HEADER DNA BINDING PROTEIN 08-JUL-11 3SSW TITLE E. COLI TRP APOREPRESSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRP OPERON REPRESSOR; COMPND 3 CHAIN: R, N; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B4393, JW4356, RTRY, TRPR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS HELIX-TURN-HELIX MOTIF, DNA BINDING, TRP OPERATOR, DNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.BENOFF,J.CAREY,H.M.BERMAN,C.L.LAWSON REVDAT 5 13-SEP-23 3SSW 1 REMARK REVDAT 4 15-AUG-12 3SSW 1 SPRSDE REVDAT 3 28-DEC-11 3SSW 1 JRNL REVDAT 2 07-DEC-11 3SSW 1 JRNL REVDAT 1 20-JUL-11 3SSW 0 SPRSDE 15-AUG-12 3SSW 1P6Z JRNL AUTH J.CAREY,B.BENOFF,B.HARISH,L.YUAN,C.L.LAWSON JRNL TITL ENVIRONMENT-DEPENDENT LONG-RANGE STRUCTURAL DISTORTION IN A JRNL TITL 2 TEMPERATURE-SENSITIVE POINT MUTANT. JRNL REF PROTEIN SCI. V. 21 63 2012 JRNL REFN ISSN 0961-8368 JRNL PMID 22057811 JRNL DOI 10.1002/PRO.759 REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 23235 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 2311 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.0477 - 4.2846 0.93 1269 136 0.1890 0.1929 REMARK 3 2 4.2846 - 3.4039 0.98 1313 137 0.1461 0.1925 REMARK 3 3 3.4039 - 2.9745 1.00 1325 122 0.1691 0.2272 REMARK 3 4 2.9745 - 2.7029 1.00 1322 125 0.1816 0.2318 REMARK 3 5 2.7029 - 2.5094 0.99 1316 152 0.1763 0.2386 REMARK 3 6 2.5094 - 2.3616 0.99 1285 138 0.1694 0.2307 REMARK 3 7 2.3616 - 2.2434 0.98 1269 152 0.1677 0.2238 REMARK 3 8 2.2434 - 2.1458 0.99 1302 158 0.1489 0.2018 REMARK 3 9 2.1458 - 2.0633 0.98 1257 149 0.1647 0.2061 REMARK 3 10 2.0633 - 1.9921 0.97 1263 126 0.1818 0.2299 REMARK 3 11 1.9921 - 1.9299 0.96 1278 138 0.1749 0.2557 REMARK 3 12 1.9299 - 1.8747 0.93 1178 132 0.1858 0.2624 REMARK 3 13 1.8747 - 1.8254 0.90 1198 143 0.1785 0.2311 REMARK 3 14 1.8254 - 1.7809 0.89 1157 131 0.1933 0.2251 REMARK 3 15 1.7809 - 1.7404 0.88 1160 121 0.1856 0.2296 REMARK 3 16 1.7404 - 1.7034 0.83 1037 128 0.2071 0.2621 REMARK 3 17 1.7034 - 1.6693 0.76 995 123 0.2369 0.2786 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.42 REMARK 3 B_SOL : 69.94 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.48030 REMARK 3 B22 (A**2) : -2.35740 REMARK 3 B33 (A**2) : 7.83770 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -5.50990 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.022 1657 REMARK 3 ANGLE : 1.491 2249 REMARK 3 CHIRALITY : 0.112 258 REMARK 3 PLANARITY : 0.008 295 REMARK 3 DIHEDRAL : 14.795 649 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -0.7226 0.1041 17.9897 REMARK 3 T TENSOR REMARK 3 T11: 0.1766 T22: 0.1491 REMARK 3 T33: 0.1618 T12: -0.0025 REMARK 3 T13: -0.0061 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 1.3753 L22: 0.5821 REMARK 3 L33: 0.9709 L12: 0.1030 REMARK 3 L13: -0.0407 L23: -0.0259 REMARK 3 S TENSOR REMARK 3 S11: 0.0232 S12: 0.1373 S13: 0.0341 REMARK 3 S21: -0.0805 S22: -0.0168 S23: 0.0593 REMARK 3 S31: 0.0731 S32: -0.0432 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3SSW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1000066610. