HEADER VIRAL PROTEIN 01-JUN-00 1F39 TITLE CRYSTAL STRUCTURE OF THE LAMBDA REPRESSOR C-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPRESSOR PROTEIN CI; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE LAMBDA; SOURCE 3 ORGANISM_TAXID: 10710; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-14B KEYWDS COOPERATIVE OPERATOR BINDING, RECA-MEDIATED SELF-CLEAVAGE, GENE KEYWDS 2 REGULATION, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.E.BELL,P.FRESCURA,A.HOCHSCHILD,M.LEWIS REVDAT 3 30-OCT-24 1F39 1 SEQADV REVDAT 2 24-FEB-09 1F39 1 VERSN REVDAT 1 26-JUL-00 1F39 0 JRNL AUTH C.E.BELL,P.FRESCURA,A.HOCHSCHILD,M.LEWIS JRNL TITL CRYSTAL STRUCTURE OF THE LAMBDA REPRESSOR C-TERMINAL DOMAIN JRNL TITL 2 PROVIDES A MODEL FOR COOPERATIVE OPERATOR BINDING. JRNL REF CELL(CAMBRIDGE,MASS.) V. 101 801 2000 JRNL REFN ISSN 0092-8674 JRNL PMID 10892750 JRNL DOI 10.1016/S0092-8674(00)80891-0 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 961024.470 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 19858 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) : 0.228 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1974 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2844 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 318 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1534 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 12.49000 REMARK 3 B22 (A**2) : -5.18000 REMARK 3 B33 (A**2) : -7.31000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.930 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) : 0.930 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.670 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.220 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.900 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.48 REMARK 3 BSOL : 55.43 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 1F39 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1000011189. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JAN-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS - B4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22468 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 17.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.1 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.10500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 59.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M NAH2PO4, 1.05 M KH2PO4, 0.075 M REMARK 280 HEPES, 25% GLYCEROL, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 57.16000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.16000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 23.00700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.66750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 23.00700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.66750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.16000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 23.00700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.66750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.16000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 23.00700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.66750 REMARK 290 SMTRY3 8 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A TETRAMER REMARK 300 CONSTRUCTED FROM CHAINS A AND B AND REMARK 300 SYMMETRY PARTNERS GENERATED BY THE REMARK 300 CRYSTALLOGRAPHIC 2-FOLD AXIS ALONG A. 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 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 101.33500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 114.32000 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 33 LIES ON A SPECIAL POSITION. 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 ASN A 216 -144.47 -112.01 REMARK 500 ASP B 187 14.99 52.41 REMARK 500 ASN B 216 -149.55 -95.64 REMARK 500 SER B 218 3.98 133.74 REMARK 500 REMARK 500 REMARK: NULL DBREF 1F39 A 136 236 UNP P03034 RPC1_LAMBD 136 236 DBREF 1F39 B 136 236 UNP P03034 RPC1_LAMBD 136 236 SEQADV 1F39 ALA A 138 UNP P03034 ASP 138 CONFLICT SEQADV 1F39 ALA B 138 UNP P03034 ASP 138 CONFLICT SEQRES 1 A 101 ALA SER ALA SER ALA PHE TRP LEU GLU VAL GLU GLY ASN SEQRES 2 A 101 SER MET THR ALA PRO THR GLY SER LYS PRO SER PHE PRO SEQRES 3 A 101 ASP GLY MET LEU ILE LEU VAL ASP PRO GLU GLN ALA VAL SEQRES 4 A 101 GLU PRO GLY ASP PHE CYS ILE ALA ARG LEU GLY GLY ASP SEQRES 5 A 101 GLU PHE THR PHE LYS LYS LEU ILE ARG ASP SER GLY GLN SEQRES 6 A 101 VAL PHE LEU GLN PRO LEU ASN PRO GLN TYR PRO MET ILE SEQRES 7 A 101 PRO CYS ASN GLU SER CYS SER VAL VAL GLY LYS VAL ILE SEQRES 8 A 101 ALA SER GLN TRP PRO GLU GLU THR PHE GLY SEQRES 1 B 101 ALA SER ALA SER ALA PHE TRP LEU GLU VAL GLU GLY ASN SEQRES 2 B 101 SER MET THR ALA PRO THR GLY SER LYS PRO SER PHE PRO SEQRES 3 B 101 ASP GLY MET LEU ILE LEU VAL ASP PRO GLU GLN ALA VAL SEQRES 4 B 101 GLU PRO GLY ASP PHE CYS ILE ALA ARG LEU GLY GLY ASP SEQRES 5 B 101 GLU PHE THR PHE LYS LYS LEU ILE ARG ASP SER GLY GLN SEQRES 6 B 101 VAL PHE LEU GLN PRO LEU ASN PRO GLN TYR PRO MET ILE SEQRES 7 B 101 PRO CYS ASN GLU SER CYS SER VAL VAL GLY LYS VAL ILE SEQRES 8 B 101 ALA SER GLN TRP PRO GLU GLU THR PHE GLY FORMUL 3 HOH *119(H2 O) HELIX 1 1 PRO A 231 GLY A 236 5 6 HELIX 2 2 PRO B 231 GLY B 236 5 6 SHEET 1 A 7 PHE A 141 GLU A 144 0 SHEET 2 A 7 LEU A 165 ASP A 169 -1 N ILE A 166 O LEU A 143 SHEET 3 A 7 SER A 220 GLN A 229 -1 O LYS A 224 N ASP A 169 SHEET 4 A 7 PHE A 179 ARG A 183 -1 O PHE A 179 N VAL A 225 SHEET 5 A 7 PHE A 189 ASP A 197 -1 O THR A 190 N ALA A 182 SHEET 6 A 7 GLN A 200 GLN A 204 -1 N GLN A 200 O ASP A 197 SHEET 7 A 7 ILE A 213 PRO A 214 -1 O ILE A 213 N LEU A 203 SHEET 1 B 7 PHE B 141 GLU B 144 0 SHEET 2 B 7 LEU B 165 ASP B 169 -1 N ILE B 166 O LEU B 143 SHEET 3 B 7 SER B 220 GLN B 229 -1 O LYS B 224 N ASP B 169 SHEET 4 B 7 PHE B 179 ARG B 183 -1 O PHE B 179 N VAL B 225 SHEET 5 B 7 PHE B 189 ASP B 197 -1 O THR B 190 N ALA B 182 SHEET 6 B 7 GLN B 200 GLN B 204 -1 O GLN B 200 N ASP B 197 SHEET 7 B 7 ILE B 213 PRO B 214 -1 O ILE B 213 N LEU B 203 SSBOND 1 CYS A 215 CYS A 219 1555 1555 2.96 SSBOND 2 CYS B 215 CYS B 219 1555 1555 2.93 CISPEP 1 LYS A 157 PRO A 158 0 -0.86 CISPEP 2 LYS B 157 PRO B 158 0 0.34 CRYST1 46.014 101.335 114.320 90.00 90.00 90.00 C 2 2 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 0.021733 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009868 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008747 0.00000