HEADER TRANSCRIPTION/DNA 22-AUG-07 2R1J TITLE CRYSTAL STRUCTURE OF THE P22 C2 REPRESSOR PROTEIN IN COMPLEX WITH THE TITLE 2 SYNTHETIC OPERATOR 9T COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*DCP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*D COMPND 3 TP*DTP*DAP*DAP*DAP*DTP*DA)-3'; COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*DTP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*D COMPND 8 TP*DTP*DAP*DAP*DAP*DTP*DG)-3'; COMPND 9 CHAIN: A; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: REPRESSOR PROTEIN C2; COMPND 13 CHAIN: L, R; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE P22; SOURCE 7 ORGANISM_TAXID: 10754; SOURCE 8 GENE: C2; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: XA90; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PUC18 KEYWDS PROTEIN-DNA COMPLEX, HELIX-TURN-HELIX, DNA-BINDING, REPRESSOR, KEYWDS 2 TRANSCRIPTION, TRANSCRIPTION REGULATION, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.D.WILLIAMS,G.B.KOUDELKA,D.WATKINS,C.HSIAO,K.WOODS REVDAT 4 21-FEB-24 2R1J 1 REMARK REVDAT 3 25-OCT-17 2R1J 1 REMARK REVDAT 2 24-FEB-09 2R1J 1 VERSN REVDAT 1 29-APR-08 2R1J 0 JRNL AUTH D.WATKINS,C.HSIAO,K.K.WOODS,G.B.KOUDELKA,L.D.WILLIAMS JRNL TITL P22 C2 REPRESSOR-OPERATOR COMPLEX: MECHANISMS OF DIRECT AND JRNL TITL 2 INDIRECT READOUT JRNL REF BIOCHEMISTRY V. 47 2325 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18237194 JRNL DOI 10.1021/BI701826F REMARK 2 REMARK 2 RESOLUTION. 1.53 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.00 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) (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 59833 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) : 0.204 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 6068 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) : 1.53 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3560 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 535 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 : 1030 REMARK 3 NUCLEIC ACID ATOMS : 814 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 331 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.05 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.334 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : 1.278 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.006 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.983 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.050 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 58.05 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 : DNA-RNA_REP_TINOUSH.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA_TINOUSH.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2R1J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000044309. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99997 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60878 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 47.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.65900 REMARK 200 R SYM FOR SHELL (I) : 0.65900 REMARK 200 FOR SHELL : 2.120 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE INITIAL CRYSTALLIZATION SOLUTION REMARK 280 CONTAINED 0.42 MM P22R NTD, 0.42 MM DUPLEX D(5 REMARK 280 TATTTAAGATATCTTAAATG3 ) -D(5 CATTTAAGATATCTTAAATA3 ), 45 MM REMARK 280 TRIS.HCL (PH 7.8), 19 MM NACL, 1.9 MM GLYCEROL, 11% PEG 400, 4.5 REMARK 280 MM LICL, 2.3MM MGCL2 AND 0.91% MPD IN A VOLUME OF 5.3 UL. THE REMARK 280 CRYSTALLIZATION SOLUTION WAS EQUILIBRATED AGAINST A RESERVOIR OF REMARK 280 100 MM TRIS.HCL (PH 7.8), 25% PEG 400, 10 MM LICL, 5 MM MGCL2 REMARK 280 AND 2% MPD, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 50.84250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 76.26375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.42125 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A, L, R 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 MET L 1 REMARK 465 ASN L 2 REMARK 465 MET R 1 REMARK 465 ASN R 2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DT B 5 0.08 SIDE CHAIN REMARK 500 DT A 24 0.07 SIDE CHAIN REMARK 500 DT A 34 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2R1J L 1 68 UNP P69202 RPC2_BPP22 1 68 DBREF 2R1J R 1 68 UNP P69202 RPC2_BPP22 1 68 DBREF 2R1J B 1 20 PDB 2R1J 2R1J 1 20 DBREF 2R1J A 21 40 PDB 2R1J 2R1J 21 40 SEQRES 1 B 20 DC DA DT DT DT DA DA DG DA DT DA DT DC SEQRES 2 B 20 DT DT DA DA DA DT DA SEQRES 1 A 20 DT DA DT DT DT DA DA DG DA DT DA DT DC SEQRES 2 A 20 DT DT DA DA DA DT DG SEQRES 1 L 68 MET ASN THR GLN LEU MET GLY GLU ARG ILE ARG ALA ARG SEQRES 2 L 68 ARG LYS LYS LEU LYS ILE ARG GLN ALA ALA LEU GLY LYS SEQRES 3 L 68 MET VAL GLY VAL SER ASN VAL ALA ILE SER GLN TRP GLU SEQRES 4 L 68 ARG SER GLU THR GLU PRO ASN GLY GLU ASN LEU LEU ALA SEQRES 5 L 68 LEU SER LYS ALA LEU GLN CYS SER PRO ASP TYR LEU LEU SEQRES 6 L 68 LYS GLY ASP SEQRES 1 R 68 MET ASN THR GLN LEU MET GLY GLU ARG ILE ARG ALA ARG SEQRES 2 R 68 ARG LYS LYS LEU LYS ILE ARG GLN ALA ALA LEU GLY LYS SEQRES 3 R 68 MET VAL GLY VAL SER ASN VAL ALA ILE SER GLN TRP GLU SEQRES 4 R 68 ARG SER GLU THR GLU PRO ASN GLY GLU ASN LEU LEU ALA SEQRES 5 R 68 LEU SER LYS ALA LEU GLN CYS SER PRO ASP TYR LEU LEU SEQRES 6 R 68 LYS GLY ASP FORMUL 5 HOH *331(H2 O) HELIX 1 1 LEU L 5 LYS L 18 1 14 HELIX 2 2 ARG L 20 GLY L 29 1 10 HELIX 3 3 SER L 31 ARG L 40 1 10 HELIX 4 4 ASN L 46 LEU L 57 1 12 HELIX 5 5 SER L 60 GLY L 67 1 8 HELIX 6 6 LEU R 5 LYS R 18 1 14 HELIX 7 7 ARG R 20 GLY R 29 1 10 HELIX 8 8 SER R 31 ARG R 40 1 10 HELIX 9 9 ASN R 46 LEU R 57 1 12 HELIX 10 10 SER R 60 GLY R 67 1 8 CRYST1 64.105 64.105 101.685 90.00 90.00 90.00 P 43 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 0.015599 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015599 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009834 0.00000