HEADER DNA BINDING PROTEIN 31-MAR-05 1Z91 TITLE X-RAY CRYSTAL STRUCTURE OF APO-OHRRC15S IN REDUCED FORM: MARR FAMILY TITLE 2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORGANIC HYDROPEROXIDE RESISTANCE TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: OHRR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)/PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET16X KEYWDS OHRR, MARR FAMILY, BACTERIAL TRANSCRIPTION FACTOR, DNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.HONG,M.FUANGTHONG,J.D.HELMANN,R.G.BRENNAN REVDAT 7 14-FEB-24 1Z91 1 REMARK REVDAT 6 20-OCT-21 1Z91 1 SEQADV REVDAT 5 16-NOV-11 1Z91 1 HETATM REVDAT 4 13-JUL-11 1Z91 1 VERSN REVDAT 3 24-FEB-09 1Z91 1 VERSN REVDAT 2 06-DEC-05 1Z91 1 REMARK REVDAT 1 25-OCT-05 1Z91 0 JRNL AUTH M.HONG,M.FUANGTHONG,J.D.HELMANN,R.G.BRENNAN JRNL TITL STRUCTURE OF AN OHRR-OHRA OPERATOR COMPLEX REVEALS THE DNA JRNL TITL 2 BINDING MECHANISM OF THE MARR FAMILY. JRNL REF MOL.CELL V. 20 131 2005 JRNL REFN ISSN 1097-2765 JRNL PMID 16209951 JRNL DOI 10.1016/J.MOLCEL.2005.09.013 REMARK 2 REMARK 2 RESOLUTION. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 4233231.340 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 4484 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) : 0.223 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.700 REMARK 3 FREE R VALUE TEST SET COUNT : 482 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.014 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 640 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE : 0.3870 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 77 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.044 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1101 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.50000 REMARK 3 B22 (A**2) : -3.50000 REMARK 3 B33 (A**2) : 7.01000 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) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.32 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) : 0.49 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.51 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.780 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) : 3.430 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.930 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.400 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.390 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 40.63 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Z91 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032450. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-03; 30-SEP-03 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ALS; ALS REMARK 200 BEAMLINE : 8.2.1; 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794; 0.9794, 0.9184, 0.9796 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111); DOUBLE REMARK 200 CRYSTAL SI(111) REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; ADSC QUANTUM REMARK 200 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4532 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 45.175 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 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) : NULL 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; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD 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 (%): 26.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 TO 33 % PEG 1450, 0.1 M AMMONIUM REMARK 280 ACETATE (OR SODIUM ACETATE), AND 0.1M SODIUM ACETATE, PH 4.5., REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 38.62100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.67750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.67750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.31050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.67750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.67750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 57.93150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.67750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.67750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 19.31050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.67750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.67750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 57.93150 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 38.62100 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE TWO FOLD AXIS 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 38.62100 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 178 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 1 REMARK 465 GLU A 2 REMARK 465 ASN A 3 REMARK 465 LYS A 4 REMARK 465 PHE A 5 REMARK 465 ASP A 6 REMARK 465 HIS A 7 REMARK 465 GLN A 145 REMARK 465 LYS A 146 REMARK 465 ASN A 147 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 LYS A 27 -17.98 -48.63 REMARK 500 LYS A 30 -51.17 -28.72 REMARK 500 ASN A 37 -27.84 76.73 REMARK 500 GLU A 53 -53.07 63.10 REMARK 500 LEU A 64 -18.34 168.05 REMARK 500 LYS A 87 118.90 179.64 REMARK 500 ASP A 92 90.97 -162.44 REMARK 500 GLU A 93 -17.56 -48.40 REMARK 500 LEU A 143 24.14 -70.27 REMARK 500 REMARK 500 REMARK: NULL DBREF 1Z91 A 1 147 UNP O34777 OHRR_BACSU 1 147 SEQADV 1Z91 SER A 15 UNP O34777 CYS 15 ENGINEERED MUTATION SEQRES 1 A 147 MET GLU ASN LYS PHE ASP HIS MET LYS LEU GLU ASN GLN SEQRES 2 A 147 LEU SER PHE LEU LEU TYR ALA SER SER ARG GLU MET THR SEQRES 3 A 147 LYS GLN TYR LYS PRO LEU LEU ASP LYS LEU ASN ILE THR SEQRES 4 A 147 TYR PRO GLN TYR LEU ALA LEU LEU LEU LEU TRP GLU HIS SEQRES 5 A 147 GLU THR LEU THR VAL LYS LYS MET GLY GLU GLN LEU TYR SEQRES 6 A 147 LEU ASP SER GLY THR LEU THR PRO MET LEU LYS ARG MET SEQRES 7 A 147 GLU GLN GLN GLY LEU ILE THR ARG LYS ARG SER GLU GLU SEQRES 8 A 147 ASP GLU ARG SER VAL LEU ILE SER LEU THR GLU ASP GLY SEQRES 9 A 147 ALA LEU LEU LYS GLU LYS ALA VAL ASP ILE PRO GLY THR SEQRES 10 A 147 ILE LEU GLY LEU SER LYS GLN SER GLY GLU ASP LEU LYS SEQRES 11 A 147 GLN LEU LYS SER ALA LEU TYR THR LEU LEU GLU THR LEU SEQRES 12 A 147 HIS GLN LYS ASN FORMUL 2 HOH *36(H2 O) HELIX 1 1 LYS A 9 ASN A 12 5 4 HELIX 2 2 GLN A 13 LYS A 27 1 15 HELIX 3 3 TYR A 29 ASP A 34 1 6 HELIX 4 4 THR A 39 GLU A 53 1 15 HELIX 5 5 VAL A 57 GLN A 63 1 7 HELIX 6 6 ASP A 67 GLY A 82 1 16 HELIX 7 7 THR A 101 LEU A 106 1 6 HELIX 8 8 LEU A 107 ALA A 111 5 5 HELIX 9 9 ASP A 113 SER A 122 1 10 HELIX 10 10 GLY A 126 LEU A 143 1 18 SHEET 1 A 3 THR A 54 THR A 56 0 SHEET 2 A 3 LEU A 97 LEU A 100 -1 O ILE A 98 N LEU A 55 SHEET 3 A 3 ILE A 84 THR A 85 -1 N THR A 85 O SER A 99 CRYST1 55.355 55.355 77.242 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 0.018065 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018065 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012946 0.00000