HEADER TRANSCRIPTION 12-SEP-09 3JTH TITLE CRYSTAL STRUCTURE OF A TRANSCRIPTIONAL REGULATOR HLYU FROM VIBRIO TITLE 2 VULNIFICUS CMCP6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION ACTIVATOR HLYU; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 3 ORGANISM_TAXID: 216895; SOURCE 4 STRAIN: CMCP6; SOURCE 5 GENE: VV1_0512; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPROEXHTC KEYWDS TRANSCRIPTION FACTOR, HLYU, RTXA, DNA-BINDING, TRANSCRIPTION, KEYWDS 2 TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR K.NISHI,H.J.LEE,S.Y.PARK,J.S.KIM REVDAT 2 13-NOV-24 3JTH 1 LINK REVDAT 1 16-MAR-10 3JTH 0 JRNL AUTH K.NISHI,H.J.LEE,S.Y.PARK,S.J.BAE,S.E.LEE,P.D.ADAMS,J.H.RHEE, JRNL AUTH 2 J.S.KIM JRNL TITL CRYSTAL STRUCTURE OF THE TRANSCRIPTIONAL ACTIVATOR HLYU FROM JRNL TITL 2 VIBRIO VULNIFICUS CMCP6. JRNL REF FEBS LETT. 2010 JRNL REFN ISSN 0014-5793 JRNL PMID 20178784 JRNL DOI 10.1016/J.FEBSLET.2010.02.052 REMARK 2 REMARK 2 RESOLUTION. 2.00 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 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) (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 11174 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) : 0.231 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1132 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 : 1492 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 60 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.110 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 3JTH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055138. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 6C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12896 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 94.0 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : 0.06500 REMARK 200 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 (%) : 76.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.26900 REMARK 200 R SYM FOR SHELL (I) : 0.22500 REMARK 200 FOR SHELL : 2.940 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 36.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9~11% POLYETHYLENE GLYCOL 20000, 0.1M REMARK 280 SODIUM ACETATE, 0.1M (N-MORPHOLINO) PROPANESULFONIC ACID, PH6.5, REMARK 280 10MM B-MERCAPTOETHANOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K 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 26.39500 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: 2450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 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 GLU A 97 REMARK 465 GLU A 98 REMARK 465 MET B 201 REMARK 465 ASN B 202 REMARK 465 LEU B 203 REMARK 465 LYS B 204 REMARK 465 GLU B 297 REMARK 465 GLU B 298 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 A 1 CG SD CE 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 LYS A 70 -179.73 -66.76 REMARK 500 GLU A 71 105.51 167.20 REMARK 500 ALA A 72 53.70 33.05 REMARK 500 GLN A 73 -0.79 78.13 REMARK 500 GLN B 235 93.13 162.47 REMARK 500 GLN B 273 -16.68 77.