAL TYR ARG PRO GLY SER PRO LEU ARG SER ARG SEQRES 16 A 219 TYR GLU GLN LEU ALA GLU ALA ILE ARG ALA ARG MET ASP SEQRES 17 A 219 GLY HIS PHE ASP LYS VAL LEU LYS GLN ALA VAL FORMUL 2 HOH *59(H2 O) HELIX 1 1 VAL A 101 PHE A 117 1 17 HELIX 2 2 GLN A 128 SER A 138 1 11 HELIX 3 3 VAL A 149 GLU A 153 5 5 HELIX 4 4 HIS A 173 ARG A 178 5 6 HELIX 5 5 ALA A 184 ALA A 187 5 4 HELIX 6 6 SER A 223 ALA A 233 1 11 HELIX 7 7 LEU A 243 VAL A 245 5 3 HELIX 8 8 LEU A 278 ASP A 294 1 17 SHEET 1 A 5 LEU A 120 GLU A 126 0 SHEET 2 A 5 GLY A 91 LEU A 97 1 O GLY A 91 N GLU A 121 SHEET 3 A 5 ARG A 265 TYR A 272 -1 N GLY A 269 O LEU A 146 SHEET 4 A 5 ILE A 156 TYR A 170 -1 N ILE A 156 O TYR A 272 SHEET 5 A 5 THR A 238 PRO A 241 -1 O THR A 238 N ALA A 168 SHEET 1 B 6 LEU A 120 GLU A 126 0 SHEET 2 B 6 GLY A 91 LEU A 97 1 O GLY A 91 N GLU A 121 SHEET 3 B 6 ARG A 265 TYR A 272 -1 N GLY A 269 O LEU A 146 SHEET 4 B 6 ILE A 156 TYR A 170 -1 N ILE A 156 O TYR A 272 SHEET 5 B 6 VAL A 254 LEU A 257 -1 N VAL A 255 O ILE A 169 SHEET 6 B 6 LYS A 250 ARG A 251 -1 N ARG A 251 O VAL A 254 SHEET 1 C 1 VAL A 181 PRO A 182 0 SHEET 1 D 2 LYS A 190 LEU A 192 0 SHEET 2 D 2 ASP A 214 ASP A 216 1 O ASP A 214 N LEU A 191 SSBOND 1 CYS A 199 CYS A 208 1555 1555 2.03 CISPEP 1 LYS A 261 PRO A 262 0 -0.14 CRYST1 96.830 45.850 53.420 90.00 117.90 90.00 C 1 2 1 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 0.010327 0.000000 0.005468 0.00000 SCALE2 0.000000 0.021810 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021182 0.00000