HEADER TRANSCRIPTION 13-MAY-15 4ZSB TITLE CRYSTAL STRUCTURE OF THE LIGAND-FREE EFFECTOR-BINDING DOMAIN OF DASR TITLE 2 (DASR-EBD) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HTH-TYPE TRANSCRIPTIONAL REPRESSOR DASR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 89-254; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: DASR-EBD COMPRISES RESIDUES 88-254 OF FULL-LENGTH DASR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES COELICOLOR A3(2); SOURCE 3 ORGANISM_TAXID: 100226; SOURCE 4 GENE: DASR, SCO5231, SC7E4.28C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION, REPRESSOR, BACTERIAL TRANSCRIPTION REGULATION, KEYWDS 2 TRANSCRIPTION FACTOR, GNTR/HUTC FAMILY, EFFECTOR-BINDING DOMAIN, N- KEYWDS 3 ACETYLGLUCOSAMINE UTILIZATION, LIGAND-FREE, MASTER REGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR S.B.FILLENBERG,F.C.GRAU,Y.A.MULLER REVDAT 3 10-JAN-24 4ZSB 1 REMARK REVDAT 2 13-JUL-16 4ZSB 1 JRNL REVDAT 1 08-JUN-16 4ZSB 0 JRNL AUTH S.B.FILLENBERG,M.D.FRIESS,S.KORNER,R.A.BOCKMANN,Y.A.MULLER JRNL TITL CRYSTAL STRUCTURES OF THE GLOBAL REGULATOR DASR FROM JRNL TITL 2 STREPTOMYCES COELICOLOR: IMPLICATIONS FOR THE ALLOSTERIC JRNL TITL 3 REGULATION OF GNTR/HUTC REPRESSORS. JRNL REF PLOS ONE V. 11 57691 2016 JRNL REFN ESSN 1932-6203 JRNL PMID 27337024 JRNL DOI 10.1371/JOURNAL.PONE.0157691 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.210 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 14016 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1288 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 44.7379 - 4.1675 0.96 2669 141 0.1695 0.2144 REMARK 3 2 4.1675 - 3.3082 0.98 2674 150 0.1974 0.2205 REMARK 3 3 3.3082 - 2.8901 0.99 2772 147 0.2124 0.2657 REMARK 3 4 2.8901 - 2.6259 0.99 2745 148 0.2300 0.2716 REMARK 3 5 2.6259 - 2.4377 0.99 2748 145 0.2485 0.3446 REMARK 3 6 2.4377 - 2.2940 1.00 2781 144 0.2512 0.3027 REMARK 3 7 2.2940 - 2.1791 0.99 2705 137 0.2616 0.3590 REMARK 3 8 2.1791 - 2.0842 0.97 2713 143 0.2872 0.3018 REMARK 3 9 2.0842 - 2.0040 0.86 2410 133 0.3381 0.3403 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.460 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 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 : 0.009 1308 REMARK 3 ANGLE : 1.101 1773 REMARK 3 CHIRALITY : 0.043 205 REMARK 3 PLANARITY : 0.005 229 REMARK 3 DIHEDRAL : 15.017 505 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4ZSB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000209803. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : SI-111 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14018 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.80600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: EFFECTOR-BINDING DOMAIN OF ENTRY 2WV0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE PH 9.0, 4.0 M REMARK 280 POTASSIUM FORMATE, 20 % (W/V) PEG MONOMETHYL ETHER 2,000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 292.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.33167 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 72.66333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 72.66333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.33167 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: 3520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 349 LIES ON A SPECIAL POSITION. 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 GLY A 85 REMARK 465 SER A 86 REMARK 465 HIS A 87 REMARK 465 MET A 88 REMARK 465 VAL A 89 REMARK 465 SER A 90 REMARK 465 GLN A 253 REMARK 465 ASP A 254 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 122 O HOH A 301 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 ALA A 92 36.44 70.07 REMARK 500 REMARK 500 REMARK: NULL DBREF 4ZSB A 89 254 UNP Q9K492 DASR_STRCO 89 254 SEQADV 4ZSB GLY A 85 UNP Q9K492 EXPRESSION TAG SEQADV 4ZSB SER A 86 UNP Q9K492 EXPRESSION TAG SEQADV 4ZSB HIS A 87 UNP Q9K492 EXPRESSION TAG SEQADV 4ZSB MET A 88 UNP Q9K492 EXPRESSION TAG SEQRES 1 A 170 GLY SER HIS MET VAL SER GLN ALA LEU GLN LEU THR SER SEQRES 2 A 170 TYR THR GLU ASP MET ARG ALA GLN GLY LEU GLU PRO THR SEQRES 3 A 170 SER GLN LEU LEU ASP ILE GLY TYR ILE THR ALA ASP ASP SEQRES 4 A 170 ARG LEU ALA GLY LEU LEU ASP ILE THR ALA GLY GLY ARG SEQRES 5 A 170 VAL LEU ARG ILE GLU ARG LEU ARG MET ALA ASN GLY GLU SEQRES 6 A 170 PRO MET ALA ILE GLU THR THR HIS LEU SER ALA LYS ARG SEQRES 7 A 170 PHE PRO ALA LEU ARG ARG SER LEU VAL LYS TYR THR SER SEQRES 8 A 170 LEU TYR THR ALA LEU ALA GLU VAL TYR ASP VAL HIS LEU SEQRES 9 A 170 ALA GLU ALA GLU GLU THR ILE GLU THR SER LEU ALA THR SEQRES 10 A 170 PRO ARG GLU ALA GLY LEU LEU GLY THR ASP VAL GLY LEU SEQRES 11 A 170 PRO MET LEU MET LEU SER ARG HIS SER GLN ASP ARG THR SEQRES 12 A 170 GLY GLN PRO VAL GLU TRP VAL ARG SER VAL TYR ARG GLY SEQRES 13 A 170 ASP ARG TYR LYS PHE VAL ALA ARG LEU LYS ARG PRO GLN SEQRES 14 A 170 ASP FORMUL 2 HOH *75(H2 O) HELIX 1 AA1 SER A 97 ALA A 104 1 8 HELIX 2 AA2 ASP A 122 ASP A 130 1 9 HELIX 3 AA3 ALA A 165 LEU A 170 1 6 HELIX 4 AA4 VAL A 171 TYR A 173 5 3 HELIX 5 AA5 SER A 175 ASP A 185 1 11 HELIX 6 AA6 THR A 201 LEU A 208 1 8 SHEET 1 AA1 6 PRO A 109 THR A 120 0 SHEET 2 AA1 6 ARG A 136 ALA A 146 -1 O MET A 145 N THR A 110 SHEET 3 AA1 6 GLU A 149 SER A 159 -1 O ALA A 152 N ARG A 144 SHEET 4 AA1 6 PRO A 230 ARG A 239 -1 O ARG A 235 N THR A 155 SHEET 5 AA1 6 MET A 216 ASP A 225 -1 N LEU A 217 O TYR A 238 SHEET 6 AA1 6 LEU A 188 SER A 198 -1 N GLU A 196 O MET A 218 CRYST1 56.634 56.634 108.995 90.00 90.00 120.00 P 31 2 1 6 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 0.017657 0.010194 0.000000 0.00000 SCALE2 0.000000 0.020389 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009175 0.00000