PDB Short entry for 1BAZ HEADER TRANSCRIPTION REGULATION 21-APR-98 1BAZ TITLE ARC REPRESSOR MUTANT PHE10VAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARC REPRESSOR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: REGULATORY PROTEIN ARC; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE P22; SOURCE 3 ORGANISM_TAXID: 10754; SOURCE 4 GENE: ARC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: UA2F; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PTA200-FV10; SOURCE 9 EXPRESSION_SYSTEM_GENE: ARC KEYWDS TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR J.F.SCHILDBACH,B.E.RAUMANN,R.T.SAUER REVDAT 5 07-FEB-24 1BAZ 1 REMARK REVDAT 4 03-NOV-21 1BAZ 1 SEQADV REVDAT 3 24-FEB-09 1BAZ 1 VERSN REVDAT 2 03-FEB-99 1BAZ 1 JRNL REVDAT 1 17-JUN-98 1BAZ 0 JRNL AUTH J.F.SCHILDBACH,A.W.KARZAI,B.E.RAUMANN,R.T.SAUER JRNL TITL ORIGINS OF DNA-BINDING SPECIFICITY: ROLE OF PROTEIN CONTACTS JRNL TITL 2 WITH THE DNA BACKBONE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 96 811 1999 JRNL REFN ISSN 0027-8424 JRNL PMID 9927650 JRNL DOI 10.1073/PNAS.96.3.811 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. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 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) (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 16211 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) : 0.213 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1633 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 50.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 810 REMARK 3 BIN R VALUE (WORKING SET) : 0.3836 REMARK 3 BIN FREE R VALUE : 0.4641 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 98 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 : 1463 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 67 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.10 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.494 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.490 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 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SCALE REMARK 3 UNCONVENTIONAL ORTHORHOMBIC CELL, WITH A AND C SWAPPED. REMARK 4 REMARK 4 1BAZ 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_1000171543. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : OCT-93 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.0 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16796 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 90.0 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.08700 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.7 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 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE ARC MUTANT FV10 CRYSTALLIZED NEARLY ISOMORPHOUSLY WITH REMARK 200 THE WILD TYPE WHEN CRYSTALLIZING USING MACROSEEDING. THEREFORE, REMARK 200 THE WILD TYPE ARC STRUCTURE WAS USED AS THE INITIAL MODEL FOR REMARK 200 THE MUTANT. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 40-45% REMARK 280 SATURATED AMMONIUM PHOSPHATE, PH 8.0, BY MACROSEEDING USING REMARK 280 CRYSTALS OF THE WILD TYPE PROTEIN REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 45.95000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.66000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.28500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.66000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.95000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.28500 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 A 1 REMARK 465 LYS A 2 REMARK 465 GLY A 3 REMARK 465 MET A 4 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 LYS B 47 REMARK 465 GLU B 48 REMARK 465 GLY B 49 REMARK 465 ARG B 50 REMARK 465 ILE B 51 REMARK 465 GLY B 52 REMARK 465 ALA B 53 REMARK 465 MET C 1 REMARK 465 LYS C 2 REMARK 465 GLY C 3 REMARK 465 MET C 4 REMARK 465 SER C 5 REMARK 465 LYS C 6 REMARK 465 ALA C 53 REMARK 465 MET D 1 REMARK 465 LYS D 2 REMARK 465 GLY D 3 REMARK 465 MET D 4 REMARK 465 SER D 5 REMARK 465 LYS D 6 REMARK 465 LYS D 47 REMARK 465 GLU D 48 REMARK 465 GLY D 49 REMARK 465 ARG D 50 REMARK 465 ILE D 51 REMARK 465 GLY D 52 REMARK 465 ALA D 53 DBREF 1BAZ A 1 53 UNP P03050 RARC_BPP22 1 53 DBREF 1BAZ B 1 53 UNP P03050 RARC_BPP22 1 53 DBREF 1BAZ C 1 53 UNP P03050 RARC_BPP22 1 53 DBREF 1BAZ D 1 53 UNP P03050 RARC_BPP22 1 53 SEQADV 1BAZ VAL A 10 UNP P03050 PHE 10 ENGINEERED MUTATION SEQADV 1BAZ VAL B 10 UNP P03050 PHE 10 ENGINEERED MUTATION SEQADV 1BAZ VAL C 10 UNP P03050 PHE 10 ENGINEERED MUTATION SEQADV 1BAZ VAL D 10 UNP P03050 PHE 10 ENGINEERED MUTATION SEQRES 1 A 53 MET LYS GLY MET SER LYS MET PRO GLN VAL 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 PRO GLN VAL 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 SEQRES 1 C 53 MET LYS GLY MET SER LYS MET PRO GLN VAL ASN LEU ARG SEQRES 2 C 53 TRP PRO ARG GLU VAL LEU ASP LEU VAL ARG LYS VAL ALA SEQRES 3 C 53 GLU GLU ASN GLY ARG SER VAL ASN SER GLU ILE TYR GLN SEQRES 4 C 53 ARG VAL MET GLU SER PHE LYS LYS GLU GLY ARG ILE GLY SEQRES 5 C 53 ALA SEQRES 1 D 53 MET LYS GLY MET SER LYS MET PRO GLN VAL ASN LEU ARG SEQRES 2 D 53 TRP PRO ARG GLU VAL LEU ASP LEU VAL ARG LYS VAL ALA SEQRES 3 D 53 GLU GLU ASN GLY ARG SER VAL ASN SER GLU ILE TYR GLN SEQRES 4 D 53 ARG VAL MET GLU SER PHE LYS LYS GLU GLY ARG ILE GLY SEQRES 5 D 53 ALA FORMUL 5 HOH *67(H2 O) HELIX 1 1 ARG A 16 GLU A 28 1 13 HELIX 2 2 VAL A 33 LYS A 47 1 15 HELIX 3 3 ARG B 16 GLU B 28 1 13 HELIX 4 4 VAL B 33 SER B 44 1 12 HELIX 5 5 ARG C 16 ASN C 29 1 14 HELIX 6 6 VAL C 33 LYS C 47 1 15 HELIX 7 7 ARG D 16 ASN D 29 1 14 HELIX 8 8 VAL D 33 SER D 44 1 12 SHEET 1 A 2 GLN A 9 ARG A 13 0 SHEET 2 A 2 GLN B 9 ARG B 13 -1 O VAL B 10 N LEU A 12 SHEET 1 B 2 GLN C 9 ARG C 13 0 SHEET 2 B 2 GLN D 9 ARG D 13 -1 O VAL D 10 N LEU C 12 CRYST1 91.900 52.570 47.320 90.00 90.00 90.00 P 21 21 21 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 0.010881 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021133 0.00000