HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 17-MAY-05 2COH OBSLTE 04-DEC-07 2COH 2ZCW TITLE CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR TTHA1359 TITLE 2 FORM THERMUS THERMOPHILUS HB8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_COMMON: BACTERIA; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS HELIX-TURN-HELIX, STRUCTURAL GENOMICS, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL GENOMICS, KEYWDS 3 UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.AGARI,S.YOKOYAMA,S.KURAMITSU,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 2 04-DEC-07 2COH 1 OBSLTE REVDAT 1 17-NOV-05 2COH 0 JRNL AUTH Y.AGARI,S.YOKOYAMA,S.KURAMITSU JRNL TITL CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR JRNL TITL 2 TTHA1359 FORM THERMUS THERMOPHILUS HB8 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1701323.010 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 36036 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) : 0.223 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3592 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5255 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE : 0.2510 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 608 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1506 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.54000 REMARK 3 B22 (A**2) : -0.54000 REMARK 3 B33 (A**2) : 1.08000 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) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.08 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) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.79 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) : 1.380 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.960 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.010 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.510 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 48.85 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 : MPD_XPLOR.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : MPD_XPLOR.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2COH COMPLIES WITH FORMAT V. 3.1, 1-AUG-2007 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE RCSB ID CODE IS RCSB024449. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-2004 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.10 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97974, 0.9, 0.97939 REMARK 200 MONOCHROMATOR : SI DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 13.100 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 50.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : 0.26600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD 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 (%): 48.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 31% MPD, 0.1M SODIUM ACETATE, 0.02M REMARK 280 CALCIUM CHLORIDE, PH 5.1, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 3555 1/2-Y,1/2+X,1/4+Z REMARK 290 4555 1/2+Y,1/2-X,3/4+Z REMARK 290 5555 1/2-X,1/2+Y,1/4-Z REMARK 290 6555 1/2+X,1/2-Y,3/4-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,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 73.85900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.02500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.02500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.92950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.02500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.02500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 110.78850 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.02500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.02500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 36.92950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.02500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.02500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 110.78850 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 73.85900 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND 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: MONOMER REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSEQI REMARK 465 MSE A 1 REMARK 465 THR A 2 REMARK 465 GLN A 3 REMARK 465 VAL A 4 REMARK 465 ARG A 5 REMARK 465 GLN A 200 REMARK 465 GLY A 201 REMARK 465 ARG A 202 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 PRO A 134 2.69 -68.00 REMARK 500 SER A 158 -160.41 -118.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M=MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1118 DISTANCE = 6.86 ANGSTROMS REMARK 525 HOH A1119 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A1120 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH A1124 DISTANCE = 8.76 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003001019.1 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES REMARK 999 NOT CURRENTLY EXIST. SEQRES 1 A 202 MSE THR GLN VAL ARG GLU THR VAL SER PHE LYS ALA GLY SEQRES 2 A 202 ASP VAL ILE LEU TYR PRO GLY VAL PRO GLY PRO ARG ASP SEQRES 3 A 202 ARG ALA TYR ARG VAL LEU GLU GLY LEU VAL ARG LEU GLU SEQRES 4 A 202 ALA VAL ASP GLU GLU GLY ASN ALA LEU THR LEU ARG LEU SEQRES 5 A 202 VAL ARG PRO GLY GLY PHE PHE GLY GLU GLU ALA LEU PHE SEQRES 6 A 202 GLY GLN GLU ARG ILE TYR PHE ALA GLU ALA ALA THR ASP SEQRES 7 A 202 VAL ARG LEU GLU PRO LEU PRO GLU ASN PRO ASP PRO GLU SEQRES 8 A 202 LEU LEU LYS ASP LEU ALA GLN HIS LEU SER GLN GLY LEU SEQRES 9 A 202 ALA GLU ALA TYR ARG ARG ILE GLU ARG LEU ALA THR GLN SEQRES 10 A 202 ARG LEU LYS ASN ARG MSE ALA ALA ALA LEU LEU GLU LEU SEQRES 11 A 202 SER GLU THR PRO LEU ALA HIS GLU GLU GLU GLY LYS VAL SEQRES 12 A 202 VAL LEU LYS ALA THR HIS ASP GLU LEU ALA ALA ALA VAL SEQRES 13 A 202 GLY SER VAL ARG GLU THR VAL THR LYS VAL ILE GLY GLU SEQRES 14 A 202 LEU ALA ARG GLU GLY TYR ILE ARG SER GLY TYR GLY LYS SEQRES 15 A 202 ILE GLN LEU LEU ASP LEU LYS GLY LEU LYS GLU LEU ALA SEQRES 16 A 202 GLU SER ARG GLY GLN GLY ARG MODRES 2COH MSE A 123 MET SELENOMETHIONINE HET MSE A 123 8 HET MPD A1001 8 HET MPD A1002 8 HET MPD A1003 8 HETNAM MSE SELENOMETHIONINE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 MPD 3(C6 H14 O2) FORMUL 5 HOH *141(H2 O) HELIX 1 1 GLY A 60 PHE A 65 5 6 HELIX 2 2 ASP A 89 GLN A 117 1 29 HELIX 3 3 ARG A 118 SER A 131 1 14 HELIX 4 4 THR A 148 GLY A 157 1 10 HELIX 5 5 VAL A 159 GLU A 173 1 15 HELIX 6 6 ASP A 187 GLU A 196 1 10 SHEET 1 A 4 VAL A 8 PHE A 10 0 SHEET 2 A 4 VAL A 79 PRO A 83 -1 O LEU A 81 N VAL A 8 SHEET 3 A 4 TYR A 29 GLU A 33 -1 N LEU A 32 O ARG A 80 SHEET 4 A 4 PHE A 58 PHE A 59 -1 O PHE A 59 N TYR A 29 SHEET 1 B 4 VAL A 15 LEU A 17 0 SHEET 2 B 4 PHE A 72 ALA A 75 -1 O ALA A 73 N ILE A 16 SHEET 3 B 4 VAL A 36 VAL A 41 -1 N ARG A 37 O GLU A 74 SHEET 4 B 4 ALA A 47 VAL A 53 -1 O VAL A 53 N VAL A 36 SHEET 1 C 4 ALA A 136 GLU A 139 0 SHEET 2 C 4 LYS A 142 LYS A 146 -1 O VAL A 144 N HIS A 137 SHEET 3 C 4 LYS A 182 LEU A 185 -1 O ILE A 183 N LEU A 145 SHEET 4 C 4 ILE A 176 GLY A 179 -1 N ARG A 177 O GLN A 184 CRYST1 54.050 54.050 147.718 90.00 90.00 90.00 P 41 21 2 8 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 0.018501 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018501 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006770 0.00000