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 3JTH A 1 98 UNP Q8DES3 Q8DES3_VIBVU 1 98 DBREF 3JTH B 201 298 UNP Q8DES3 Q8DES3_VIBVU 1 98 SEQRES 1 A 98 MET ASN LEU LYS ASP MSE GLU GLN ASN SER ALA LYS ALA SEQRES 2 A 98 VAL VAL LEU LEU LYS ALA MSE ALA ASN GLU ARG ARG LEU SEQRES 3 A 98 GLN ILE LEU CYS MSE LEU HIS ASN GLN GLU LEU SER VAL SEQRES 4 A 98 GLY GLU LEU CYS ALA LYS LEU GLN LEU SER GLN SER ALA SEQRES 5 A 98 LEU SER GLN HIS LEU ALA TRP LEU ARG ARG ASP GLY LEU SEQRES 6 A 98 VAL THR THR ARG LYS GLU ALA GLN THR VAL TYR TYR THR SEQRES 7 A 98 LEU LYS SER GLU GLU VAL LYS ALA MSE ILE LYS LEU LEU SEQRES 8 A 98 HIS SER LEU TYR CYS GLU GLU SEQRES 1 B 98 MET ASN LEU LYS ASP MSE GLU GLN ASN SER ALA LYS ALA SEQRES 2 B 98 VAL VAL LEU LEU LYS ALA MSE ALA ASN GLU ARG ARG LEU SEQRES 3 B 98 GLN ILE LEU CYS MSE LEU HIS ASN GLN GLU LEU SER VAL SEQRES 4 B 98 GLY GLU LEU CYS ALA LYS LEU GLN LEU SER GLN SER ALA SEQRES 5 B 98 LEU SER GLN HIS LEU ALA TRP LEU ARG ARG ASP GLY LEU SEQRES 6 B 98 VAL THR THR ARG LYS GLU ALA GLN THR VAL TYR TYR THR SEQRES 7 B 98 LEU LYS SER GLU GLU VAL LYS ALA MSE ILE LYS LEU LEU SEQRES 8 B 98 HIS SER LEU TYR CYS GLU GLU MODRES 3JTH MSE A 6 MET SELENOMETHIONINE MODRES 3JTH MSE A 20 MET SELENOMETHIONINE MODRES 3JTH MSE A 31 MET SELENOMETHIONINE MODRES 3JTH MSE A 87 MET SELENOMETHIONINE MODRES 3JTH MSE B 206 MET SELENOMETHIONINE MODRES 3JTH MSE B 220 MET SELENOMETHIONINE MODRES 3JTH MSE B 231 MET SELENOMETHIONINE MODRES 3JTH MSE B 287 MET SELENOMETHIONINE HET MSE A 6 8 HET MSE A 20 8 HET MSE A 31 8 HET MSE A 87 8 HET MSE B 206 8 HET MSE B 220 8 HET MSE B 231 8 HET MSE B 287 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 3 HOH *60(H2 O) HELIX 1 1 MET A 1 ALA A 21 1 21 HELIX 2 2 ASN A 22 LEU A 32 1 11 HELIX 3 3 VAL A 39 GLN A 47 1 9 HELIX 4 4 SER A 49 ASP A 63 1 15 HELIX 5 5 SER A 81 TYR A 95 1 15 HELIX 6 6 ASP B 205 ALA B 221 1 17 HELIX 7 7 ASN B 222 HIS B 233 1 12 HELIX 8 8 VAL B 239 GLN B 247 1 9 HELIX 9 9 SER B 249 ASP B 263 1 15 HELIX 10 10 SER B 281 TYR B 295 1 15 SHEET 1 A 3 LEU A 37 SER A 38 0 SHEET 2 A 3 TYR A 76 LEU A 79 -1 O TYR A 77 N LEU A 37 SHEET 3 A 3 VAL A 66 ARG A 69 -1 N THR A 67 O THR A 78 SHEET 1 B 3 LEU B 237 SER B 238 0 SHEET 2 B 3 THR B 274 LEU B 279 -1 O TYR B 277 N LEU B 237 SHEET 3 B 3 VAL B 266 GLU B 271 -1 N ARG B 269 O TYR B 276 LINK C ASP A 5 N MSE A 6 1555 1555 1.33 LINK C MSE A 6 N GLU A 7 1555 1555 1.33 LINK C ALA A 19 N MSE A 20 1555 1555 1.33 LINK C MSE A 20 N ALA A 21 1555 1555 1.33 LINK C CYS A 30 N MSE A 31 1555 1555 1.33 LINK C MSE A 31 N LEU A 32 1555 1555 1.33 LINK C ALA A 86 N MSE A 87 1555 1555 1.33 LINK C MSE A 87 N ILE A 88 1555 1555 1.33 LINK C ASP B 205 N MSE B 206 1555 1555 1.33 LINK C MSE B 206 N GLU B 207 1555 1555 1.33 LINK C ALA B 219 N MSE B 220 1555 1555 1.32 LINK C MSE B 220 N ALA B 221 1555 1555 1.33 LINK C CYS B 230 N MSE B 231 1555 1555 1.33 LINK C MSE B 231 N LEU B 232 1555 1555 1.33 LINK C ALA B 286 N MSE B 287 1555 1555 1.33 LINK C MSE B 287 N ILE B 288 1555 1555 1.33 CRYST1 35.946 52.790 47.862 90.00 103.92 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 0.027820 0.000000 0.006895 0.00000 SCALE2 0.000000 0.018943 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021526 0.00000