HEADER TRANSCRIPTION REGULATION 12-OCT-94 1MYK TITLE CRYSTAL STRUCTURE, FOLDING, AND OPERATOR BINDING OF THE HYPERSTABLE TITLE 2 ARC REPRESSOR MUTANT PL8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARC REPRESSOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE P22; SOURCE 3 ORGANISM_TAXID: 10754; SOURCE 4 GENE: MUTATED ARC GENE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PTA200-PL8 KEYWDS TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR J.F.SCHILDBACH,M.E.MILLA,P.D.JEFFREY,B.E.RAUMANN,R.T.SAUER REVDAT 3 14-FEB-24 1MYK 1 SEQADV REVDAT 2 24-FEB-09 1MYK 1 VERSN REVDAT 1 26-JAN-95 1MYK 0 JRNL AUTH J.F.SCHILDBACH,M.E.MILLA,P.D.JEFFREY,B.E.RAUMANN,R.T.SAUER JRNL TITL CRYSTAL STRUCTURE, FOLDING, AND OPERATOR BINDING OF THE JRNL TITL 2 HYPERSTABLE ARC REPRESSOR MUTANT PL8. JRNL REF BIOCHEMISTRY V. 34 1405 1995 JRNL REFN ISSN 0006-2960 JRNL PMID 7827088 JRNL DOI 10.1021/BI00004A035 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.E.RAUMANN,M.A.ROULD,C.O.PABO,R.T.SAUER REMARK 1 TITL DNA RECOGNITION BY BETA-SHEETS IN THE ARC REPRESSOR-OPERATOR REMARK 1 TITL 2 CRYSTAL STRUCTURE REMARK 1 REF NATURE V. 367 754 1994 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 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) (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 5340 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) : 0.217 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL 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 : 764 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.50 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) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.490 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.99 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.180 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) : 1.500 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 4.150 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 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 1MYK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175190. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5340 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 55.35000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.90000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.67500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.90000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.90000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 83.02500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.90000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.90000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.67500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.90000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.90000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 83.02500 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 55.35000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 400 REMARK 400 COMPOUND REMARK 400 PL8 IS HYPERSTABLE RELATIVE TO ARC, BUT HAS REDUCED REMARK 400 AFFINITY FOR DNA. PL8 DIMER IS 2.5 KCALMOL MORE STABLE REMARK 400 THAN WILD TYPE DIMER BY THERMAL OR CHEMICAL DENATURATION. REMARK 400 DNA AFFINITY IS DOWN 5.0 KCALMOL FOR REACTION OF TWO REMARK 400 DIMERS BINDING ARC OPERATOR. ARC AND PL8 ARE DIMERIC IN REMARK 400 SOLUTION. 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 LYS A 2 REMARK 465 GLY A 3 REMARK 465 MET A 4 REMARK 465 SER A 5 REMARK 465 ALA A 53 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 GLY B 3 REMARK 465 MET B 4 REMARK 465 SER B 5 REMARK 465 ILE B 51 REMARK 465 GLY B 52 REMARK 465 ALA B 53 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 LYS A 6 CG CD CE NZ REMARK 470 LYS B 6 CG CD CE NZ REMARK 470 ARG B 50 CG CD NE CZ NH1 NH2 DBREF 1MYK A 1 53 UNP P03050 RARC_BPP22 1 53 DBREF 1MYK B 1 53 UNP P03050 RARC_BPP22 1 53 SEQADV 1MYK LEU A 8 UNP P03050 PRO 8 CONFLICT SEQADV 1MYK LEU B 8 UNP P03050 PRO 8 CONFLICT SEQRES 1 A 53 MET LYS GLY MET SER LYS MET LEU GLN PHE ASN LEU ARG SEQRES 2 A 53 TRP PRO ARG GLU VAL LEU ASP LEU VAL ARG LYS VAL ALA SEQRES 3 A 53 GLU GLU ASN GLY ARG SER VAL ASN SER GLU ILE TYR GLN SEQRES 4 A 53 ARG VAL MET GLU SER PHE LYS LYS GLU GLY ARG ILE GLY SEQRES 5 A 53 ALA SEQRES 1 B 53 MET LYS GLY MET SER LYS MET LEU GLN PHE ASN LEU ARG SEQRES 2 B 53 TRP PRO ARG GLU VAL LEU ASP LEU VAL ARG LYS VAL ALA SEQRES 3 B 53 GLU GLU ASN GLY ARG SER VAL ASN SER GLU ILE TYR GLN SEQRES 4 B 53 ARG VAL MET GLU SER PHE LYS LYS GLU GLY ARG ILE GLY SEQRES 5 B 53 ALA FORMUL 3 HOH *16(H2 O) HELIX 1 1 ARG A 16 ASN A 29 1 14 HELIX 2 2 SER A 32 GLU A 48 1 17 HELIX 3 3 ARG B 16 ASN B 29 1 14 HELIX 4 4 SER B 32 GLU B 48 1 17 SHEET 1 A 2 MET A 7 PRO A 15 0 SHEET 2 A 2 MET B 7 PRO B 15 -1 N LEU B 8 O TRP A 14 CRYST1 51.800 51.800 110.700 90.00 90.00 90.00 P 41 21 2 16 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 0.019305 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009033 0.00000