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : CHANNEL-CUT SI(111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24536 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.669 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.59700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.520 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2OZ9 DIMER REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HAMPTON RESEARCH CRYSTAL SCREEN REMARK 280 CONDITION #6: 30% (W/V) PEG 4000, 200 MM MGCL2, 100 MM TRIS HCL REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 27.16750 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: R, N 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 ALA R 2 REMARK 465 GLN R 3 REMARK 465 GLN R 4 REMARK 465 LYS R 106 REMARK 465 SER R 107 REMARK 465 ASP R 108 REMARK 465 ALA N 2 REMARK 465 GLN N 3 REMARK 465 GLN N 4 REMARK 465 SER N 5 REMARK 465 PRO N 6 REMARK 465 TYR N 7 REMARK 465 LYS N 106 REMARK 465 SER N 107 REMARK 465 ASP N 108 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 MET N 11 CG SD CE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SSX RELATED DB: PDB REMARK 900 E. COLI TRP APOREPORESSOR L75F MUTANT DBREF 3SSW R 2 108 UNP P0A881 TRPR_ECOLI 2 108 DBREF 3SSW N 2 108 UNP P0A881 TRPR_ECOLI 2 108 SEQRES 1 R 107 ALA GLN GLN SER PRO TYR SER ALA ALA MET ALA GLU GLN SEQRES 2 R 107 ARG HIS GLN GLU TRP LEU ARG PHE VAL ASP LEU LEU LYS SEQRES 3 R 107 ASN ALA TYR GLN ASN ASP LEU HIS LEU PRO LEU LEU ASN SEQRES 4 R 107 LEU MET LEU THR PRO ASP GLU ARG GLU ALA LEU GLY THR SEQRES 5 R 107 ARG VAL ARG ILE VAL GLU GLU LEU LEU ARG GLY GLU MET SEQRES 6 R 107 SER GLN ARG GLU LEU LYS ASN GLU LEU GLY ALA GLY ILE SEQRES 7 R 107 ALA THR ILE THR ARG GLY SER ASN SER LEU LYS ALA ALA SEQRES 8 R 107 PRO VAL GLU LEU ARG GLN TRP LEU GLU GLU VAL LEU LEU SEQRES 9 R 107 LYS SER ASP SEQRES 1 N 107 ALA GLN GLN SER PRO TYR SER ALA ALA MET ALA GLU GLN SEQRES 2 N 107 ARG HIS GLN GLU TRP LEU ARG PHE VAL ASP LEU LEU LYS SEQRES 3 N 107 ASN ALA TYR GLN ASN ASP LEU HIS LEU PRO LEU LEU ASN SEQRES 4 N 107 LEU MET LEU THR PRO ASP GLU ARG GLU ALA LEU GLY THR SEQRES 5 N 107 ARG VAL ARG ILE VAL GLU GLU LEU LEU ARG GLY GLU MET SEQRES 6 N 107 SER GLN ARG GLU LEU LYS ASN GLU LEU GLY ALA GLY ILE SEQRES 7 N 107 ALA THR ILE THR ARG GLY SER ASN SER LEU LYS ALA ALA SEQRES 8 N 107 PRO VAL GLU LEU ARG GLN TRP LEU GLU GLU VAL LEU LEU SEQRES 9 N 107 LYS SER ASP FORMUL 3 HOH *201(H2 O) HELIX 1 1 ALA R 9 GLN R 31 1 23 HELIX 2 2 HIS R 35 MET R 42 1 8 HELIX 3 3 PRO R 45 ARG R 63 1 19 HELIX 4 4 GLN R 68 LEU R 75 1 8 HELIX 5 5 ILE R 79 ALA R 91 1 13 HELIX 6 6 VAL R 94 LEU R 104 1 11 HELIX 7 7 ALA N 9 GLN N 31 1 23 HELIX 8 8 HIS N 35 MET N 42 1 8 HELIX 9 9 PRO N 45 ARG N 63 1 19 HELIX 10 10 GLN N 68 LEU N 75 1 8 HELIX 11 11 ILE N 79 ALA N 91 1 13 HELIX 12 12 VAL N 94 LEU N 104 1 11 CRYST1 35.692 54.335 56.945 90.00 103.21 90.00 P 1 21 1 4 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 0.028017 0.000000 0.006577 0.00000 SCALE2 0.000000 0.018404 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018038 0.00000