HEADER DNA BINDING PROTEIN 07-NOV-05 2EWT TITLE CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF BLDD COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE DNA-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA-BINDING DOMAIN; COMPND 5 SYNONYM: BLDD; COMPND 6 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: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS THE DNA-BINDING DOMAIN OF BLDD, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.K.KIM,C.J.LEE,M.K.KIM,J.M.KIM,J.H.KIM,H.S.YIM,S.S.CHA,S.O.KANG REVDAT 4 13-MAR-24 2EWT 1 REMARK REVDAT 3 13-JUL-11 2EWT 1 VERSN REVDAT 2 24-FEB-09 2EWT 1 VERSN REVDAT 1 13-JUN-06 2EWT 0 JRNL AUTH I.K.KIM,C.J.LEE,M.K.KIM,J.M.KIM,J.H.KIM,H.S.YIM,S.S.CHA, JRNL AUTH 2 S.O.KANG JRNL TITL CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF BLDD, A JRNL TITL 2 CENTRAL REGULATOR OF AERIAL MYCELIUM FORMATION IN JRNL TITL 3 STREPTOMYCES COELICOLOR A3(2) JRNL REF MOL.MICROBIOL. V. 60 1179 2006 JRNL REFN ISSN 0950-382X JRNL PMID 16689794 JRNL DOI 10.1111/J.1365-2958.2006.05176.X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.K.KIM,M.K.KIM,C.J.LEE,H.S.YIM,S.S.CHA,S.O.KANG REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY CRYSTALLOGRAPHIC REMARK 1 TITL 2 ANALYSIS OF THE DNA-BINDING DOMAIN OF BLDD FROM STREPTOMYCES REMARK 1 TITL 3 COELICOLOR A3(2) REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 60 1115 2004 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 15159573 REMARK 1 DOI 10.1107/S0907444904006961 REMARK 2 REMARK 2 RESOLUTION. 1.81 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) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1438212.220 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 7031 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) : 0.188 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 381 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 999 REMARK 3 BIN R VALUE (WORKING SET) : 0.1860 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 : 551 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.97000 REMARK 3 B22 (A**2) : 0.86000 REMARK 3 B33 (A**2) : -1.83000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.04 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 54.40 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 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2EWT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1000035189. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 6B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97932, 0.97942, 0.98722 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE DIP-2030B REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7031 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 51.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 4000, 0.1M SODIUM ACETATE (PH REMARK 280 4.6), 0.2M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 38.59950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.88700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.59950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.88700 REMARK 290 SMTRY3 4 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE TWO FOLD AXIS: -X+1, -Y, Z+3/2 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 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 -17.57418 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 64.95247 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 LYS A 7 CG CD CE NZ REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2015 DBREF 2EWT A 1 71 GB 21219990 NP_625769 1 71 SEQRES 1 A 71 MET SER SER GLU TYR ALA LYS GLN LEU GLY ALA LYS LEU SEQRES 2 A 71 ARG ALA ILE ARG THR GLN GLN GLY LEU SER LEU HIS GLY SEQRES 3 A 71 VAL GLU GLU LYS SER GLN GLY ARG TRP LYS ALA VAL VAL SEQRES 4 A 71 VAL GLY SER TYR GLU ARG GLY ASP ARG ALA VAL THR VAL SEQRES 5 A 71 GLN ARG LEU ALA GLU LEU ALA ASP PHE TYR GLY VAL PRO SEQRES 6 A 71 VAL GLN GLU LEU LEU PRO HET SO4 A2001 5 HET SO4 A2002 5 HET SO4 A2015 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *147(H2 O) HELIX 1 1 SER A 2 GLN A 20 1 19 HELIX 2 2 SER A 23 SER A 31 1 9 HELIX 3 3 LYS A 36 ARG A 45 1 10 HELIX 4 4 THR A 51 GLY A 63 1 13 HELIX 5 5 PRO A 65 LEU A 70 5 6 SITE 1 AC1 5 ARG A 45 HOH A2063 HOH A2069 HOH A2111 SITE 2 AC1 5 HOH A2151 SITE 1 AC2 6 TYR A 43 ARG A 48 ARG A 54 HOH A2049 SITE 2 AC2 6 HOH A2077 HOH A2121 SITE 1 AC3 8 SER A 2 SER A 3 LYS A 36 HOH A2059 SITE 2 AC3 8 HOH A2081 HOH A2125 HOH A2126 HOH A2157 CRYST1 77.199 31.774 33.644 90.00 105.14 90.00 C 1 2 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 0.012954 0.000000 0.003506 0.00000 SCALE2 0.000000 0.031472 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030792 0.00000