HEADER DNA BINDING PROTEIN 08-JUL-11 3SSX TITLE E. COLI TRP APOREPORESSOR L75F MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRP OPERON REPRESSOR; COMPND 3 CHAIN: R, N; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: 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 4 13-SEP-23 3SSX 1 REMARK SEQADV REVDAT 3 28-DEC-11 3SSX 1 JRNL REVDAT 2 07-DEC-11 3SSX 1 JRNL REVDAT 1 20-JUL-11 3SSX 0 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. 1.58 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 26533 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1323 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 27.3898 - 3.2851 0.94 2924 151 0.1645 0.1976 REMARK 3 2 3.2851 - 2.6081 1.00 3047 154 0.1666 0.2347 REMARK 3 3 2.6081 - 2.2786 1.00 3028 150 0.1664 0.2043 REMARK 3 4 2.2786 - 2.0703 1.00 3012 171 0.1608 0.1953 REMARK 3 5 2.0703 - 1.9220 1.00 3010 174 0.1686 0.2332 REMARK 3 6 1.9220 - 1.8087 0.99 2985 160 0.2001 0.2379 REMARK 3 7 1.8087 - 1.7181 0.94 2856 131 0.2235 0.2895 REMARK 3 8 1.7181 - 1.6434 0.81 2438 131 0.2532 0.2775 REMARK 3 9 1.6434 - 1.5801 0.64 1910 101 0.2487 0.2898 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 : 0.41 REMARK 3 B_SOL : 78.36 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.020 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.13260 REMARK 3 B22 (A**2) : -4.83880 REMARK 3 B33 (A**2) : 14.97140 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -6.98370 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 : 0.024 1729 REMARK 3 ANGLE : 1.788 2345 REMARK 3 CHIRALITY : 0.151 261 REMARK 3 PLANARITY : 0.011 307 REMARK 3 DIHEDRAL : 16.320 698 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): 0.2543 0.0476 18.0010 REMARK 3 T TENSOR REMARK 3 T11: 0.1830 T22: 0.1788 REMARK 3 T33: 0.1820 T12: -0.0033 REMARK 3 T13: 0.0063 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 1.0407 L22: 0.4898 REMARK 3 L33: 0.7006 L12: 0.1108 REMARK 3 L13: 0.4056 L23: 0.0858 REMARK 3 S TENSOR REMARK 3 S11: -0.0166 S12: 0.1473 S13: 0.0532 REMARK 3 S21: -0.0196 S22: 0.0080 S23: 0.0555 REMARK 3 S31: 0.0154 S32: 0.0343 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 3SSX 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_1000066611. 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 : 28206 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.680 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.940 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 (%): 42.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 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 27.05250 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: 5060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 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 SER N 107 REMARK 465 ASP N 108 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAM N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SSW RELATED DB: PDB REMARK 900 E. COLI TRP APOREPRESSOR DBREF 3SSX R 2 108 UNP P0A881 TRPR_ECOLI 2 108 DBREF 3SSX N 2 108 UNP P0A881 TRPR_ECOLI 2 108 SEQADV 3SSX PHE R 75 UNP P0A881 LEU 75 ENGINEERED MUTATION SEQADV 3SSX PHE N 75 UNP P0A881 LEU 75 ENGINEERED MUTATION 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 PHE 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 PHE 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 HET TAM N 1 11 HETNAM TAM TRIS(HYDROXYETHYL)AMINOMETHANE FORMUL 3 TAM C7 H17 N O3 FORMUL 4 HOH *238(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 PHE R 75 1 8 HELIX 5 5 GLY R 76 ILE R 79 5 4 HELIX 6 6 ALA R 80 THR R 83 1 4 HELIX 7 7 VAL R 94 LEU R 104 1 11 HELIX 8 8 ALA N 9 GLN N 31 1 23 HELIX 9 9 HIS N 35 MET N 42 1 8 HELIX 10 10 PRO N 45 ARG N 63 1 19 HELIX 11 11 GLN N 68 PHE N 75 1 8 HELIX 12 12 ILE N 79 ALA N 91 1 13 HELIX 13 13 VAL N 94 LEU N 105 1 12 SITE 1 AC1 12 ARG N 54 ILE N 57 THR N 81 ARG N 84 SITE 2 AC1 12 GLY N 85 SER N 88 HOH N 335 HOH N 337 SITE 3 AC1 12 LEU R 41 MET R 42 LEU R 43 HOH R 334 CRYST1 35.716 54.105 55.633 90.00 100.10 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 0.027999 0.000000 0.004986 0.00000 SCALE2 0.000000 0.018483 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018258 0.00000