HEADER GENE REGULATION 08-MAR-06 2DG7 TITLE CRYSTAL STRUCTURE OF THE PUTATIVE TRANSCRIPTIONAL REGULATOR SCO0337 TITLE 2 FROM STREPTOMYCES COELICOLOR A3(2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES COELICOLOR; SOURCE 3 ORGANISM_TAXID: 100226; SOURCE 4 STRAIN: A3(2); SOURCE 5 EXPRESSION_SYSTEM: RHODOCOCCUS ERYTHROPOLIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1833; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: L-88; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTIP-QC2 KEYWDS HELIX-TURN-HELIX MOTIF, TETR FAMILY, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR T.HAYASHI,Y.TANAKA,N.SAKAI,M.YAO,T.TAMURA,I.TANAKA REVDAT 3 13-JUL-11 2DG7 1 VERSN REVDAT 2 24-FEB-09 2DG7 1 VERSN REVDAT 1 13-MAR-07 2DG7 0 JRNL AUTH T.HAYASHI,Y.TANAKA,N.SAKAI,M.YAO,T.TAMURA,I.TANAKA JRNL TITL CRYSTAL STRUCTURE OF THE PUTATIVE TRANSCRIPTIONAL REGULATOR JRNL TITL 2 SCO0337 FROM STREPTOMYCES COELICOLOR A3(2) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1105378.100 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 8970 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) : 0.230 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 879 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1285 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 164 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1426 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 55 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.37000 REMARK 3 B22 (A**2) : 7.95000 REMARK 3 B33 (A**2) : -6.58000 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) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.11 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) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.003 REMARK 3 BOND ANGLES (DEGREES) : 0.90 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.59 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) : 1.520 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.540 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.410 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.720 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.55 REMARK 3 BSOL : 65.82 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 2DG7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAR-06. REMARK 100 THE RCSB ID CODE IS RCSB025380. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934, 0.97950, 0.98338 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9138 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.20400 REMARK 200 FOR SHELL : NULL 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 (%): 45.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES PH7.0, 9% JEFFAMINE ED- REMARK 280 2001 REAGENT PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 51.47600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.43200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 51.47600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.43200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 DIMER GENERATED FROM THE REMARK 300 MONOMER IN THE ASYMMETRIC UNIT BY THE OPERATIONS: -X+1, -Y+1, Z. 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: 2440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 102.95200 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 42.86400 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LEU A 188 REMARK 465 GLU A 189 REMARK 465 HIS A 190 REMARK 465 HIS A 191 REMARK 465 HIS A 192 REMARK 465 HIS A 193 REMARK 465 HIS A 194 REMARK 465 HIS A 195 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 ASP A 5 73.80 -163.90 REMARK 500 GLU A 22 -81.25 -56.13 REMARK 500 HIS A 23 -146.17 -74.20 REMARK 500 PRO A 75 -6.13 -59.48 REMARK 500 VAL A 95 39.56 -80.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QPI RELATED DB: PDB REMARK 900 A PROTEIN STRUCTURE WHICH IS CATEGORIZED INTO THE SAME REMARK 900 FAMILY DBREF 2DG7 A 1 187 GB 5912516 CAB56142 1 187 SEQADV 2DG7 MSE A 1 GB 5912516 MET 1 MODIFIED RESIDUE SEQADV 2DG7 MSE A 87 GB 5912516 MET 87 MODIFIED RESIDUE SEQADV 2DG7 LEU A 188 GB 5912516 EXPRESSION TAG SEQADV 2DG7 GLU A 189 GB 5912516 EXPRESSION TAG SEQADV 2DG7 HIS A 190 GB 5912516 EXPRESSION TAG SEQADV 2DG7 HIS A 191 GB 5912516 EXPRESSION TAG SEQADV 2DG7 HIS A 192 GB 5912516 EXPRESSION TAG SEQADV 2DG7 HIS A 193 GB 5912516 EXPRESSION TAG SEQADV 2DG7 HIS A 194 GB 5912516 EXPRESSION TAG SEQADV 2DG7 HIS A 195 GB 5912516 EXPRESSION TAG SEQRES 1 A 195 MSE ALA ARG TRP ASP PRO GLY ALA GLU GLN ARG LEU LYS SEQRES 2 A 195 ARG ALA ALA LEU GLU LEU TYR SER GLU HIS GLY TYR ASP SEQRES 3 A 195 ASN VAL THR VAL THR ASP ILE ALA GLU ARG ALA GLY LEU SEQRES 4 A 195 THR ARG ARG SER TYR PHE ARG TYR PHE PRO ASP LYS ARG SEQRES 5 A 195 GLU VAL LEU PHE GLY GLY SER GLU LEU LEU PRO PRO ALA SEQRES 6 A 195 VAL ALA ARG ALA VAL LEU ALA ALA ASP PRO GLY ALA ALA SEQRES 7 A 195 PRO LEU THR ALA VAL LEU ASP ALA MSE SER GLN VAL GLY SEQRES 8 A 195 ALA GLN LEU VAL ALA GLN VAL GLU GLY ALA ALA GLN ARG SEQRES 9 A 195 ARG ALA VAL ILE ASP ALA SER PRO GLU LEU GLN GLU ARG SEQRES 10 A 195 GLU ARG THR LYS SER ALA ALA ILE SER ARG ALA VAL GLN SEQRES 11 A 195 ASP ALA LEU VAL ARG ARG GLN VAL ASP ALA ASP THR ALA SEQRES 12 A 195 GLU LEU VAL ALA GLN LEU ALA THR VAL ALA PHE GLY SER SEQRES 13 A 195 ALA PHE ARG ARG TRP ILE ASP ALA GLU GLY HIS ALA ASP SEQRES 14 A 195 PHE GLY SER CYS LEU ASP THR VAL THR ASP ARG LEU ARG SEQRES 15 A 195 ALA VAL LEU THR GLY LEU GLU HIS HIS HIS HIS HIS HIS MODRES 2DG7 MSE A 1 MET SELENOMETHIONINE MODRES 2DG7 MSE A 87 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 87 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *55(H2 O) HELIX 1 1 GLY A 7 HIS A 23 1 17 HELIX 2 2 GLY A 24 VAL A 28 5 5 HELIX 3 3 THR A 29 ALA A 37 1 9 HELIX 4 4 THR A 40 PHE A 48 1 9 HELIX 5 5 ARG A 52 PHE A 56 5 5 HELIX 6 6 LEU A 62 ALA A 72 1 11 HELIX 7 7 ALA A 78 GLY A 91 1 14 HELIX 8 8 GLY A 100 ALA A 110 1 11 HELIX 9 9 SER A 111 ARG A 136 1 26 HELIX 10 10 ASP A 139 ALA A 164 1 26 HELIX 11 11 ASP A 169 GLY A 187 1 19 LINK C MSE A 1 N ALA A 2 1555 1555 1.33 LINK C ALA A 86 N MSE A 87 1555 1555 1.33 LINK C MSE A 87 N SER A 88 1555 1555 1.33 CRYST1 102.952 42.864 43.933 90.00 90.00 90.00 P 21 21 2 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 0.009713 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023330 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022762 0.00000 HETATM 1 N MSE A 1 20.910 17.247 40.956 1.00 71.57 N HETATM 2 CA MSE A 1 21.371 18.661 41.071 1.00 70.48 C HETATM 3 C MSE A 1 20.914 19.493 39.884 1.00 66.58 C HETATM 4 O MSE A 1 20.485 20.635 40.044 1.00 67.64 O HETATM 5 CB MSE A 1 22.896 18.711 41.188 1.00 74.52 C HETATM 6 CG MSE A 1 23.413 18.114 42.479 1.00 78.87 C HETATM 7 SE MSE A 1 22.943 19.170 44.014 1.00 86.50 SE HETATM 8 CE MSE A 1 24.559 18.898 45.045 1.00 84.81 C